Compositions Containing, Methods Involving, and Uses of Non-Natural Amino Acids and Polypeptides

Abstract

Disclosed herein are non-natural amino acids and polypeptides that include at least one non-natural amino acid, and methods for making such non-natural amino acids and polypeptides. The non-natural amino acids, by themselves or as a part of a polypeptide, can include a wide range of possible functionalities, but typical have at least one aromatic amine group. Also disclosed herein are non-natural amino acid polypeptides that are further modified post-translationally, methods for effecting such modifications, and methods for purifying such polypeptides. Typically, the modified non-natural amino acid polypeptides include at least one alkylated amine group. Further disclosed are methods for using such non-natural amino acid polypeptides and modified non-natural amino acid polypeptides, including therapeutic, diagnostic, and other biotechnology uses.

1 . A compound or salt thereof selected from the group consisting of: 
       
         
           
           
               
               
           
         
         wherein each R a  is independently selected from the group consisting of H, halogen, alkyl, —NO 2 , —CN, substituted alkyl, —N(R′) 2 , —C(O) k R′, —C(O)N(R′) 2 , —OR′, and —S(O) k R′, where k is 1, 2, or 3; 
         M is H or —CH 2 R 5 ; or the M-N—C(R 5 ) moiety may form a 4 to 7 membered ring structure; 
         R 1  is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 2  is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 5  is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, —C(O)R″, —C(O)OR″, —C(O)N(R″) 2 , —C(O)NHCH(R″) 2 , -(alkylene or substituted alkylene)-N(R″) 2 , -(alkenylene or substituted alkenylene)-N(R″) 2 , -(alkylene or substituted alkylene)-(aryl or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl or substituted aryl), -(alkylene or substituted alkylene)-ON(R″) 2 , -(alkylene or substituted alkylene)-C(O)SR″, -(alkylene or substituted alkylene)-S—S-(aryl or substituted aryl), wherein each R″ is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, or —C(O)OR′; 
         or R 5  is L-X, where, X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a ligand; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; an inhibitory ribonucleic acid; a radionucleotide; a neutron-capture agent; a derivative of biotin; quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme, an activated complex activator, a virus, an adjuvant, an aglycan, an allergan, an angiostatin, an antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a receptor, a reverse micelle, and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, —O—, —O-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-O—, —C(O)—, —C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)—, —C(O)N(R′)—, —C(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)N(R′), —OC(O)N(R′)—, —OC(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-OC(O)N(R′)—, —N(R′)C(O)—, —NR′C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-NR′C(O)—, —S—, —S-(alkylene or substituted alkylene)-, —S(O) k — where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(S)—, —C(S)-(alkylene or substituted alkylene)-, —CSN(R′)—, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, —N(R′)C(O)O—, -(alkylene or substituted alkylene)-O—N═CR′—, -(alkylene or substituted alkylene)-C(O)NR′-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-S(O) k -(alkylene or substituted alkylene)-S—, -(alkylene or substituted alkylene)-S—S—, —S(O) k N(R′)—, —N(R′)C(O)N(R′)—, —N(R′)C(S)N(R′)—, —N(R′)S(O) k N(R′)—, —N(R′)—N═, —C(R′)═N—, —C(R′)═N—N(R′)—, —C(R′)═N—N═, —C(R′) 2 —N═N—, and —C(R′) 2 —N(R′)—N(R′)—; 
         or R 5  and any R a  optionally form a cycloalkyl or a heterocycloalkyl; and 
         each R′ is independently H, alkyl, or substituted alkyl. 
       
     
     
         2 . The compound of  claim 1 , wherein R 1  is H and R 2  is OH. 
     
     
         3 . The compound of  claim 1 , wherein R a  is a halogen. 
     
     
         4 . The compound of  claim 1 , wherein both R 1  and R 2  are polypeptides. 
     
     
         5 . The compound of  claim 1 , wherein X is a biologically active agent selected from the group consisting of a peptide, protein, enzyme, antibody, drug, dye, lipid, nucleosides, oligonucleotide, cell, virus, liposome, microparticle, and micelle. 
     
     
         6 . The compound of  claim 5 , wherein X is a drug selected from the group consisting of an antibiotic, fungicide, anti-viral agent, anti-inflammatory agent, anti-tumor agent, cardiovascular agent, anti-anxiety agent, hormone, growth factor, and steroidal agent. 
     
     
         7 . The compound of  claim 5 , wherein X is an enzyme selected from the group consisting of horseradish peroxidase, alkaline phosphatase, β-galactosidase, and glucose oxidase. 
     
     
         8 . The compound of  claim 1 , wherein X is a detectable label selected from the group consisting of a fluorescent, phosphorescent, chemiluminescent, chelating, electron dense, magnetic, intercalating, radioactive, chromophoric, and energy transfer moiety. 
     
     
         9 . The compound of  claim 1 , wherein X is a polymer comprising alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl. 
     
     
         10 . The compound of  claim 9 , wherein the polymer comprises polyalkylene oxide or substituted polyalkylene oxide. 
     
     
         11 . The compound of  claim 9 , wherein the polymer comprises -[(alkylene or substituted alkylene)-O-(hydrogen, alkyl, or substituted alkyl)] x , wherein x is from 20-10,000. 
     
     
         12 . The compound of  claim 9 , wherein the polymer is m-PEG having a molecular weight ranging from about 2 to about 40 KDa. 
     
     
         13 . A polypeptide, or salt thereof, containing at least one compound of  claim 1  selected from the group: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       wherein X is a halogen. 
     
     
         14 . A polypeptide, or salt thereof, containing at least one compound of  claim 1  selected from the group: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         15 . A polypeptide, or salt thereof, containing at least one compound of  claim 1  selected from the group: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       wherein X is a halogen. 
     
     
         16 . A compound or salt thereof having the structure: 
       
         
           
           
               
               
           
         
         wherein each R a  is independently selected from the group consisting of H, halogen, alkyl, —NO 2 , —CN, substituted alkyl, —N(R′) 2 , —C(O) k R′, —C(O)N(R′) 2 , —OR′, and —S(O) k R′, where k is 1, 2, or 3; 
         R 1  is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and 
         R 2  is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         each of R 3  and R 4  is independently H, halogen, lower alkyl, or substituted lower alkyl, or R 3  and R 4  or two R 3  groups optionally form a cycloalkyl or a heterocycloalkyl; 
         M is H or —CH 2 R 5 ; 
         R 5  is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, —C(O)R″, —C(O)OR″, —C(O)N(R″) 2 , —C(O)NHCH(R″) 2 , -(alkylene or substituted alkylene)-N(R″) 2 , -(alkenylene or substituted alkenylene)-N(R″) 2 , -(alkylene or substituted alkylene)-(aryl or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl or substituted aryl), -(alkylene or substituted alkylene)-ON(R″) 2 , -(alkylene or substituted alkylene)-C(O)SR″, -(alkylene or substituted alkylene)-S—S-(aryl or substituted aryl), wherein each R″ is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, or —C(O)OR′; 
         or R 5  is L-X, where, X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a ligand; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; an inhibitory ribonucleic acid; a radionucleotide; a neutron-capture agent; a derivative of biotin; quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme, an activated complex activator, a virus, an adjuvant, an aglycan, an allergan, an angiostatin, an antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a receptor, a reverse micelle, and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, —O—, —O-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-O—, —C(O)—, —C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)—, —C(O)N(R′)—, —C(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)N(R′), —OC(O)N(R′)—, —OC(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-OC(O)N(R′)—, —N(R′)C(O)—, —NR′C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-NR′C(O)—, —S—, —S-(alkylene or substituted alkylene)-, —S(O) k — where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(S)—, —C(S)-(alkylene or substituted alkylene)-, —CSN(R′)—, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, —N(R′)C(O)O—, -(alkylene or substituted alkylene)-O—N═CR′—, -(alkylene or substituted alkylene)-C(O)NR′-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-S(O) k -(alkylene or substituted alkylene)-S—, -(alkylene or substituted alkylene)-S—S—, —S(O) k N(R′)—, —N(R′)C(O)N(R′)—, —N(R′)C(S)N(R′)—, —N(R′)S(O) k N(R′)—, —N(R′)—N═, —C(R′)═N—, —C(R′)═N—N(R′)—, —C(R′)═N—N═, —C(R′) 2 —N═N—, and —C(R′) 2 —N(R′)—N(R′)—; 
         or two R 5  groups optionally form a cycloalkyl or a heterocycloalkyl; 
         or R 5  and any R a  optionally form a cycloalkyl or a heterocycloalkyl; 
         with a proviso that when R 1  is H then R 2  is not OH, or when R 2  is OH then R 1  is not H; and 
         G is an amine protecting group. 
       
     
     
         17 . The compound of  claim 16 , wherein the amine protecting group is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         18 . The compound of  claim 16 , wherein both R 1  and R 2  are polypeptides. 
     
     
         19 . A compound or salt thereof having the structure of: 
       
         
           
           
               
               
           
         
         wherein L is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene; 
         Q is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, —O-(alkylene or substituted alkylene)-, —S-(alkylene or substituted alkylene)-, where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(O)-(alkylene or substituted alkylene)-, —C(S)-(alkylene or substituted alkylene)-, —NR′-(alkylene or substituted alkylene)-, —CON(R″)-(alkylene or substituted alkylene)-, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, and where each R′ is independently H, alkyl, or substituted alkyl; 
         R 1  is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and 
         R 2  is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         each of R 3  and R 4  is independently H, halogen, lower alkyl, or substituted lower alkyl, or R 3  and R 4  or two R 3  groups optionally form a cycloalkyl or a heterocycloalkyl; 
         each R a  is independently selected from the group consisting of H, halogen, alkyl, —NO 2 , —CN, substituted alkyl, —N(R′) 2 , —C(O) k R′, —C(O)N(R′) 2 , —OR′, and —S(O) k R′, where k is 1, 2, or 3; 
         R 6  is a protected aldehyde or a masked aldehyde, wherein the protecting group includes, but is not limited to, 
       
       
         
           
           
               
               
           
         
       
       where each X 1  is independently selected from the group consisting of —O—, —S—, —N(H)—, —N(R)—, —N(Ac)—, and —N(OMe)-; X 2  is —OR, —OAc, —SR, —N(R) 2 , —N(R)(Ac), —N(R)(OMe), or N 3 , and where each R′ and R is independently H, alkyl, or substituted alkyl. 
     
     
         20 . The compound of  claim 19  wherein X 1  is O. 
     
     
         21 . The compound of  claim 19  wherein both R 1  and R 2  are polypeptides. 
     
     
         22 . A polypeptide containing at least one compound of  claim 19  selected from the group: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         23 . A method of making a compound containing at least one non-natural amino acid selected from the group consisting of: 
       
         
           
           
               
               
           
         
         wherein the compound is formed by a reductive alkylation of an aromatic amino moiety on at least one non-natural amino acid with at least one reactant comprising at least one aldehyde moiety; 
         each R a  is independently selected from the group consisting of H, halogen, alkyl, —NO 2 , —CN, substituted alkyl, —N(R′) 2 , —C(O) k R′, —C(O)N(R′) 2 , —OR′, and —S(O) k R′, where k is 1, 2, or 3; 
         M is H or —CH 2 R 5 ; or the M-N—C(R 5 ) moiety may form a 4 to 7 membered ring structure; 
         R 1  is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 2  is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 5  is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, —C(O)R″, —C(O)OR″, —C(O)N(R″) 2 , —C(O)NHCH(R″) 2 , -(alkylene or substituted alkylene)-N(R″) 2 , -(alkenylene or substituted alkenylene)-N(R″) 2 , -(alkylene or substituted alkylene)-(aryl or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl or substituted aryl), -(alkylene or substituted alkylene)-ON(R″) 2 , -(alkylene or substituted alkylene)-C(O)SR″, -(alkylene or substituted alkylene)-S—S-(aryl or substituted aryl), wherein each R″ is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, or —C(O)OR′; 
         or R 5  is L-X, where, X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a ligand; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; an inhibitory ribonucleic acid; a radionucleotide; a neutron-capture agent; a derivative of biotin; quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme, an activated complex activator, a virus, an adjuvant, an aglycan, an allergan, an angiostatin, an antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a receptor, a reverse micelle, and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, —O—, —O-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-O—, —C(O)—, —C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)—, —C(O)N(R′)—, —C(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)N(R′), —OC(O)N(R′)—, —OC(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-OC(O)N(R′)—, —N(R′)C(O)—, —NR′C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-NR′C(O)—, —S—, —S-(alkylene or substituted alkylene)-, —S(O) k — where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(S)—, —C(S)-(alkylene or substituted alkylene)-, —CSN(R′)—, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, —N(R′)C(O)O—, -(alkylene or substituted alkylene)-O—N═CR′—, -(alkylene or substituted alkylene)-C(O)NR′-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-S(O) k -(alkylene or substituted alkylene)-S—, -(alkylene or substituted alkylene)-S—S—, —S(O) k N(R′)—, —N(R′)C(O)N(R′)—, —N(R′)C(S)N(R′)—, —N(R′)S(O) k N(R′)—, —N(R′)—N═, —C(R′)═N—, —C(R′)═N—N(R′)—, —C(R′)═N—N═, —C(R′) 2 —N═N—, and —C(R′) 2 —N(R′)—N(R′)—; 
         or R 5  and any R a  optionally form a cycloalkyl or a heterocycloalkyl; and 
         each R′ is independently H, alkyl, or substituted alkyl. 
       
     
     
         24 . The method of  claim 23 , wherein R 1  and R 2  of the at least one non-natural amino acid is H and OH respectively. 
     
     
         25 . The method of  claim 23 , wherein R a  of the at least one non-natural amino acid is a halogen. 
     
     
         26 . The method of  claim 23 , wherein both R 1  and R 2  of the at least one non-natural amino acid are polypeptides. 
     
     
         27 . The method of  claim 23 , wherein X of the at least one non-natural amino acid is a biologically active agent selected from the group consisting of a peptide, protein, enzyme, antibody, drug, dye, lipid, nucleosides, oligonucleotide, cell, virus, liposome, microparticle, and micelle. 
     
     
         28 . The method of  claim 27 , wherein X of the at least one non-natural amino acid is a drug selected from the group consisting of an antibiotic, fungicide, anti-viral agent, anti-inflammatory agent, anti-tumor agent, cardiovascular agent, anti-anxiety agent, hormone, growth factor, and steroidal agent. 
     
     
         29 . The method of  claim 27 , wherein X of the at least one non-natural amino acid is an enzyme selected from the group consisting of horseradish peroxidase, alkaline phosphatase, β-galactosidase, and glucose oxidase. 
     
     
         30 . The method of  claim 23 , wherein X of the at least one non-natural amino acid is a detectable label selected from the group consisting of a fluorescent, phosphorescent, chemiluminescent, chelating, electron dense, magnetic, intercalating, radioactive, chromophoric, and energy transfer moiety. 
     
     
         31 . The method of  claim 23 , wherein X of the non-natural amino acid is a polymer comprising alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, alkaryl, substituted alkaryl, aralkyl, or substituted aralkyl. 
     
     
         32 . The method of  claim 31 , wherein the polymer comprises polyalkylene oxide or substituted polyalkylene oxide. 
     
     
         33 . The method of  claim 31 , wherein the polymer comprises -[(alkylene or substituted alkylene)-O-(hydrogen, alkyl, or substituted alkyl)] x , wherein x is from 20-10,000. 
     
     
         34 . The method of  claim 31 , wherein the polymer is m-PEG having a molecular weight ranging from about 2 to about 40 KDa. 
     
     
         35 . The method of  claim 23  wherein the at least one non-natural amino acid is selected from a group: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         36 . The method of  claim 23  wherein the at least one non-natural amino acid is selected from a group: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         37 . The method of  claim 23  wherein the at least one non-natural amino acid is selected from a group: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         38 . A method of making a polypeptide containing at least one non-natural amino acid selected from the group consisting of: 
       
         
           
           
               
               
           
         
         wherein the polypeptide is formed by a reductive alkylation of an aromatic amino moiety on at least one non-natural amino acid with at least one reactant comprising at least one aldehyde moiety; 
         each R a  is independently selected from the group consisting of H, halogen, alkyl, —NO 2 , —CN, substituted alkyl, —N(R′) 2 , —C(O) k R′, —C(O)N(R′) 2 , —OR′, and —S(O) k R′, where k is 1, 2, or 3; 
         R 1  is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and 
         R 2  is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         each of R 3  and R 4  is independently H, halogen, lower alkyl, or substituted lower alkyl, or R 3  and R 4  or two R 3  groups optionally form a cycloalkyl or a heterocycloalkyl; 
         M is —CH 2 R 5 ; 
         R 5  is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, —C(O)R″, —C(O)OR″, —C(O)N(R″) 2 , —C(O)NHCH(R″) 2 , -(alkylene or substituted alkylene)-N(R″) 2 , -(alkenylene or substituted alkenylene)-N(R″) 2 , -(alkylene or substituted alkylene)-(aryl or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl or substituted aryl), -(alkylene or substituted alkylene)-ON(R″) 2 , -(alkylene or substituted alkylene)-C(O)SR″, -(alkylene or substituted alkylene)-S—S-(aryl or substituted aryl), wherein each R″ is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, or —C(O)OR′; 
         or R 5  is L-X, where, X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a ligand; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; an inhibitory ribonucleic acid; a radionucleotide; a neutron-capture agent; a derivative of biotin; quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme, an activated complex activator, a virus, an adjuvant, an aglycan, an allergan, an angiostatin, an antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a receptor, a reverse micelle, and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, —O—, —O-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-O—, —C(O)—, —C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)—, —C(O)N(R′)—, —C(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)N(R′), —OC(O)N(R′)—, —OC(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-OC(O)N(R′)—, —N(R′)C(O)—, —NR′C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-NR′C(O)—, —S—, —S-(alkylene or substituted alkylene)-, —S(O) k — where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(S)—, —C(S)-(alkylene or substituted alkylene)-, —CSN(R′)—, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, —N(R′)C(O)O—, -(alkylene or substituted alkylene)-O—N═CR′—, -(alkylene or substituted alkylene)-C(O)NR′-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-S(O) k -(alkylene or substituted alkylene)-S—, -(alkylene or substituted alkylene)-S—S—, —S(O) k N(R′)—, —N(R′)C(O)N(R′)—, —N(R′)C(S)N(R′)—, —N(R′)S(O) k N(R′)—, —N(R′)—N═, —C(R′)═N—, —C(R′)═N—N(R′)—, —C(R′)═N—N═, —C(R′) 2 —N═N—, and —C(R′) 2 —N(R′)—N(R′)—; 
         or two R 5  groups optionally form a cycloalkyl or a heterocycloalkyl; 
         or R 5  and any R a  optionally form a cycloalkyl or a heterocycloalkyl; 
         with a proviso that when R 1  is H then R 2  is not OH, or when R 2  is OH then R 1  is not H; and
 G is an amine protecting group. 
 
       
     
     
         39 . The method of  claim 38  wherein the amine protecting group is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         40 . The method of  claim 38  wherein both R 1  and R 2  are polypeptides. 
     
     
         41 . The method of  claim 38  wherein the at least one aldehyde moiety has the structure corresponding to: 
       
         
           
           
               
               
           
         
         wherein:
 R 5  is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, —C(O)R″, —C(O)OR″, —C(O)N(R″) 2 , —C(O)NHCH(R″) 2 , -(alkylene or substituted alkylene)-N(R″) 2 , -(alkenylene or substituted alkenylene)-N(R″) 2 , -(alkylene or substituted alkylene)-(aryl or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl or substituted aryl), -(alkylene or substituted alkylene)-ON(R″) 2 , -(alkylene or substituted alkylene)-C(O)SR″, -(alkylene or substituted alkylene)-S—S-(aryl or substituted aryl), wherein each R″ is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, or —C(O)OR′; 
 or R 5  is L-X, where, X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a ligand; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; an inhibitory ribonucleic acid; a radionucleotide; a neutron-capture agent; a derivative of biotin; quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme, an activated complex activator, a virus, an adjuvant, an aglycan, an allergan, an angiostatin, an antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a receptor, a reverse micelle, and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, —O—, —O-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-O—, —C(O)—, —C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)—, —C(O)N(R′)—, —C(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)N(R′), —OC(O)N(R′)—, —OC(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-OC(O)N(R′)—, —N(R′)C(O)—, —NR′C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-NR′C(O)—, —S—, —S-(alkylene or substituted alkylene)-, —S(O) k — where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(S)—, —C(S)-(alkylene or substituted alkylene)-, —CSN(R′)—, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, —N(R′)C(O)O—, -(alkylene or substituted alkylene)-O—N═CR′—, -(alkylene or substituted alkylene)-C(O)NR′-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-S(O) k -(alkylene or substituted alkylene)-S—, -(alkylene or substituted alkylene)-S—S—, —S(O) k N(R′)—, —N(R′)C(O)N(R′)—, —N(R′)C(S)N(R′)—, —N(R′)S(O) k N(R′)—, —N(R′)—N═, —C(R′)═N—, —C(R′)═N—N(R′)—, —C(R′)═N—N═, —C(R′) 2 —N═N—, and —C(R′) 2 —N(R′)—N(R′)—. 
 
       
     
     
         42 . A method for treating a disorder, condition or disease comprising administering a therapeutically effective amount of a polypeptide comprising at least one non-natural amino acid selected from the group consisting of: 
       
         
           
           
               
               
           
         
         wherein each R a  is independently selected from the group consisting of H, halogen, alkyl, —NO 2 , —CN, substituted alkyl, —N(R′) 2 , —C(O) k R′, —C(O)N(R′) 2 , —OR′, and —S(O) k R′, where k is 1, 2, or 3; 
         M is H or —CH 2 R 5 ; or the M-N—C(R 5 ) moiety may form a 4 to 7 membered ring structure; 
         R 1  is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 2  is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 5  is alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, alkylalkoxy, substituted alkylalkoxy, polyalkylene oxide, substituted polyalkylene oxide, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, —C(O)R″, —C(O)OR″, —C(O)N(R″) 2 , —C(O)NHCH(R″) 2 , -(alkylene or substituted alkylene)-N(R″) 2 , -(alkenylene or substituted alkenylene)-N(R″) 2 , -(alkylene or substituted alkylene)-(aryl or substituted aryl), -(alkenylene or substituted alkenylene)-(aryl or substituted aryl), -(alkylene or substituted alkylene)-ON(R″) 2 , -(alkylene or substituted alkylene)-C(O)SR″, -(alkylene or substituted alkylene)-S—S-(aryl or substituted aryl), wherein each R″ is independently hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkoxy, substituted alkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle, substituted heterocycle, alkaryl, substituted alkaryl, aralkyl, substituted aralkyl, or —C(O)OR′; 
         or R 5  is L-X, where, X is a selected from the group consisting of a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide, a water-soluble dendrimer, a cyclodextrin, a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a ligand; a photoisomerizable moiety; biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; an inhibitory ribonucleic acid; a radionucleotide; a neutron-capture agent; a derivative of biotin; quantum dot(s); a nanotransmitter; a radiotransmitter; an abzyme, an activated complex activator, a virus, an adjuvant, an aglycan, an allergan, an angiostatin, an antihormone, an antioxidant, an aptamer, a guide RNA, a saponin, a shuttle vector, a macromolecule, a mimotope, a receptor, a reverse micelle, and any combination thereof; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, —O—, —O-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-O—, —C(O)—, —C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)—, —C(O)N(R′)—, —C(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)N(R′), —OC(O)N(R′)—, —OC(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-OC(O)N(R′)—, —N(R′)C(O)—, —NR′C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-NR′C(O)—, —S—, —S-(alkylene or substituted alkylene)-, —S(O) k — where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(S)—, —C(S)-(alkylene or substituted alkylene)-, —CSN(R′)—, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, —N(R′)C(O)O—, -(alkylene or substituted alkylene)-O—N═CR′—, -(alkylene or substituted alkylene)-C(O)NR′-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-S(O) k -(alkylene or substituted alkylene)-S—, -(alkylene or substituted alkylene)-S—S—, —S(O) k N(R′)—, —N(R′)C(O)N(R′)—, —N(R′)C(S)N(R′)—, —N(R′)S(O) k N(R′)—, —N(R′)—N═, C(R′)═N—, —C(R′)═N—N(R′)—, —C(R′)═N—N═, —C(R′) 2 —N═N—, and —C(R′) 2 —N(R′)—N(R′)—; 
         or R 5  and any R a  optionally form a cycloalkyl or a heterocycloalkyl; and 
         each R′ is independently H, alkyl, or substituted alkyl. 
         with a proviso that when R 1  is H then R 2  is not OH, or when R 2  is OH then R 1  is not H. 
       
     
     
         43 . The method of  claim 42 , further comprising administering a pharmaceutically acceptable carrier with the therapeutically effective amount of the polypeptide. 
     
     
         44 . The method of  claim 42 , wherein R 1  and R 2  are both polypeptides. 
     
     
         45 . The method of  claim 42 , wherein X is a water-soluble polymer. 
     
     
         46 . The method of  claim 42 , wherein X is a derivative of polyethylene glycol. 
     
     
         47 . The method of  claim 42 , wherein X is a cytotoxic compound. 
     
     
         48 . The method of  claim 42 , wherein X is a drug. 
     
     
         49 . The method of  claim 42 , wherein X is a second polypeptide. 
     
     
         50 . The method of  claim 49 , wherein the second polypeptide is a peptide containing a non-natural amino acid polypeptide. 
     
     
         51 . The method of  claim 42 , wherein the polypeptide is a protein homologous to a therapeutic protein selected from the group consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic factor, antibody, antibody fragment, apolipoprotein, apoprotein, atrial natriuretic factor, atrial natriuretic polypeptide, atrial peptide, C-X-C chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10, GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine, CC chemokine, monocyte chemoattractant protein-1, monocyte chemoattractant protein-2, monocyte chemoattractant protein-3, monocyte inflammatory protein-1 alpha, monocyte inflammatory protein-i beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262, CD40, CD40 ligand, c-kit ligand, collagen, colony stimulating factor (CSF), complement factor 5a, complement inhibitor, complement receptor 1, cytokine, epithelial neutrophil activating peptide-78, MIP-16, MCP-1, epidermal growth factor (EGF), epithelial neutrophil activating peptide, erythropoietin (EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII, Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin, four-helical bundle protein, G-CSF, glp-1, GM-CSF, glucocerebrosidase, gonadotropin, growth factor, growth factor receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth factor (hGF), hirudin, human growth hormone (hGH), human serum albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin, insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN), IFN-alpha, IFN-beta, IFN-gamma, interleukin (IL), IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, keratinocyte growth factor (KGF), lactoferrin, leukemia inhibitory factor, luciferase, neurturin, neutrophil inhibitory factor (NIF), oncostatin M, osteogenic protein, oncogene product, paracitonin, parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin, protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small biosynthetic protein, soluble complement receptor I, soluble I-CAM 1, soluble interleukin receptor, soluble TNF receptor, somatomedin, somatostatin, somatotropin, streptokinase, superantigens, staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE, steroid hormone receptor, superoxide dismutase, toxic shock syndrome toxin, thymosin alpha 1, tissue plasminogen activator, tumor growth factor (TGF), tumor necrosis factor, tumor necrosis factor alpha, tumor necrosis factor beta, tumor necrosis factor receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular endothelial growth factor (VEGF), urokinase, mos, ras, raf, met, p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone receptor, testosterone receptor, aldosterone receptor, LDL receptor, and corticosterone. 
     
     
         52 . The method of  claim 42 , wherein the at least one non-natural acid is incorporated at a specific site within the polypeptide. 
     
     
         53 . The method of  claim 42 , wherein the non-natural amino acid is incorporated using a translation system. 
     
     
         54 . The method of  claim 42 , wherein the non-natural amino acid is incorporated into the polypeptide using a translation system and a post translation modification system. 
     
     
         55 . The method of  claim 42 , wherein the polypeptide comprising at least one non-natural amino acid is stable for at least 1 month. 
     
     
         56 . The method of  claim 42 , wherein the polypeptide comprising at least one non-natural amino acid is stable for at least 2 weeks. 
     
     
         57 . A method for detecting the presence of a polypeptide in a patient, the method comprising administering an effective amount of a homologous non-natural amino acid polypeptide comprising at least one non-natural amino acid selected from the group consisting of: 
       
         
           
           
               
               
           
         
         and detecting an indicator on the polypeptide selected from the group consisting of a label; a dye; an affinity label; a photoaffinity label; a spin label; a second protein or polypeptide or polypeptide analog; a fluorophore; a radioactive moiety; a moiety incorporating a heavy atom; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; biotin, a biotin analogue; an electron dense group; a magnetic group; a chromophore; an energy transfer agent; a detectable label; a radiotransmitter, and any combination of the above; wherein each R a  is independently selected from the group consisting of H, halogen, alkyl, —NO 2 , —CN, substituted alkyl, —N(R′) 2 , —C(O) k R′, —C(O)N(R′) 2 , —OR′, and —S(O) k R′, where k is 1, 2, or 3; 
         M is H or —CH 2 R 5 ; or the M-N—C(R 5 ) moiety may form a 4 to 7 membered ring structure; 
         R 1  is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 2  is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide; 
         R 5  is L-X, where, X is a selected from the group consisting of a label; a dye; an affinity label; a photoaffinity label; a spin label; a second protein or polypeptide or polypeptide analog; a fluorophore; a radioactive moiety; a moiety incorporating a heavy atom; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; biotin, a biotin analogue; an electron dense group; a magnetic group; a chromophore; an energy transfer agent; a detectable label; a radiotransmitter, and any combination of the above; and L is optional, and when present is a linker selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, —O—, —O-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-O—, —C(O)—, —C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)—, —C(O)N(R′)—, —C(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-C(O)N(R′), —OC(O)N(R′)—, —OC(O)N(R′)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-OC(O)N(R′)—, —N(R′)C(O)—, —NR′C(O)-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-NR′C(O)—, —S—, —S-(alkylene or substituted alkylene)-, —S(O) k — where k is 1, 2, or 3, —S(O) k (alkylene or substituted alkylene)-, —C(S)—, —C(S)-(alkylene or substituted alkylene)-, —CSN(R′)—, —CSN(R′)-(alkylene or substituted alkylene)-, —N(R′)CO-(alkylene or substituted alkylene)-, —N(R′)C(O)O—, -(alkylene or substituted alkylene)-O—N═CR′—, -(alkylene or substituted alkylene)-C(O)NR′-(alkylene or substituted alkylene)-, -(alkylene or substituted alkylene)-S(O) k -(alkylene or substituted alkylene)-S—, -(alkylene or substituted alkylene)-S—S—, —S(O) k N(R′)—, —N(R′)C(O)N(R′)—, —N(R′)C(S)N(R′)—, —N(R′)S(O) k N(R′)—, —N(R′)—N═, —C(R′)═N—, —C(R′)═N—N(R′)—, —C(R′)═N—N═, —C(R′) 2 —N═N—, and —C(R′) 2 —N(R′)—N(R′)—; 
         or R 5  and any R a  optionally form a cycloalkyl or a heterocycloalkyl; 
         each R′ is independently H, alkyl, or substituted alkyl; and 
         with a proviso that when R 1  is H then R 2  is not OH, or when R 2  is OH then R 1  is not H. 
       
     
     
         58 . The method of  claim 57 , wherein the at least one non-natural acid is incorporated at a specific site within the polypeptide. 
     
     
         59 . The method of  claim 57 , wherein the non-natural amino acid is incorporated using a translation system. 
     
     
         60 . The method of  claim 57 , wherein the non-natural amino acid is incorporated into the polypeptide using a translation system and a post translation modification system. 
     
     
         61 . The method of  claim 57 , wherein the at least one non-natural amino acid is stable in aqueous solution for at least 1 month. 
     
     
         62 . The method of  claim 57 , wherein the at least one non-natural amino acid is stable for at least 2 weeks. 
     
     
         63 . The method of  claim 57 , wherein the at least one non-natural amino acid is stable for at least 5 days. 
     
     
         64 . The method of  claim 57 , wherein the polypeptide is a protein homologous to a therapeutic protein selected from the group consisting of: alpha-1 antitrypsin, angiostatin, antihemolytic factor, antibody, apolipoprotein, apoprotein, atrial natriuretic factor, atrial natriuretic polypeptide, atrial peptide, C-X-C chemokine, T39765, NAP-2, ENA-78, gro-a, gro-b, gro-c, IP-10, GCP-2, NAP-4, SDF-1, PF4, MIG, calcitonin, c-kit ligand, cytokine, CC chemokine, monocyte chemoattractant protein-1, monocyte chemoattractant protein-2, monocyte chemoattractant protein-3, monocyte inflammatory protein-1 alpha, monocyte inflammatory protein-i beta, RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262, CD40, CD40 ligand, c-kit ligand, collagen, colony stimulating factor (CSF), complement factor 5a, complement inhibitor, complement receptor 1, cytokine, epithelial neutrophil activating peptide-78, MIP-16, MCP-1, epidermal growth factor (EGF), epithelial neutrophil activating peptide, erythropoietin (EPO), exfoliating toxin, Factor IX, Factor VII, Factor VIII, Factor X, fibroblast growth factor (FGF), fibrinogen, fibronectin, four-helical bundle protein, G-CSF, glp-1, GM-CSF, glucocerebrosidase, gonadotropin, growth factor, growth factor receptor, grf, hedgehog protein, hemoglobin, hepatocyte growth factor (hGF), hirudin, human growth hormone (hGH), human serum albumin, ICAM-1, ICAM-1 receptor, LFA-1, LFA-1 receptor, insulin, insulin-like growth factor (IGF), IGF-I, IGF-II, interferon (IFN), IFN-alpha, IFN-beta, IFN-gamma, interleukin (IL), IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, keratinocyte growth factor (KGF), lactoferrin, leukemia inhibitory factor, luciferase, neurturin, neutrophil inhibitory factor (NIF), oncostatin M, osteogenic protein, oncogene product, paracitonin, parathyroid hormone, PD-ECSF, PDGF, peptide hormone, pleiotropin, protein A, protein G, pth, pyrogenic exotoxin A, pyrogenic exotoxin B, pyrogenic exotoxin C, pyy, relaxin, renin, SCF, small biosynthetic protein, soluble complement receptor I, soluble I-CAM 1, soluble interleukin receptor, soluble TNF receptor, somatomedin, somatostatin, somatotropin, streptokinase, superantigens, staphylococcal enterotoxin, SEA, SEB, SEC1, SEC2, SEC3, SED, SEE, steroid hormone receptor, superoxide dismutase, toxic shock syndrome toxin, thymosin alpha 1, tissue plasminogen activator, tumor growth factor (TGF), tumor necrosis factor, tumor necrosis factor alpha, tumor necrosis factor beta, tumor necrosis factor receptor (TNFR), VLA-4 protein, VCAM-1 protein, vascular endothelial growth factor (VEGF), urokinase, mos, ras, raf, met, p53, tat, fos, myc, jun, myb, rel, estrogen receptor, progesterone receptor, testosterone receptor, aldosterone receptor, LDL receptor, and corticosterone.