[1] | Sali A, Shakhnovich E, Karplus M (1994) How does a protein fold? Nature 369: 248–251. doi: 10.1038/369248a0
|
[2] | Uversky VN, Dunker AK (2010) Understanding protein non-folding. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1804(6): 1231–1264. doi: 10.1016/j.bbapap.2010.01.017
|
[3] | Uversky VN (2013) Under-folded proteins: Conformational ensembles and their roles in protein folding, function and pathogenesis. Biopolymers 99: 870–887. doi: 10.1002/bip.22298
|
[4] | Lesk AM, Chothia C (1980) How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 136(3): 225–70. doi: 10.1016/0022-2836(80)90373-3
|
[5] | Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4): 823–826.
|
[6] | Wagner A (2007) Robustness and Evolvability in Living Systems. Princeton: Princeton Univ. Press. 384 p.
|
[7] | Bloom JD, Labthavikul ST, Otey CR, Arnold FH (2006) Protein stability promotes evolvability. Proc. Natl. Acad. Sci. USA 103(15): 5869–5874. doi: 10.1073/pnas.0510098103
|
[8] | Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc. Natl. Acad. Sci. USA 104(41): 16152–16157. doi: 10.1073/pnas.0705366104
|
[9] | Bornscheuer UT, Huisman GW, Kazlauskas RJ, Lutz S, Moore JC, et al. (2012) Engineering the third wave of biocatalysis. Nature 485: 185–194. doi: 10.1038/nature11117
|
[10] | Shoichet BK, Baase WA, Kuroki R, Matthews BW (1995) A relationship between protein stability and protein function. Proc. Natl. Acad. Sci. USA 92(2): 452–456. doi: 10.1073/pnas.92.2.452
|
[11] | Beadle BM, Shoichet BK (2002) Structural bases of stability–function tradeoffs in enzymes. J Mol Biol 321(2): 285–296. doi: 10.1016/s0022-2836(02)00599-5
|
[12] | Gr?ger H, Asano Y (2012) Introduction–Principles and Historical Landmarks of Enzyme Catalysis in Organic Synthesis. In: Drauz K, Gr?ger H, May O, editors. Enzyme Catalysis in Organic Synthesis, Third Edition. Weinheim: Wiley-VCH. pp.1–42
|
[13] | Shaw A, Bott R (1996) Engineering enzymes for stability. Curr Opin Struct Biol 6(4): 546–550.
|
[14] | Eijsink VG, Bj?rk A, G?seidnes S, Sirev?g R, Synstad B, et al. (2004) Rational engineering of enzyme stability. J Biotechnol 113(1): 105–120. doi: 10.1016/j.jbiotec.2004.03.026
|
[15] | Eijsink VG, G?seidnes S, Borchert TV, van den Burg B (2005) Directed evolution of enzyme stability. Biomol Eng 22(1): 21–30. doi: 10.1016/j.bioeng.2004.12.003
|
[16] | Iyer PV, Ananthanarayan L (2008) Enzyme stability and stabilization – aqueous and non-aqueous environment. Process Biochem 43(10): 1019–1032. doi: 10.1016/j.procbio.2008.06.004
|
[17] | O'Fagain C (2011) Engineering protein stability. Methods Mol. Biol 681: 103–136. doi: 10.1007/978-1-60761-913-0_7
|
[18] | Bruggink A, Roos EC, de Vroom E (1998) Penicillin acylase in the industrial production of β-lactam antibiotics. Org Process Res Dev 2(2): 128–133. doi: 10.1021/op9700643
|
[19] | Arroyo M, De la Mata I, Acebal C, Castillón MP (2003) Biotechnological applications of penicillin acylases: state-of-the-art. Appl Microbiol Biotechnol 60(5): 507–514. doi: 10.1007/s00253-002-1113-6
|
[20] | Duggleby HJ, Tolley SP, Hill CP, Dodson EJ, Dodson G, et al. (1995) Penicillin acylase has a single-amino-acid catalytic centre. Nature 373: 264–268. doi: 10.1038/373264a0
|
[21] | Guranda DT, van Langen LM, van Rantwijk F, Sheldon RA, ?vedas VK (2001) Highly efficient and enantioselective enzymatic acylation of amines in aqueous medium. Tetrahedron Asymmetry 12(11): 1645–1650. doi: 10.1016/s0957-4166(01)00263-4
|
[22] | Guranda DT, Khimiuk AI, van Langen LM, van Rantwijk F, Sheldon RA, et al. (2004) An ‘easy-on, easy-off’ protecting group for the enzymatic resolution of (±)-1-phenylethylamine in an aqueous medium. Tetrahedron Asymmetry 15(18): 2901–2906. doi: 10.1016/j.tetasy.2004.06.051
|
[23] | Guranda DT, Ushakov GA, ?vedas VK (2010) Penicillin Acylase-Catalyzed Effective and Stereoselective Acylation of 1-phenylethylamine in Aqueous Medium using Non-Activated Acyl Donor. Acta Naturae 2(1): 94–96.
|
[24] | Chilov GG, Moody HM, Boesten WH, ?vedas VK (2003) Resolution of (RS)-phenylglycinonitrile by penicillin acylase-catalyzed acylation in aqueous medium. Tetrahedron Asymmetry 14(17): 2613–2617. doi: 10.1016/s0957-4166(03)00523-8
|
[25] | Ismail H, Lau RM, van Langen LM, van Rantwijk F, ?vedas VK, et al. (2008) A green, fully enzymatic procedure for amine resolution, using a lipase and a penicillin G acylase. Green Chemistry 10(4): 415–418. doi: 10.1039/b714088f
|
[26] | Solodenko VA, Belik MY, Galushko SV, Kukhar VP, Kozlova EV, et al. (1993) Enzymatic preparation of both L-and D-enantiomers of phosphonic and phosphonous analogues of alanine using penicillin acylase. Tetrahedron Asymmetry 4(9): 1965–1968. doi: 10.1016/s0957-4166(00)82240-5
|
[27] | Soloshonok VA, Soloshonok IV, Kukhar VP, ?vedas VK (1998) Biomimetic Transamination of α-Alkyl β-Keto Carboxylic Esters. Chemoenzymatic Approach to the Stereochemically Defined α-Alkyl β-Fluoroalkyl β-Amino Acids. J Org Chem 63(6): 1878–1884. doi: 10.1021/jo971777m
|
[28] | Deaguero AL, Blum JK, Bommarius AS (2012) Improving the Diastereoselectivity of Penicillin G Acylase for Ampicillin Synthesis from Racemic Substrates. Protein Eng Des Sel 25(3): 135–144. doi: 10.1093/protein/gzr065
|
[29] | Hanefeld U, Gardossi L, Magner E (2009) Understanding enzyme immobilisation. Chemical Society Reviews 38(2): 453–468. doi: 10.1039/b711564b
|
[30] | Margolin AL, Izumrudov VA, ?vedas VK, Zezin AB (1982) Soluble-insoluble immobilized enzymes. Biotechnol Bioeng 24(1): 237–240. doi: 10.1002/bit.260240119
|
[31] | Phadtare S, Parekh P, Gole A, Patil M, Pundle A, et al. (2002) Penicillin G Acylase-Fatty Lipid Biocomposite Films Show Excellent Catalytic Activity and Long Term Stability/Reusability. Biotechnol Prog 18(3): 483–488. doi: 10.1021/bp015504v
|
[32] | Margolin AL (1996) Novel crystalline catalysts. Trends Biotechnol 14(7): 223–230. doi: 10.1016/0167-7799(96)10031-7
|
[33] | Kallenberg AI, van Rantwijk F, Sheldon RA (2005) Immobilization of penicillin G acylase: the key to optimum performance. Adv Synth Catal 347(7–8): 905–926. doi: 10.1002/adsc.200505042
|
[34] | Pchelintsev NA, Youshko MI, ?vedas VK (2009) Quantitative characteristic of the catalytic properties and microstructure of cross-linked enzyme aggregates of penicillin acylase. J Mol Catal B Enzym 56(4): 202–207. doi: 10.1016/j.molcatb.2008.05.006
|
[35] | Katchalski-Katzir E, Kraemer DM (2000) Eupergit C, a carrier for immobilization of enzymes of industrial potential. J Mol Catal B Enzym 10(1): 157–176. doi: 10.1016/s1381-1177(00)00124-7
|
[36] | Mateo C, Abian O, Fernández-Lorente G, Pedroche J, Fernández-Lafuente R, et al. (2002) Epoxy Sepabeads: A novel epoxy support for stabilization of industrial enzymes via very intense multipoint covalent attachment. Biotechnol Prog 18(3): 629–634. doi: 10.1021/bp010171n
|
[37] | Basso A, Braiuca P, Cantone S, Ebert C, Linda P, et al. (2007) In silico analysis of enzyme surface and glycosylation effect as a tool for efficient covalent immobilisation of CalB and PGA on Sepabeads. Adv Synth Catal 349(6): 877–886. doi: 10.1002/adsc.200600337
|
[38] | Basso A, De Martin L, Ebert C, Gardossi L, Linda P, et al. (2001) Activity of covalently immobilised PGA in water miscible solvents at controlled aw. J Mol Catal B Enzym 11(4): 851–855. doi: 10.1016/s1381-1177(00)00070-9
|
[39] | Azevedo AM, Fonseca LP, Prazeres DMF (1999) Stability and stabilisation of penicillin acylase. J Chem Technol Biotechnol 74(11): 1110–16. doi: 10.1002/(sici)1097-4660(199911)74:11<1110::aid-jctb149>3.0.co;2-b
|
[40] | del Rio G, Rodríguez ME, Munguía ME, LóPez-Munguí A, Soberón X (1995) Mutant Escherichia coli penicillin acylase with enhanced stability at alkaline pH. Biotechnol Bioeng 48(2): 141–148.
|
[41] | Polizzi KM, Chaparro-Riggers JF, Vazquez-Figueroa E, Bommarius AS (2006) Structure-guided consensus approach to create a more thermostable penicillin G acylase. J Biotechnol 1(5): 531–536. doi: 10.1002/biot.200600029
|
[42] | Guranda DT, Volovik TS, ?vedas VK (2004) pH stability of penicillin acylase from Escherichia coli. Biochem (Mosc) 69(12): 1386–1390. doi: 10.1007/s10541-005-0085-4
|
[43] | Cunningham BC, Wells JA (1987) Improvement in the alkaline stability of subtilisin using an efficient random mutagenesis and screening procedure. Protein Eng 1(4): 319–325. doi: 10.1093/protein/1.4.319
|
[44] | Bessler C, Schmitt J, Maurer KH, Schmid RD (2003) Directed evolution of a bacterial α-amylase: Toward enhanced pH-performance and higher specific activity. Protein science 12(10): 2141–2149. doi: 10.1110/ps.0384403
|
[45] | Qin Y, Wei X, Song X, Qu Y (2008) Engineering endoglucanase II from Trichoderma reesei to improve the catalytic efficiency at a higher pH optimum. J Biotechnol 135(2): 190–195. doi: 10.1016/j.jbiotec.2008.03.016
|
[46] | Stephens DE, Singh S, Permaul K (2009) Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability. FEMS Microbiol Lett 293(1): 42–47. doi: 10.1111/j.1574-6968.2009.01519.x
|
[47] | Liu YH, Hu B, Xu YJ, Bo JX, Fan S, et al. (2012) Improvement of the acid stability of Bacillus licheniformis alpha amylase by error-prone PCR. J Appl Microbiol 113(3): 541–549. doi: 10.1111/j.1365-2672.2012.05359.x
|
[48] | Akke M, Forsén S (1990) Protein stability and electrostatic interactions between solvent exposed charged side chains. Proteins 8(1): 23–29. doi: 10.1002/prot.340080106
|
[49] | Shirai T, Suzuki A, Yamane T, Ashida T, Kobayashi T, et al. (1997) High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism. Protein Eng 10(6): 627–634. doi: 10.1093/protein/10.6.627
|
[50] | Shirai T, Ishida H, Noda JI, Yamane T, Ozaki K, et al. (2001) Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme. J Mol Biol 310(5): 1079–1087. doi: 10.1006/jmbi.2001.4835
|
[51] | Fushinobu S, Ito K, Konno M, Wakagi T, Matsuzawa H (1998) Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Protein Eng 11(12): 1121–1128. doi: 10.1093/protein/11.12.1121
|
[52] | Wang T, Liu X, Yu Q, Zhang X, Qu Y, et al. (2005) Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei. Biomol Eng 22(1): 89–94. doi: 10.1016/j.bioeng.2004.10.003
|
[53] | Liu L, Wang B, Chen H, Wang S, Wang M, et al. (2009) Rational pH-engineering of the thermostable xylanase based on computational model. Process Biochem 44(8): 912–915. doi: 10.1016/j.procbio.2009.02.013
|
[54] | Yang H, Liu L, Shin HD, Chen RR, Li J, et al. (2013) Structure-based engineering of histidine residues in the catalytic domain of α-amylase from Bacillus subtilis for improved protein stability and catalytic efficiency under acidic conditions. J Biotechnol 164(1): 59–66. doi: 10.1016/j.jbiotec.2012.12.007
|
[55] | Robinson NE (2002) Protein deamidation. Proc Natl Acad Sci U S A 99(8): 5283–5288. doi: 10.1073/pnas.082102799
|
[56] | Gülich S, Linhult M, St?hl S, Hober S (2002) Engineering streptococcal protein G for increased alkaline stability. Protein Eng 15(10): 835–842.
|
[57] | Palmer B, Angus K, Taylor L, Warwicker J, Derrick JP (2008) Design of stability at extreme alkaline pH in streptococcal protein G. J Biotechnol 134(3): 222–230. doi: 10.1016/j.jbiotec.2007.12.009
|
[58] | Beli?n T, Joye IJ, Delcour JA, Courtin CM (2009) Computational design-based molecular engineering of the glycosyl hydrolase family 11 B. subtilis XynA endoxylanase improves its acid stability. Protein Eng Des Sel 22(10): 587–596. doi: 10.1093/protein/gzp024
|
[59] | Xu H, Zhang F, Shang H, Li X, Wang J, et al. (2013) Alkalophilic adaptation of XynB endoxylanase from Aspergillus niger via rational design of pKa of catalytic residues. J Biosci Bioeng 115(6): 618–622. doi: 10.1016/j.jbiosc.2012.12.006
|
[60] | Potapov V, Cohen M, Schreiber G (2009) Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 22(9): 553–560. doi: 10.1093/protein/gzp030
|
[61] | Khan S, Vihinen M (2010) Performance of protein stability predictors. Hum Mutat 31(6): 675–684. doi: 10.1002/humu.21242
|
[62] | Yang AS, Honig B (1993) On the pH dependence of protein stability. J Mol Biol 231(2): 459. doi: 10.1006/jmbi.1993.1294
|
[63] | Pakula AA, Sauer RT (1989) Genetic analysis of protein stability and function. Annu Rev Genet 23(1): 289–310. doi: 10.1146/annurev.ge.23.120189.001445
|
[64] | Matthews BW (1993) Structural and genetic analysis of protein stability. Annu Rev Biochem 62(1): 139–160. doi: 10.1146/annurev.bi.62.070193.001035
|
[65] | McVey CE, Walsh MA, Dodson GG, Wilson KS, Brannigan JA (2001) Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism. J Mol Biol 313(1): 139–150. doi: 10.1006/jmbi.2001.5043
|
[66] | Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, et al. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res 41(D1): D490–D498. doi: 10.1093/nar/gks1211
|
[67] | Oinonen C, Rouvinen J (2000) Structural comparison of Ntn-hydrolases. Protein Science 9(12): 2329–2337. doi: 10.1110/ps.9.12.2329
|
[68] | Suplatov D, Shalaeva D, Kirilin E, Arzhanik V, ?vedas V (2014) Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity. J Biomol Struct Dyn 32(1): 75–87. doi: 10.1080/07391102.2012.750249
|
[69] | Suplatov DA, Besenmatter W, ?vedas VK, Svendsen A (2012) Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. Protein Eng Des Sel 25(11): 689–697. doi: 10.1093/protein/gzs068
|
[70] | Grinberg VY, Burova TV, Grinberg NV, Shcherbakova TA, Guranda DT (2008) Thermodynamic and kinetic stability of penicillin acylase from Escherichia coli. Biochim Biophys Acta 1784(5): 736–746. doi: 10.1016/j.bbapap.2008.01.016
|
[71] | Fersht AR, Daggett V (2002) Protein folding and unfolding at atomic resolution. Cell 108(4): 573. doi: 10.1016/s0092-8674(02)00620-7
|
[72] | Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol 9(9): 646–652. doi: 10.1038/nsb0902-646
|
[73] | Trodler P, Pleiss J (2008) Modeling structure and flexibility of Candida antarctica lipase B in organic solvents. BMC Struct Biol 8(1): 9. doi: 10.1186/1472-6807-8-9
|
[74] | Rehm S, Trodler P, Pleiss J (2010) Solvent-induced lid opening in lipases: A molecular dynamics study. Protein Science 19(11): 2122–2130. doi: 10.1002/pro.493
|
[75] | Pleiss J (2012) Rational Design of Enzymes. In: Drauz K, Gr?ger H, May O, editors. Enzyme Catalysis in Organic Synthesis, Third Edition. Weinheim: Wiley-VCH. pp.89–117
|
[76] | Sawyer L, James MN (1982) Carboxyl–carboxylate interactions in proteins. Nature 295: 79–80. doi: 10.1038/295079a0
|
[77] | Wohlfahrt G, Pellikka T, Boer H, Teeri TT, Koivula A (2003) Probing pH-dependent functional elements in proteins: modification of carboxylic acid pairs in Trichoderma reesei cellobiohydrolase Cel6A. Biochemistry 42(34): 10095–10103. doi: 10.1021/bi034954o
|
[78] | Park S, Saven JG (2005) Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins 60(3): 450–463. doi: 10.1002/prot.20511
|
[79] | Finkelstein AV, Ptitsyn O (2002) “Lecture 17”. In: Protein physics: a course of lectures (soft condensed matter, complex fluids and biomaterials). London–San Diego: Academic. pp. 207–226
|
[80] | ?vedas V, Guranda D, van Langen L, van Rantwijk F, Sheldon R (1997) Kinetic study of penicillin acylase from Alcaligenes faecalis. FEBS Lett 417(3): 414–418. doi: 10.1016/s0014-5793(97)01289-1
|
[81] | Aharoni A, Gaidukov L, Khersonsky O, Gould SM, Roodveldt C, et al. (2004) The evolvability of promiscuous protein functions. Nat Genet 37(1): 73–76. doi: 10.1038/ng1482
|
[82] | Tokuriki N, Stricher F, Serrano L, Tawfik DS (2008) How protein stability and new functions trade off. PLoS Comput Biol 4(2): e1000002. doi: 10.1371/journal.pcbi.1000002
|
[83] | Serrano L, Day AG, Fersht AR (1993) Step-wise mutation of barnase to binase: a procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J Mol Biol 233(2): 305–312. doi: 10.1006/jmbi.1993.1508
|
[84] | ?vedas VK, Beltser AI (1998) Totally Enzymatic Synthesis of Peptides: Penicillin Acylase-Catalyzed Protection and Deprotection of Amino Groups as Important Building Blocks of This Strategy. Ann N Y Acad Sci 864(1): 524–527. doi: 10.1111/j.1749-6632.1998.tb10373.x
|
[85] | van Rantwijk F, Sheldon RA (2004) Enantioselective acylation of chiral amines catalysed by serine hydrolases. Tetrahedron 60(3): 501–519. doi: 10.1016/j.tet.2003.10.018
|
[86] | Mongan J, Case DA (2005) Biomolecular simulations at constant pH. Curr Opin Struct Biol 15(2): 157–163. doi: 10.1016/j.sbi.2005.02.002
|
[87] | Scheraga HA, Khalili M, Liwo A (2007) Protein-folding dynamics: overview of molecular simulation techniques. Annu Rev Phys Chem 58: 57–83. doi: 10.1146/annurev.physchem.58.032806.104614
|
[88] | Mongan J, Case DA, McCammon JA (2004) Constant pH molecular dynamics in generalized Born implicit solvent. J Comp Chem 25(16): 2038–2048. doi: 10.1002/jcc.20139
|
[89] | Day R, Bennion BJ, Ham S, Daggett V (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J Mol Biol 322(1): 189–203. doi: 10.1016/s0022-2836(02)00672-1
|
[90] | Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1): 33–38. doi: 10.1016/0263-7855(96)00018-5
|
[91] | Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, et al. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30(16): 2785–2791. doi: 10.1002/jcc.21256
|
[92] | Shumway RH, Stoffer DS (2010) Time series analysis and its applications: with R examples. New York – Dordrecht – Heidelberg – London: Springer. 604 p.
|
[93] | Giorgino T (2009) Computing and visualizing dynamic time warping alignments in R: the dtw package. J Stat Softw 31(7): 1–24.
|
[94] | Chen L (2005) Similarity Search Over Time Series and Trajectory Data. A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Computer Science.
|
[95] | Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16): 1781–1802. doi: 10.1002/jcc.20289
|
[96] | Novikov FN, Stroganov OV, Khaliullin IG, Panin NV, Shapovalova IV, et al. (2013) Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis. FEBS J 280(1): 115–126. doi: 10.1111/febs.12054
|
[97] | Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, et al.. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res (suppl 2): W522–W525.
|
[98] | Li H, Robertson AD, Jensen JH (2005) Very fast empirical prediction and rationalization of protein pKa values. Proteins 61(4): 704–721. doi: 10.1002/prot.20660
|
[99] | Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60(12): 2256–2268. doi: 10.1107/s0907444904026460
|
[100] | Altschul SF, Madden TL, Sch?ffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17): 3389–3402. doi: 10.1093/nar/25.17.3389
|
[101] | Fischer JD, Mayer CE, S?ding J (2008) Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 24(5): 613–20. doi: 10.1093/bioinformatics/btm626
|
[102] | Menke M, Berger B, Cowen L (2008) Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol 4(1): e10. doi: 10.1371/journal.pcbi.0040010
|
[103] | Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, et al. (2011) Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nat Protoc 6(11): 1669–1682. doi: 10.1038/nprot.2011.393
|
[104] | Suplatov D, Kirilin E, Takhaveev V, ?vedas V (2013). Zebra: web-server for bioinformatic analysis of diverse protein families, J Biomol Struct Dyn, in press, DOI:10.1080/07391102.2013.834514.
|
[105] | Jasnaya AS, Jamskova OV, Guranda DT, Shcherbakova TA, Tishkov VI, et al. (2008) Cloning of penicillin acylase from Escherichia coli. Catalytic properties of recombinant enzymes. Moscow University Chemistry Bulletin 49(2): 127. doi: 10.3103/s0027131408020120
|
[106] | Gardossi L, Poulsen PB, Ballesteros A, Hult K, ?vedas VK, et al. (2010) Guidelines for reporting of biocatalytic reactions. Trends Biotechnol 28(4): 171–180. doi: 10.1016/j.tibtech.2010.01.001
|
[107] | ?vedas VK, Margolin AL, Sherstiuk SF, Klyosov AA, Berezin IV (1977) Inactivation of soluble and immobilized penicillin amidase from E. coli by phenylmethylsulfonylfluoride, kinetic analysis and titration of enzyme active sites. Bioorg. Khimiya (Russ.) 3: 546–553.
|
[108] | Voevodin VlV, Zhumatiy SA, Sobolev SI, Antonov AS, Bryzgalov PA, et al. (2012) Practice of "Lomonosov" Supercomputer. Open Systems J. (Russ.) 7: 36–39.
|