Pharmaceutical and industrial protein engineering: Where we are?

Pakistan Journal of Pharmaceutical Sciences

Volumn 26, Issue 1, 2013, Pages 217-232

  Amara, Amro Abd Al Fattah ^a  

^a KING SAUD UNIVERSITY   (Saudi Arabia)

Author keywords

Applications; Directed evolution; Protein engineering; Rational design

Indexed keywords

BASIC PROTEIN; BETA LACTAMASE; CATALYTIC ANTIBODY; DNA; DORNASE ALFA; HYBRID PROTEIN; INFLIXIMAB; INSULIN; OLIGONUCLEOTIDE; PANCREATIC RIBONUCLEASE; POLYKETIDE SYNTHASE; PROTEIN VARIANT; RNA;

ALGORITHM; AMINO ACID SEQUENCE; COVALENT BOND; DELETION MUTANT; DNA SHUFFLING; GENETIC ENGINEERING; IMMUNOGENICITY; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; MUTAGENESIS; PHARMACEUTICAL ENGINEERING; PROTEIN ENGINEERING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REGENERATIVE MEDICINE; REVIEW; SIGNAL TRANSDUCTION; SITE DIRECTED MUTAGENESIS; SYNTHESIS; TISSUE ENGINEERING;

ANIMALS; BIOTECHNOLOGY; DATABASES, GENETIC; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; HUMANS; KNOWLEDGE BASES; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEINS; RECOMBINANT PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; TECHNOLOGY, PHARMACEUTICAL;

EID: 84872193737     PISSN: 1011601X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (230)

1. Abendroth J, McCormick MS, Edwards TE, Staker B, Loewen R, Gifford M, Rifkin J, Mayer C, Guo W, Zhang Y, Myler P, Kelley A, Analau E, Hewitt SN, Napuli AJ, Kuhn P, Ruth RD and Stewart LJ (2010). X-ray structure determination of the glycine cleavage system protein H of Mycobacterium tuberculosis using an inverse Compton synchrotron X-ray source. J. Struct. Funct. Genomics, 11: 91-100.
2. Akarsu H, Burmeister WP, Petosa C, Petit I, Muller CW, Ruigrok RW and Baudin F (2003). Crystal structure of the M1 protein-binding domain of the influenza A virus nuclear export protein (NEP/NS2). EMBO J., 22: 4646-4655.
3. Alahuhta M, Salin M, Casteleijn MG, Kemmer C, El-Sayed I, Augustyns K, Neubauer P and Wierenga RK (2008). Structure-based protein engineering efforts with a monomeric TIM variant: The importance of a single point mutation for generating an active site with suitable binding properties. Protein Eng. Des. Sel., 21: 257-266.
4. Alekseyev VY, Liu CW, Cane DE, Puglisi JD and Khosla C (2007). Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Protein Sci., 16: 2093-2107.
5. Ali M, Hariharan AG, Mishra N and Jainal S (2009). Catalytic antibodies as potential therapeutics. Indian J. Biotechnol., 8: 253-258
6. Amara AA (2003). Ph.D. Thesis. Biochemical and Molecular Characterization of PHA synthases from Pseudomonas aeruginosa, Ralstonia eutropha, Aeromonas punctata as well as of the (R)-3- hydroxyacyl-ACP:CoA transacylase from Pseudomonas putida. Münster University.
7. Amara AA and Rehm BH (2003). Replacement of the catalytic nucleophile cysteine-296 by serine in class II polyhydroxyalkanoate synthase from Pseudomonas aeruginosa -mediated synthesis of a new polyester: Identification of catalytic residues. Biochem J., 374(2): 413-421.
8. Amara AA and Serour EA (2008). Wool quality improvement using thermophilic crude proteolytic microbial enzymes. American-Eurasian J. Agric. Environ. Sci., 3(4): 554-560.
9. Amara AA, Rehm BHA and Steinbüchel A (2001). Biopolymer overproduction by new mutants using simple methods for selection. In: DAAD-Bioforum-Berlin "Grenzenlos forschen" DAAD Biotechnologische Methoden, pp.231-239.
10. Amara AA, Steinbüchel A and Rehm BHA (2002). In vivo evolution of the Aeromonas punctata polyhydroxyalkanoate (PHA) synthase: Isolation and characterization of modified PHA synthases with enhanced activity. Appl. Microbiol. Biotechnol., 59: 477-482.
11. Anfinsen C (1972). The formation and stabilization of protein structure. Biochem. J., 128 (4): 737-749.
12. Anthea M, Hopkins J, McLaughlin CW, Maryanna SJ, Warner Q, LaHart D and Wright JD (1993). Human Biology and Health. Englewood Cliffs, New Jersey, Prentice Hall, USA.
13. Arulmuthu E, Williams D and Versteeg H (2009). The arrival of genetic engineering. IEEE Eng. Med. Biol. Mag., 28(1): 40-54.
14. Bai Y, Feng H and Zhou Z (2007). Population and structure determination of hidden folding intermediates by native-state hydrogen exchange-directed protein engineering and nuclear magnetic resonance. Methods Mol. Biol., 350: 69-81.
15. Ball P (2008). Complexity crystallised: Protein x-ray crystallography has come a long way from a 12 year search for the structure of a single protein. Chemistry World, pp.50-56.
16. Bang D, Makhatadze GI, Tereshko V, Kossiakoff AA and Kent SB (2005). Total chemical synthesis and X-ray crystal structure of a protein diastereomer: [D-Gln 35]ubiquitin. Angew. Chem. Int. Ed. Engl., 44: 3852-3856.
17. Baum C, Kalle C, Staal FJT, Fehse B, Schmidt M, Weerkamp F, Karlsson S, Wagemaker G and Williams DA (2004). Chance or necessity? Insertional mutagenesis in gene therapy and its consequences. Molecular Therapy, 9(1): 5-13.
18. Beese LS and Steitz TA (1991). Structural basis for the 39-59 exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism. EMBO J., 10: 25-33.
19. Bennett EJ, Bjerregaard J, Knapp JE, Chavous DA, Friedman AM, Royer WE Jr. and O'Connor CM (2003). Catalytic implications from the Drosophila protein L-isoaspartyl methyltransferase structure and site-directed mutagenesis. Biochem., 42: 12844-12853.
20. Best RB, Fowler SB, Herrera JL, Steward A, Paci E and Clarke J (2003). Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations. J. Mol. Biol., 330: 867-877.
21. Boeris V, Farruggia B, Romanini D and Pico G (2009). How flexible polymers interact with proteins and its relationship with the protein separation method by protein-polymer complex formation. Protein J., 28: 233-239.
22. Boes M, Dake BL, Booth BA, Sandra A, Bateman M, Knudtson K and Bar RS (2002). Structure-function relationships of insulin-like growth factor binding protein 6 (IGFBP-6) and its chimeras. Growth Horm. IGF. Res., 12: 91-98.
23. Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J and Schwede T (2009). Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc., 4: 1-13.
24. Branningan JA and Wilkinson AJ (2002). Protein engineering 20 years on, Nature Rev. Mol. Cell Biol., 3: 964-970.
25. Brautigam CA and Steitz TA (1998). Structural principles for the inhibition of the 39-59 exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J. Mol. Biol., 277: 363-377.
26. Bray BL (2003). Large-scale manufacture ofpeptide therapeutics by chemical synthesis. Nat. Rev. Drug Discov., 2: 587-593.
27. Breedveld FC (2000). Therapeutic monoclonal antibodies. Lancet, 355: 735-740.
28. Briki F, Doucet J and Etchebest C (2002). A procedure for refining a coiled coil protein structure using x-ray fiber diffraction and modeling. Biophys. J., 83:1774-83.
29. Brode PF, Erwin CR, Rauch DS, Barnett BL, Armpriester JM, Wang ESF and Rubingh DN (1966). Subtilisin BPN' variants: Increased hydrolytic activity on surface-bound substrates via decreased surface activity. Biochem., 36: 3162-3169.
30. Brode PF. Erwin CR. Rauch DS. Barnett BL, Armpriester JM, Wang ESF and Rubingh DN (1966). Subtilisin BPN' variants: Increased hydrolytic activity on surface-bound substrates via decreased surface activity. Biochem., 36: 3162-3169.
31. Brown E and fMaloy S (2006). Facile approach for constructing TEV insertions to probe protein structure in vivo. Biotechniques., 41: 721-724
32. Bryson JW, Desjarlais JR, Handel TM and DeGrado WF (1998). From coiled coils to small globular proteins: design of a native-like three-helix bundle. Protein Sci., 7(6): 1404-1414.
33. Calderone V (2004). Practical aspects of the integration of different software in protein structure solution. Acta. Crystallogr. D. Biol. Crystallogr., 60: 2150-2155.
34. Calderone V, Trabucco M, Vujicic A, Battistutta R, Giacometti GM, Andreucci F, Barbato R and Zanotti G (2003). Crystal structure of the PsbQ protein of photosystem II from higher plants. EMBO Rep., 4: 900-905
35. Caraglia1 M. Vitale G. Marra M. S. Del Prete, A. Lentini, A. Budillon, S. Beninati and A. Abbruzzese (2004). Translational and post-translational modifications of proteins as a new mechanism of action of Alpha-Interferon: Review article Amino Acids, 26: 409-417.
36. Cavasotto CN, Orry AJ, Murgolo NJ, Czarniecki MF, Kocsi SA, Hawes BE, O'Neill KA, Hine H, Burton MS, Voigt JH, Abagyan RA, Bayne ML and Monsma FJ, Jr. (2008). Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J. Med. Chem., 51: 581-588.
37. Chandrashekaran IR, Yao S, Wang CC, Bansal PS, Alewood PF, Forbes BE, Wallace JC, Bach LA and Norton RS (2007). The N-terminal subdomain of insulin-like growth factor (IGF) binding protein 6. Structure and interaction with IGFs. Biochem., 46: 3065-3074.
38. Chappell JD, Prota AE, Dermody TS, Stehle T (2002). Crystal structure of reovirus attachment protein sigma1 reveals evolutionary relationship to adenovirus fiber. EMBO J., 21: 1-11.
39. Chen C, Hyytinen E-R, Sun X, Helin HJ, Koivisto PA, Frierson HF, Jr, Vessella RL and Dong JT (2003). Deletion, Mutation, and Loss of Expression of KLF6 in Human Prostate Cancer. Am. J. Pathol., 162(4): 1349-1354
40. Chen QL, Tang XS, Yao WJ and Lu SQ (2009). Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein. Int. J. Biol. Sci., 5: 596-602.
41. Chen X and Shi Z (2009). Sequence Analysis of the Full-length cDNA and Protein Structure Homology Modeling of FABP2 from Paralichthys Olivaceus. Bioinform. Biol. Insights, 3: 29-35.
42. Chen X, Christopher A, Jones JP, Bell SG, Guo Q, Xu F, Rao Z and Wong LL (2002). Crystal structure of the F87W/Y96F/V247L mutant of cytochrome P-450cam with 1,3,5-trichlorobenzene bound and further protein engineering for the oxidation of pentachlorobenzene and hexachlorobenzene. J. Biol. Chem. 277: 37519-37526.
43. Chen Y, Tan W, Lu X, Lu Y, Qin S, Li S, Zeng Y, Bu H, Li Y and Cheng J (2007). Full-length cDNA cloning and protein three-dimensional structure modeling of porcine prothrombin. Blood Cells Mol. Dis., 38: 93-99.
44. Chiang SJ (2004). Strain improvement for fermentation and biocatalysis processes by genetic engineering technology. J. Ind. Microbiol. Biotechnol., 31: 99-108.
45. Chie L, Chung D and Pincus MR (2005). Specificity of inhibition of ras-p21 signal transduction by peptides from GTPase activating protein (GAP) and the son-of sevenless (SOS) ras-specific guanine nucleotide exchange protein. Protein J., 24: 253-258.
46. Chie L, Friedman FK, Duncan T, Chen JM, Chung D and Pincus M (2004). Loop domain peptides from the SOS ras-guanine nucleotide exchange protein, identified from molecular dynamics calculations, strongly inhibit ras signaling. Protein J., 23: 229-234.
47. Chin KH, Chou CC, Wang AH and Chou SH (2006). Crystal structure of XC5357 from Xanthomonas campestris: a putative tetracenomycin polyketide synthesis protein adopting a novel cupin subfamily structure. Proteins, 65: 1046-1050.
48. Choi JH, May BC, Govaerts C and Cohen FE (2009). Site-directed mutagenesis demonstrates the plasticity of the beta helix: implications for the structure of the misfolded prion protein. Structure, 17: 1014-1023.
49. Choi SB, Normi YM and Wahab HA (2009). Why hypothetical protein KPN00728 of Klebsiella pneumoniae should be classified as chain C of succinate dehydrogenase? Protein J., 28: 415-427.
50. Christendat D, Saridakis V, Kim Y, Kumar PA, Xu X and Semesi A, Joachimiak A, Arrowsmith CH, Edwards AM (2002). The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum. Protein Sci., 11: 1409-1414.
51. Coenraad JH and Hendriksen FM (2005). Refinement of polyclonal antibody production by combining oral immunization of chicken swith harvest of antibodies from the egg yolk. ILAR J. 46: 294-299.
52. Connor SJO', Meng YG, Rezaie AR and Presta LZ (1998). Humanization of anantibody against human protein C and calcium-dependence involving framework residues. Protein Engineering, 11(4): 321-328.
53. Costa MH, Quintilio W, Sant'Anna OA, Faljoni-Alario A and de Araujo PS (2002). The use of protein structure/activity relationships in the rational design of stable particulate delivery systems. Braz. J. Med. Biol. Res., 35: 727-730.
54. Cowan D (1996). Industrial enzyme technology. Trends Biotechnol., 14(6): 177-178.
55. Crameri A, Raillard SA, Bermudez E and Stemmer WP (1998). DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature, 391: 288-291.
56. Crawford JM, Dancy BCR, Hill EA, Udwary DW and Townsend CA (2006). Identification of astarte runit acyl-carrier protein transacylase domain in aniterative type I polyketidesynthase. PNAS, 103 (45): 16728-16733.
57. Crisman RL and Randolph TW (2009). Refolding of proteins from inclusion bodies is favored by a diminished hydrophobic effect at elevated pressures. Biotechnol. Bioeng., 102(2): 483-492.
58. Dai QH, Tommos C, Fuentes EJ, Blomberg MR, Dutton PL and Wand AJ (2002). Structure of a de novo designed protein model of radical enzymes. J. Am. Chem. Soc., 124: 10952-10953.
59. Dana CD, Bevan DR and Winkel BS (2006). Molecular modeling of the effects of mutant alleles on chalcone synthase protein structure. J. Mol. Model., 12: 905-914.
60. Debbage P (2009). Targeted drugs and nanomedicine: present and future. Curr. Pharm. Des., 15(2): 153-172.
61. Degim IT and Çelebi N (2007). Controlled delivery of peptides and proteins. Curr. Pharm. Des., 13: 99-117.
62. Du X, Cheng J and Song J (2009). Improved prediction of protein binding sites from sequences using genetic algorithm. Protein J., 28: 273-280.
63. Edelheit O, Hanukoglu A and Hanukoglu I (2009). Simple and efficient site-directed mutagenesis using two single-primer reactions in parallel to generate mutants for protein structure-function studies. BMC Biotechnol., 9: 61.
64. Ellrott K, Guo JT, Olman V and Xu Y (2007). Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays. Comput. Syst. Bioinformatics Conf., 6: 335-342.
65. Erie DA, Yager TD and von-Hippel PH (1992). The single-nucleotide addition cycle in transcription: A biophysical and biochemical perspective. Annu. Rev. Biophys. Biomol. Struct., 21: 379-415.
66. Ermakova I, Boldyreff B, Issinger OG and Niefind K (2003). Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit. J. Mol. Biol., 330: 925-934.
67. Ermakova-Gerdes S, Shestakov S and Vermaas W (1996). Random chemical mutagenesis of a specific psbDI region coding for a lumenal loop of the D2 protein of photosystem II in Synechocystis sp. PCC 6803. Plant Mol. Biol., 30: 243-254.
68. Evdokimov AG, Mekel M, Hutchings K, Narasimhan L, Holler T, McGrath T, Beattie B, Fauman E, Yan C, Heaslet H, Walter R, Finzel B, Ohren J, McConnell P, Braden T, Sun F, Spessard C, Banotai C, Al-Kassim L, Ma W, Wengender P, Kole D, Garceau N, Toogood P and Liu J (2008). Rational protein engineering in action: the first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus. J. Struct. Biol., 162: 152-169.
69. Feinberg H, Uitdehaag JC, Davies JM, Wallis R, Drickamer K and Weis WI (2003). Crystal structure of the CUB1-EGF-CUB2 region of mannose-binding protein associated serine protease-2. EMBO J., 22: 2348-2359.
70. Fernando P, Abdulle R, Mohindra A, Guillemette JG and Heikkila JJ (2002). Mutation or deletion of the Cterminal tail affects the function and structure of Xenopus laevis small heat shock protein, hsp30. Comp. Biochem. Physiol. B. Biochem. Mol. Biol., 133: 95-103.
71. Fieulaine S, Morera S, Poncet S, Monedero V, Gueguen-Chaignon V, Galinier A, Janin J, Deutscher J and Nessler S (2001). X-ray structure of HPr kinase: A bacterial protein kinase with a P-loop nucleotide-binding domain. EMBO J., 20: 3917-3927.
72. Findlow SC, Winsor C, Simpson TJ, Crosby J and Crump MP (2003). Solution structure and dynamics of oxytetracycline polyketide synthase acyl carrier protein from Streptomyces rimosus. Biochem., 42: 8423-8433.
73. Finkelstein AV and Galzitskaya OV (2004). Physics of protein folding. Physics of Life Reviews, pp.23-56.
74. Flaman AS, Chen JM, Van Iderstine SC and Byers DM (2001). Site-directed mutagenesis of acyl carrier protein (ACP) reveals amino acid residues involved in ACP structure and acyl-ACP synthetase activity. J. Biol. Chem., 276: 35934-35939.
75. Fortier LA, Kornatowski MA, Mohammed HO, Jordan MT, O'Cain LC and Stevens WB (2005). Age-related changes in serum insulin-like growth factor-I, insulin-like growth factor-I binding protein-3 and articular cartilage structure in Thoroughbred horses. Equine. Vet. J., 37: 37-42.
76. Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M and Clarke J (2002). Mechanical unfolding of a titin Ig domain: Structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J. Mol. Biol., 322: 841-849.
77. Freemont PS, Friedman JM, Beese LS, Sanderson MR and Steitz TA (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. Natl. Acad. Sci. USA., 85: 8924-8928.
78. Fukunishi Y, Nakamura H (2008). Prediction of protein-ligand complex structure by docking software guided by other complex structures. J. Mol. Graph. Model., 26: 1030-1033.
79. Gan HH, Perlow RA, Roy S, Ko J, Wu M, Huang J, Yan S, Nicoletta A, Vafai J, Sun D, Wang L, Noah JE, Pasquali S and Schlick T (2002). Analysis of Protein Sequence/Structure Similarity Relationships. Biophysical J., 83: 2781-2791.
80. Gaudier M, Gaudin Y and Knossow M (2002). Crystal structure of vesicular stomatitis virus matrix protein. EMBO J., 21: 2886-2892.
81. Gavira JA, Toh D, Lopez-Jaramillo J, Garcia-Ruiz JM and Ng JD (2002). Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling. Acta. Crystallogr. D. Biol. Crystallogr., 58: 1147-1154.
82. Glickman, BW and Radman M (1980). Escherichia coli mutator mutants deficient in methylation-instructed DNA Mismatch correction. Proc. Natl. Acad. Sci. USA. 77: 1063-1067.
83. Gomes J and Steiner W (2004). Extremophiles and Extremozymes. Food Technol. Biotechnol., 42(4): 223-235.
84. Goodenough PW (1995). A review of protein engineering for the food industry. Mol. Biotechnol., 4: 151-166.
85. Greener A, Callahan M and Jerpseth B (1997). An efficient random mutagenesis technique using an E. coli Mutator Strain. Mol. Biotechnol., 7: 189-195.
86. Gupta R, Beg QK and Lorenz P (2002b). Bacterial alkaline proteases: molecular approaches and industrial applications. Appl. Microbiol. Biotechnol., 59: 15-32.
87. Gupta R, Beg QK, Khan S and Chauhan B (2002a). An overview on fermentation, downstream processing and properties of microbial alkaline proteases. Appl. Microbiol. Biotechnol., 60: 381-395.
88. Guzmán F, Barberis S and Illanes A (2006). Peptide synthesis: chemical or enzymatic. Electron J. Biotechn., 0717-3458
89. Han KD, Park SJ, Jang SB and Lee BJ (2008). Solution structure of conserved hypothetical protein HP0892 from Helicobacter pylori. Proteins, 70: 599-602.
90. Han KD, Park SJ, Jang SB, Son WS and Lee BJ (2005). Solution structure of conserved hypothetical protein HP0894 from Helicobacter pylori. Proteins, 61: 1114-1116.
91. Harris A (1992). Cystic fibrosis gene. Brit. Med. Bull., 48: 738-753.
92. Hartely H (1951). Origin of the word 'Protein'. Nature, 168: 244.
93. Hattori M, Mizohata E, Manzoku M, Bessho Y, Murayama K, Terada T, Kuramitsu S, Shirouzu M and Yokoyama S (2005). Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8. Proteins, 61: 1117-1120.
94. Headey SJ, Keizer DW, Yao S, Brasier G, Kantharidis P, Bach LA and Norton RS (2004). C-terminal domain of insulin-like growth factor (IGF) binding protein-6: Structure and interaction with IGF-II. Mol. Endocrinol., 18: 2740-2750.
95. Herrmann T, Guntert P and Wuthrich K (2002a). Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J. Biomol. NMR., 24: 171-189.
96. Herrmann T, Guntert P and Wuthrich K (2002b). Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol., 319: 209-227.
97. Ho Y, Hsiao JC, Yang MH, Chung CS, Peng YC, Lin TH, Chang W and Tzou DL (2005). The oligomeric structure of vaccinia viral envelope protein A27L is essential for binding to heparin and heparan sulfates on cell surfaces: a structural and functional approach using site-specific mutagenesis. J. Mol. Biol., 349: 1060-1071.
98. Hoffmann N, Amara AA, Beermann BrB, Qi Q, Hinz HJ and Rehm BHA (2002). Biochemical characterization of the Pseudomonas putida 3-hydroxyacyl ACP:CoA transacylase which diverts intermediates of fatty acid de novo biosynthesis. J. Biol. Chem., 277: 42926-42936.
99. Holmes MA, Buckner FS, Van Voorhis WC, Mehlin C, Boni E, Earnest TN, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Zucker F, Schoenfeld LW, Hol WG and Merritt EA (2006). Structure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparum. Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun., 62: 180-185.
100. Holmwood G and Schindler M (2009). Protein structure based rational design of ecdysone agonists. Bioorg. Med. Chem., 17: 4064-4070.
101. Horikoshi K (1999). Alkaliphiles: some applications of their products for biotechnology. Microbiol. Mol. Biol. Rev., 63: 735-750.
102. Hua QX and Weiss MA (2004). Mechanism of insulin fibrillation: The structure of insulin under amyloidogenic conditions resembles a protein-folding intermediate. J. Biol. Chem., 279: 21449-21460.
103. Huang K, Maiti NC, Phillips NB, Carey PR and Weiss MA (2006). Structure-specific effects of protein topology on cross-beta assembly: Studies of insulin fibrillation. Biochem., 45: 10278-10293.
104. Huang RB, Du QS, Wei YT, Pang ZW, Wei H and Chou KC. (2009). Physics and chemistry-driven artificial neural network for predicting bioactivity of peptides and proteins and their design. J. Theor. Biol., 256(3): 428-435.
105. Hutchison CA, Phillips S, Edgell MH, Gillam S, Jahnke P and Smith M (1978). Mutagenesis at a specific position in a DNA sequence. J. Biol. Chem., 253(18): 6551-6560.
106. Ifuku K, Nakatsu T, Kato H and Sato F (2004). Crystal structure of the PsbP protein of photosystem II from Nicotiana tabacum. EMBO Rep., 5: 362-367.
107. Ikeda RA and Richardson CC (1986). Interactions of the RNA polymerase of bacteriophage T7 with its promoter during binding and initiation of transcription. Proc. Natl. Acad. Sci. USA., 83: 3614-3618.
108. Ito S, Kobayashi T, Ara K, Ozaki K, Kawai S and Hatada Y (1998). Alkaline detergent enzymes from alkaliphiles: enzymatic properties, genetics, and structures. Extremophiles, 2: 185-190.
109. Iwata Y, Naito S, Itai A and Miyamoto S (2001). Protein structure-based de novo design and synthesis of aldose reductase inhibitors. Drug Des. Discov., 17: 349-359.
110. Jang SB, Kwon AR, Son WS, Park SJ and Lee BJ (2009). Crystal structure of hypothetical protein HP0062 (O24902-HELPY) from Helicobacter pylori at 1.65 A resolution. J. Biochem., 146: 535-540.
111. Jiang H and Blouin C (2007). Insertions and the emergence of novel protein structure: A structure-based phylogenetic study of insertions. BMC Bioinformatics, 8: 444.
112. Jones PT, Dear PH, Foote J, Neuberger MS and Winter G (1986). Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature, 321: 522-525.
113. Kan CC (2002). Impact of recombinant DNA technology and protein engineering on structure-based drug design: case studies of HIV-1 and HCMV proteases. Curr. Top. Med. Chem., 2: 247-269.
114. Kang W and Jang J (2009). Protein engineering, expression, and activity of novel fusion protein processing keratinocyte growth factor 2 and fibronectin. Acta. Biochim. Biophys Sin., 41: 16-20.
115. Kao SL, Chong SS and Lee CGL (2000). The role of single nucleotide polymorphisms (SNPs) in understanding complex disorders and pharmacogenomics. Ann. Acad. Med. Singapore., 29: 376-382.
116. Kasrayan A, Bocola M, Sandstrom AG, Laven G and Backvall JE (2007). Prediction of the Candida antarctica lipase A protein structure by comparative modeling and site-directed mutagenesis. Chembiochem., 8: 1409-1415.
117. Kendrew J, Bodo G, Dintzis H, Parrish R, Wyckoff H and Phillips D (1958). A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature, 181(4610): 662-666.
118. Kendrew JC, Bodo G, Dintzis HM and Parrish RG (1958). A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature, 181(4610): 662-666.
119. Khodagholi F, Eftekharzadeh B and Yazdanparast R (2008). A new artificial chaperone for protein refolding: sequential use of detergent and alginate. Protein J., 27: 123-129.
120. Ki TK, Rosenberg J, Virtanen P, Lamminmäki U, Tuomola M and Saviranta P (2003). Further improvement of broad specificity hapten recognition with protein engineering. Protein Eng., 16(1): 37-46.
121. Kim SJ, Jeong DG, Jeong SK, Yoon TS and Ryu SE (2007). Crystal structure of the major diabetes autoantigen insulinoma-associated protein 2 reveals distinctive immune epitopes. Diabetes, 56: 41-48.
122. King DA, Hall BE, Iwamoto MA, Win KZ, Chang JF and Ellenberger T (2006). Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments. J. Biol. Chem., 281: 20107-20119.
123. Kiss RS, Weers PM, Narayanaswami V, Cohen J, Kay CM and Ryan RO (2003). Structure-guided protein engineering modulates helix bundle exchangeable apolipoprotein properties. J. Biol. Chem., 278: 21952-21959.
124. Klepeis JL, Wei Y, Hecht MH and Floudas CA (2005). Ab initio prediction of the three-dimensional structure of a de novo designed protein: A double-blind case study. Proteins, 58: 560-570.
125. Ko J and Ma J (2005). A rapid and efficient PCR-based mutagenesis method applicable to cell physiology study. Am. J. Physiol. Cell Physiol., 288: 1273-1278.
126. Kuang Z, Yao S, Keizer DW, Wang CC, Bach LA, Forbes BE, Wallace JC and Norton RS (2006). Structure, dynamics and heparin binding of the C-terminal domain of insulin-like growth factor-binding protein-2 (IGFBP-2). J. Mol. Biol., 364: 690-704.
127. Kurgan L (2008). On the relation between the predicted secondary structure and the protein size. Protein J., 27: 234-239.
128. Lai JR, Koglin A and Walsh CT (2006). Carrier protein structure and recognition in polyketide and nonribosomal peptide biosynthesis. Biochem., 45: 14869-14879.
129. Lazar GA, Desjarlais JR and Handel TM (1997). de novo design of the hydrophobic core of ubiquitin. Protein Sci., 6(6): 1167-1178.
130. Leuschner C and Antranikan G (1995). Heat stable enzymes from extremely thermophilic and hyperthermophilicmic microorganisms. World J. Microbiol. Biotechnol., 11: 95-114.
131. Li S, Depetris RS, Barford D, Chernoff J and Hubbard SR (2005). Crystal structure of a complex between protein tyrosine phosphatase 1B and the insulin receptor tyrosine kinase. Structure, 13: 1643-1651.
132. Lin KF, Lee TR, Tsai PH, Hsu MP, Chen CS and Lyu PC (2007). Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin. Proteins, 68: 530-540.
133. Lippincott-Schwartz J and Patterson GH (2003). Development and use of fluorescent protein markers in living cells. Science, 300: 87-91.
134. Liu H-L, Doleyres Y, Coutinho PM, Ford C and Reilly PJ (2000). Replacement and deletion mutations in the catalytic domain and belt region of Aspergillus aeamori glucoamylase to enhance thermostability. Protein Eng., 13(9): 655-659.
135. Liu J, Li C, Ke S and Satyanarayanajois SD (2007). Structure-based rational design of beta-hairpin peptides from discontinuous epitopes of cluster of differenttiation 2 (CD2) protein to modulate cell adhesion interaction. J. Med. Chem., 50: 4038-4047.
136. Ludwig K, Baljinnyam B, Herrmann A and Bottcher C (2003). The 3D structure of the fusion primed Sendai F-protein determined by electron cryomicroscopy. EMBO J., 22: 3761-3771.
137. Mark S, Kubler B, Honing S, Oesterreicher S, John H, Braulke T, Forssmann WG and Standker L (2005). Diversity of human insulin-like growth factor (IGF) binding protein-2 fragments in plasma: Primary structure, IGF-binding properties, and disulfide bonding pattern. Biochemistry, 44: 3644-3652.
138. Matagne A, Lamotte-Brasseur J and Freare J-M (1998). Catalytic properties of class A b-lactamases: Efficiency and diversity. J. Biochem., 330: 581-598.
139. Matsuura T and Pluckthun A (2004). Strategies for selection from protein libraries composed of de novo designed secondary structure modules. Orig. Life Evol. Biosph., 34: 151-157.
140. Michel MF, Zenklusen F, Müller D, Muller B and Schumperli D (2000). Positive and negative mutant selection in the human histone hairpin-binding protein using the yeast three-hybrid system. Nucleic Acids Research, pp.1594-1603.
141. Milik M, Szalma S and Olszewski KA (2003). Common Structural Cliques: a tool for protein structure and function Analysis. Protein Eng., 16(8): 543-552.
142. Mirzaei H, McBee JK, Watts J and Aebersold R (2008). Comparative evaluation of current peptide production plat forms used in absolute quantification in Proteomics . Mol. Cell Proteomics, 7(4): 813-823.
143. Miyahara A, Okamura-Oho Y, Miyashita T, Hoshika A and Yamada M (2003). Genomic structure and alternative splicing of the insulin receptor tyrosine kinase substrate of 53-kDa protein. J. Hum. Genet., 48: 410-414.
144. Molina R, Gonzalez A, Stelter M, Perez-Dorado I, Kahn R, Morales M, Moscoso M, Campuzano S, Campillo NE, Mobashery S, Garcia JL, Garcia P and Hermoso JA (2009). Crystal structure of CbpF, a bifunctional choline-binding protein and autolysis regulator from Streptococcus pneumoniae. EMBO Rep ., 10: 246-251.
145. Moore JP and Sweet RW (1993). The HIV gp120-CD4 interaction: A target for pharmacological or immunological intervention? Perspect. Drug Discov., 1: 235-250.
146. Moss AJ, Sharma S and Brindle NPJ (2009). Bionanotechnology II: From biomolecular assembly to applications rational design and protein engineering of growth factors for regenerative medicine and tissue engineering. Biochem. Soc. Trans., 37: 717-721.
147. Muirhead H and Perutz M (1963). Structure of hemoglobin. A three-dimensional fourier synthesis of reduced human hemoglobin at 5.5 A resolution. Nature, 199(4894): 633-638.
148. Muller RH and Keck CM (2004). Challenges and solutions for the delivery of biotech drugs - a review of drug nanocrystal technology and lipid nanoparticles. J. Biotechnol., 113: 151-170.
149. Munson M, O'Brien R, Sturtevant JM and Regan L (1994). Redesigning the hydrophobic core of a four-helix-bundle protein. Protein Sci., 3(11): 2015-2022.
150. Nicolini C and Pechkova E (2006). Structure and growth of ultrasmall protein microcrystals by synchrotron radiation: I. microGISAXS and microdiffraction of P450scc. J. Cell. Biochem., 97: 544-552.
151. Nielsen FS, Sauer J, Backlund J, Voldborg B, Gregorius K, Mouritsen S and Bratt T (2004). Insertion of foreign T cell epitopes in human tumor necrosis factor alpha with minimal effect on protein structure and biological activity. J. Biol. Chem., 279: 33593-33600.
152. Nielsen PK, Bonsager BC, Fukuda K and Svensson B (2004). Barley alpha-amylase/subtilisin inhibitor: Structure, biophysics and protein engineering. Biochim. Biophys. Acta., 1696: 157-164.
153. Nishijima K (2005). Attitude of pharmaceutical company toward protein structure analysis. Tanpakushitsu Kakusan Koso, 50: 862-868.
154. O'Maille PE, Bakhtina M and Tsai MD (2002). Structure-based combinatorial protein engineering (SCOPE) J. Mol. Biol., 321: 677-691.
155. O'Maille PE, Tsai MD, Greenhagen BT, Chappell J and Noel JP (2004). Gene library synthesis by structure-based combinatorial protein engineering. Methods Enzymol., 388: 75-91.
156. Ostermeier M, Nixon AE, Shim J and Benkovic SJ (1999). Combinatorial protein engineering by incremental truncation. Proc. Natl. Acad. Sci. USA., 96: 3562-3567.
157. Ozbek S, Engel J and Stetefeld J (2002). Storage function of cartilage oligomeric matrix protein: The crystal structure of the coiled-coil domain in complex with vitamin D(3). EMBO J., 21: 5960-5968.
158. Parker JS, Roe SM and Barford D (2004). Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J., 23: 4727-4737.
159. Paul S, Gabibov A and Massey R (1994). Catalytic Antibodies "Conference Overview". Mol. Biotechnol., 1: 109-111.
160. Pechkova E and Nicolini C (2006). Structure and growth of ultrasmall protein microcrystals by synchrotron radiation: II. microGISAX and microscopy of lysozyme. J. Cell Biochem., 97: 553-560.
161. Platt OS and Falcone JF (1988). Membrane Protein Lesions in Erythrocytes with Heinz Bodies J. Clin. Invest., 82:1051-1058.
162. Poza M, Sestelo AB, Ageitos JM, Vallejo JA, Veiga-Crespo P and Villa TG (2007). Cloning and expression of the XPR2 gene from Yarrowia lipolytica in Pichia pastoris. J. Agric. Food Chem., 55: 3944-3948.
163. Procopiou A, Allinson NM, Jones GR and Clarke DT (2004). Estimation of protein secondary structure from synchrotron radiation circular dichroism spectra. Conf. Proc. IEEE Eng. Med. Biol. Soc., 4: 2893-2896.
164. Qabar M, Urban J, Sia C, Klein M and Kahn M (1996). Pharmaceutical applications of peptidomimetics. Lett. Pept. Sci., 3: 25-30.
165. Quine JR, Cross TA, Chapman MS and Bertram R (2004). Mathematical aspects of protein structure determination with NMR orientational restraints. Bull. Math. Biol., 66: 1705-1730.
166. Rao M, Tankasale A, Ghatge M and Desphande V (1998). Molecular and biotechnological aspects of microbial proteases. Microbiol. Mol. Biol. Rev., 62: 597-634.
167. Rehm BHA, Antonio RV, Spiekermann P, Amara AA and Steinbüchel A (2002). Molecular characterization of the poly (3-hydroxybutyrate) (PHB) synthase from Ralstonia eutropha: in vitro evolution, site-specific mutagenesis and development of a PHB synthase protein model. Biochim. Biophys. Acta., 1594: 178-190.
168. Rubingh DN (1996a). Engineering proteases with improved properties for detergents. In: Enzyme Technology for industrial Applications Edited by Savage L. Southborough MA: IBC Biomedical Library Series, pp.98-123
169. Rubingh DN (1996b). The influence of sutfactants on enzyme activity. Curr. Opin. Colfoid. Interface Sci., 1: 598-603.
170. Runbingh DN (1997). Protein Engineering from a bioindustrial point of view. Curr. Opin. Biotechnol., 8: 417-422.
171. Sala A, Capaldi S, Campagnoli M, Faggion B, Labo S, Perduca M, Romano A, Carrizo ME, Valli M, Visai L, Minchiotti L, Galliano M and Monaco HL (2005). Structure and properties of the C-terminal domain of insulin-like growth factor-binding protein-1 isolated from human amniotic fluid. J. Biol. Chem., 280: 29812-29819.
172. Sanger F and Thompson EO (1953a). The amino-acid sequence in the glycyl chain of insulin. I. The identification of lower peptides from partial hydrolysates Biochem. J., 53(3): 353-366.
173. Sanger F and Thompson EO (1953b). The amino-acid sequence in the glycyl chain of insulin. II. The investigation of peptides from enzymic hydrolysates. Biochem. J., 53(3): 366-374.
174. Satyanarayana T, Raghukumar C and Shivaji S (2005). Extremophilic microbes: Diversity and perspectives. Current Science, 89(1): 78-90.
175. Schäfer T, Kirk O, Borchert TV, Fuglsang CC, Pedersen S, Salmon S, Olsen HS, Deinhammer R and Lund H (2005). Enzymes for technical applications. In: Biopolymers,eds Fahnestock SR and Steinbüchel A, Wiley VCH (Editor), Chapter 13, pp.377-437.
176. Scheraga HA (1985). Effect of side chain-backbone electrostatic interactions on the stability of a-helices Proc. Natl. Acad. Sci. USA, 82: 5585-5587.
177. Schmidt A, Dordick JS, Hauer B, Kiener A, Wubbolts M and Witholt B (2001). Industrial biocatalysis today and tomorrow. Nature, 409: 258-268.
178. Senesh G, Bushi D, Neta A and Yodfat O (2010). Compatibility of insulin Lispro, Aspart and Glulisine with the SoloTM MicroPump, a novel miniature insulin pump. J. Diabetes Sci. Technol., 4: 104-110.
179. Severin K, Lee DH and Kennan AJ (1997). A synthetic peptide ligase. Nature, 389(6652): 706-709.
180. Shak S, Capon DJ, Hellmiss R, Marsters SA and Baker CL (1990). Recombinant human DNase I reduces the viscosity of cystic fibrosis sputum. Proc. Natl. Acad. Sci. USA, 87: 9188-9192.
181. Shen S, Hu G and Tuszynski JA (2007). Analysis of protein three-dimension structure using amino acids depths. Protein J., 26: 183-192.
182. Shen Y-C, Wang X-H and Wang X-M (2006). High efficient mammalian expression and secretion of a functional humanized single-chain Fv/human interleukin-2 molecules World J. Gastroenterol., 12(24): 3859-3865.
183. 2+ in a de novo designed protein. Biopolymers, 91: 907-916.
184. Sivasubramanian A, Sircar A, Chaudhury S and Gray JJ (2009). Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins, 74(2): 497-514.
185. Skelton NJ, Chen YM, Dubree N, Quan C, Jackson DY, Cochran A, Zobel K, Deshayes K, Baca M, Pisabarro MT and Lowman HB (2001). Structure-function analysis of a phage display-derived peptide that binds to insulin-like growth factor binding protein 1. Biochem., 40: 8487-8498.
186. Standley DM, Kinjo AR, Kinoshita K and Nakamura H (2008). Protein structure databases with new web services for structural biology and biomedical research. Brief. Bioinform., 9: 276-285.
187. Stemmer WPC (1994). Rapid evolution of a protein in vitro by DNA shuffling. Nature, 370: 389-391.
188. Strausberg SL, Alexander PA, Gallagher DT, Gilliland GL, Barnett BL and Bryan PN (1995). Directed evolution of a subtilisin with calcium-independent stability. Bio-Technol., 13: 669-673.
189. Sueda S, Islam MN and Kondo H (2004). Protein engineering of pyruvate carboxylase: Investigation on the function of acetyl-CoA and the quaternary structure. Eur. J. Biochem., 271: 1391-1400.
190. Sugimoto I, Li Z, Yoshitome S, Ito S and Hashimoto E (2004). Mass-spectrometric identification of binding proteins of Mr 25,000 protein, a part of vitellogenin B1, detected in particulate fraction of Xenopus laevis oocytes. Protein J., 23: 467-473.
191. Sumner JB (1926). The isolation and crystallization of the enzyme urease. preliminary paper J. Biol. Chem., 69: 435-441.
192. Taguchi S, Maehara A, Takase K, Nakahara M, Nakamura H and Doi Y (2001). Analysis of mutational effects of a polyhydroxybutyrate (PHB) polymerase on bacterial PHB accumulation using an in vivo assay system. FEMS Microbiol. Lett., 198(1): 65-71.
193. Taguchi S, Nakamura H, Hiraishi T, Yamato I and Doi Y (2002). In vitro evolution of a polyhydroxybutyrate synthase by intragenic suppression-type mutagenesis. J. Biochem. (Tokyo), 131(6): 801-806.
194. Takekiyo T, Takeda N, Isogai Y, Kato M and Taniguchi Y (2007). Pressure stability of the alpha-helix structure in a de novo designed protein (alpha-l-alpha)(2) studied by FTIR spectroscopy. Biopolymers, 85: 185-188.
195. Tandang MR, Atsuta N, Maruyama N, Adachi M and Utsumi S (2005). Evaluation of the solubility and emulsifying property of soybean proglycinin and rapeseed procruciferin in relation to structure modified by protein engineering. J. Agric. Food Chem ., 53: 8736-8744.
196. Tang M, Waring AJ and Hong M (2007). Trehalose-protected lipid membranes for determining membrane protein structure and insertion. J. Magn. Reson., 184: 222-227.
197. Tang XM, Lakay FM, Shen W, Shao WL, Fang HY, Prior BA, Wang ZX and Zhuge J (2004). Purification and characterisation of an alkaline protease used in tannery industry from Bacillus licheniformis. Biotechnol. Lett., 26: 1421-1424.
198. Teixeira RJ, Silva VC, Gazolla HM, Cunha SB and Guimaraes MM (2002). The relationship between ovarian structure and serum insulin, insulin-like growth factor-I (IGF-I) and its binding protein (IGFBP-1 and IGFBP-3) levels in premature pubarche. J. Pediatr. Endocrinol. Metab., 15: 69-75.
199. Thaa B, Zahn R, Matthey U, Kroneck PM, Burkle A and Fritz G (2008). The deletion of amino acids 114-121 in the TM1 domain of mouse prion protein stabilizes its conformation but does not affect the overall structure. Biochim. Biophys. Acta. 1783: 1076-1084.
200. Thangam EB and Rajkumar GS (2002). Purification and characterization of alkaline protease from Alcaligenes faecalis. Biotechnol. Appl. Biochem., 35:149-154.
201. Thore S, Mauxion F, Seraphin B and Suck D (2003). X-ray structure and activity of the yeast Pop2 protein: A nuclease subunit of the mRNA deadenylase complex. EMBO Rep., 4: 1150-1155.
202. Timsit Y, Allemand F, Chiaruttini C and Springer M (2006). Coexistence of two protein folding states in the crystal structure of ribosomal protein L20. EMBO Rep., 7: 1013-1018.
203. Tratschin JD, Miller IL and Carter BJ (1984). Genetic-analysis of adeno-associated virus-properties of deletion mutants constructed in vitro and evidence for an adeno-associated virus-replication function. J. Virol., 51: 611-619.
204. Vajdos FF, Ultsch M, Schaffer ML, Deshayes KD, Liu J, Skelton NJ and de Vos AM (2001). Crystal structure of human insulin-like growth factor-1: Detergent binding inhibits binding protein interactions. Biochem., 40: 11022-11029.
205. Valer M (1975). Skin irritancy and sensitivity to laundry detergents containing proteolytic enzymes. Part II. Berufsdermatosen, 23: 96-115.
206. van den Burg B (2003). Extremophiles as a source for novel enzymes. Curr. Opin. Microbiol., 6: 213-218.
207. Vannini A, Volpari C, Gargioli C, Muraglia E, Cortese R, De Francesco R, Neddermann P and Marco SD (2002). The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA. EMBO J., 21: 4393-4401.
208. Venkatachalam KV, Huang W, LaRocco M and Palzkil T (1994). Characterization of TEM-1 P-Lactamase mutants from positions 238 to 241 with increased catalytic efficiency for ceftazidim. J. Boil. Chem., 269: 23444-43450.
209. Visegràdy B. Than NG. Kilàr F. Sümegi B, Than GN and Bohn H. (2001). Homology modelling and molecular dynamics studies of human placental tissue protein 13 (galectine-13). Protein Eng., 14(11): 878-880.
210. von-Hippel PH. Bear DG. Morgan WD and McSwiggen JA (1984). Protein-nucleic acid interactions in transcription: A molecular analysis. Annu. Rev. Biochem., 53: 389-416.
211. Vorberg I, Chan K and Priola SA (2001). Deletion of beta-strand and alpha-helix secondary structure in normal prion protein inhibits formation of its protease-resistant isoform. J. Virol., 75: 10024-10032.
212. Wan ZL, Huang K, Hu SQ, Whittaker J and Weiss MA (2008). The structure of a mutant insulin uncouples receptor binding from protein allostery. An electrostatic block to the TR transition. J. Biol. Chem., 283: 21198-21210.
213. Wang J, Feng J, Shi M, Qian L, Chen L, Yu M, Xu R, Shen B and Guo N (2008). De novo design of ErbB2 epitope targeting fusion protein stabilized by coiled coil structure. Mol. Immunol., 45: 106-116.
214. Wang L, Schultz PG (2002). Expanding the genetic code. Chem. Commun. 1: 1-11.
215. Weiss MA, Nakagawa SH, Jia W, Xu B, Hua QX, Chu YC, Wang RY and Katsoyannis PG (2002). Protein structure and the spandrels of San Marco: insulin's receptor-binding surface is buttressed by an invariant leucine essential for its stability. Biochem., 41: 809-819
216. Whittingham JL, Havelund S and Jonassen I (1997). Crystal structure of a prolonged-acting insulin with albumin-binding properties. Biochem 36: 2826-2831.
217. Winter G, Fersht AR, Wilkinson AJ, Zoller M and Smith M (1982). Redesigning enzyme structure by site-directed mutagenesis: Tyrosyl tRNA synthetase and ATP binding. Nature, 299 (5885): 756-758.
218. Woo EJ, Marshall J, Bauly J, Chen JG, Venis M, Napier RM and Pickersgill RW (2002). Crystal structure of auxin-binding protein 1 in complex with auxin. EMBO J., 21: 2877-2885.
219. Woods VL, Jr. and Hamuro Y (2001). High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: Utility in pharmaceutical design. J. Cell. Biochem. Suppl. Suppl., 37: 89-98.
220. Yan C, Wu F, Jernigan RL, Dobbs D and Honavar V (2008). Characterization of protein-protein interfaces. Protein J., 27: 59-70.
221. Yang C, Salerno JC and Koretz JF (2005). NH2-terminal stabilization of small heat shock protein structure: A comparison of two NH2-terminal deletion mutants of alphaA-crystallin. Mol. Vis., 11: 641-647.
222. Yang Y-R, Zhu H, Fang N, Liang X, Zhong C-Q, Tang X-F, Shen P and Tang B (2008). Cold-adapted maturation of thermophilic WF146 protease by mimicking the propeptide binding interactions of psychrophilic subtilisin S41. FEBS Letters, 582: 2620-2626.
223. Yao M, Zhou Y and Tanaka I (2006). LAFIRE: Software for automating the refinement process of protein-structure analysis. Acta Crystallogr. D Biol. Crystallogr., 62: 189-196.
224. You L and Arnold FH (1994). Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. Protein Eng., 9: 77-83.
225. Yu P, Jonker A and Gruber M (2009). Molecular basis of protein structure in proanthocyanidin and anthocyanin-enhanced Lc-transgenic alfalfa in relation to nutritive value using synchrotron-radiation FTIR micro-spectroscopy: A novel approach. Spectrochim Acta. A. Mol. Biomol. Spectrosc., 73: 846-853.
226. Yu P, McKinnon JJ, Christensen CR and Christensen DA (2004). Using synchrotron-based FTIR micro-spectroscopy to reveal chemical features of feather protein secondary structure: Comparison with other feed protein sources. J. Agric. Food Chem., 52: 7353-7361.
227. Yuen CM and Liu DR (2007). Dissecting protein structure and function using directed evolution. Nat. Methods, 4: 995-997.
228. Yun M, Bronner CE, Park CG, Cha SS, Park HW and Endow SA (2003). Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein, Ncd. EMBO J., 22: 5382-5389.
229. Zhao H and Arnold FH (1997). Optimization of DNA shuffling for high fidelity recombination. Nucleic Acids Res., 25(6): 1307-1308.
230. Zou H, Strzalka J, Xu T, Tronin A and Blasie JK (2007). Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin- binding protein maquette at soft interfaces by molecular dynamics simulations. J. Phys. Chem. B., 111: 1823-1833.