Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation

Author(s): Neerja Thakur, Nikhil Sharma, Vijay Kumar, Tek Chand Bhalla*

Journal Name: Current Proteomics

Volume 17 , Issue 2 , 2020

Become EABM
Become Reviewer
Call for Editor

Graphical Abstract:


Background: Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments.

Methods: They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides, arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic site and preferred substrate. Despite their economic importance, we lack knowledge as to how these amidases withstand elevated pH and temperature whereas others cannot.

Results: The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic organisms revealed some striking trends as to how amino acid composition varies significantly. Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L) in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant and alkali tolerant amidases.

Conclusion: The present investigation insights physiochemical properties and dominance of some crucial amino acid residues in the primary and secondary structure of some amidases from acid-tolerant, alkali tolerant and neutrophilic microorganisms.

Keywords: Amidase, acid-tolerant, alkali tolerant, neutrophilic, Tukey test (T-Test), amino acid composition, primary and secondary structure.

Banerjee, A.; Sharma, R.; Banerjee, U.C. The nitrile-degrading enzymes: current status and future prospects. Appl. Microbiol. Biotechnol., 2002, 60(1-2), 33-44.
[] [PMID: 12382040]
Sharma, M.; Sharma, N.N.; Bhalla, T.C. Amidases: versatile enzymes in nature. Rev. Environ. Sci. Bio., 2009, 8, 343.
Ghonemy, D.H.E. Microbial amidases and their industrial applications: a review. J. Med. Microb. Diagn., 2014, 4, 173.
Mehta, P.K.; Bhatia, S.K.; Bhatia, R.K.; Bhalla, T.C. Enhanced production of thermostable amidase from Geobacillus subterraneus RL-2a MTCC 11502 via optimization of physicochemical parameters using Taguchi DOE methodology. 3 Biotech, 2016, 6(1), 66.
[ 10.1007/s13205-016-0390-1] [PMID: 28330136]
Fournand, D.; Bigey, F.; Arnaud, A. Acyl transfer activity of an amidase from Rhodococcus sp. strain R312: formation of a wide range of hydroxamic acids. Appl. Environ. Microbiol., 1998, 64(8), 2844-2852.
[PMID: 9687439]
Kobayashi, M.; Goda, M.; Shimizu, S. The catalytic mechanism of amidase also involves nitrile hydrolysis. FEBS Lett., 1998, 439(3), 325-328.
[] [PMID: 9845347]
Komeda, H.; Harada, H.; Washika, S.; Sakamoto, T.; Ueda, M.; Asano, Y. S-stereoselective piperazine-2-tert-butylcarboxamide hydrolase from Pseudomonas azotoformans IAM 1603 is a novel L-amino acid amidase. Eur. J. Biochem., 2004, 271(8), 1465-1475.
[] [PMID: 15066172]
Chacko, S.; Ramteke, P.W.; Joseph, B. A comparative study on the production of amidase using immobilized and dehydrated immobilized cells of Pseudomonasputida MTCC 6809. J. Gen. Eng. Biotechnol., 2012, 10, 121-127.
Fuhshuku, K.; Watanabe, S.; Nishii, T.; Ishii, A.; Asano, Y. A novel S-enantioselective amidase acting on 3,3,3-trifluoro-2-hydroxy-2-methylpropanamide from Arthrobacter sp. S-2. Biosci. Biotechnol. Biochem., 2015, 79(10), 1587-1596.
[] [PMID: 26011254]
Li, H.; Zhu, S.; Zheng, G. Promiscuous (+)-γ-lactamase activity of an amidase from nitrile hydratase pathway for efficient synthesis of carbocyclic nucleosides intermediate. Bioorg. Med. Chem. Lett., 2018, 28(6), 1071-1076.
[] [PMID: 29486967]
Bhatia, R.K.; Bhatia, S.K.; Mehta, P.K.; Bhalla, T.C. Bench scale production of benzohydroxamic acid using acyl transfer activity of amidase from Alcaligenes sp. MTCC 10674. J. Ind. Microbiol. Biotechnol., 2013, 40(1), 21-27.
[] [PMID: 23065258]
Ismailsab, M.; Monisha, T.R.; Reddy, P.V.; Santoshkumar, M.; Anand, S.; Nayak, A.S.; Karegoudar, T.B. Biotransformation of aromatic and heterocyclic amides by amidase of whole cells of Rhodococcus sp. MTB5: biocatalytic characterization and substrate specificity. Biocatal. Biotransform., 2017, 35, 74-85.
Chen, J.; Zheng, R.C.; Zheng, Y.G.; Shen, Y.C. Microbial transformation of nitriles to high-value acids or amides. Adv. Biochem. Eng. Biotechnol., 2009, 113, 33-77.
Bhalla, T.C.; Sharma, N.; Bhatia, R.K. Microbial degradation of cyanides and nitriles. Microorganisms in environmental management: microbes and environment; Springer, 2012, pp. 569-587.
Rigoldi, F.; Donini, S.; Redaelli, A.; Parisini, E.; Gautieri, A. Review: engineering of thermostable enzymes for industrial applications. APL Bioeng., 2018, 2(1)011501
[] [PMID: 31069285]
Krasnikov, B.F.; Chien, C.H.; Nostramo, R.; Pinto, J.T.; Nieves, E.; Callaway, M.; Sun, J.; Huebner, K.; Cooper, A.J. Identification of the putative tumor suppressor Nit2 as omega-amidase, an enzyme metabolically linked to glutamine and asparagine transamination. Biochimie, 2009, 91(9), 1072-1080.
[] [PMID: 19595734]
Jaisson, S.; Veiga-da-Cunha, M.; Van Schaftingen, E. Molecular identification of omega-amidase, the enzyme that is functionally coupled with glutamine transaminases, as the putative tumor suppressor Nit2. Biochimie, 2009, 91(9), 1066-1071.
[] [PMID: 19596042]
Chien, C.H.; Gao, Q.Z.; Cooper, A.J.; Lyu, J.H.; Sheu, S.Y. Structural insights into the catalytic active site and activity of human Nit2/ω-amidase: kinetic assay and molecular dynamics simulation. J. Biol. Chem., 2012, 287(31), 25715-25726.
[] [PMID: 22674578]
Cooper, A.J.; Shurubor, Y.I.; Dorai, T.; Pinto, J.T.; Isakova, E.P.; Deryabina, Y.I.; Denton, T.T.; Krasnikov, B.F. ω-Amidase: an underappreciated, but important enzyme in L-glutamine and L-asparagine metabolism; relevance to sulfur and nitrogen metabolism, tumor biology and hyperammonemic diseases. Amino Acids, 2016, 48(1), 1-20.
[] [PMID: 26259930]
Wang, Y.S.; Cheng, F.; Zheng, R.C.; Wang, Y.J. Yu-Guo Zheng,Y.G. Characterization of an enantioselective amidase with potential application to asymmetric hydrolysis of (R, S)-2, 2-dimethylcyclopropane carboxamide. World J. Microbiol. Biotechnol., 2011, 27, 2885-2892.
Makhongela, H.S.; Glowacka, A.E.; Agarkar, V.B.; Sewell, B.T.; Weber, B.; Cameron, R.A.; Cowan, D.A.; Burton, S.G. A novel thermostable nitrilase superfamily amidase from Geobacillus pallidus showing acyl transfer activity. Appl. Microbiol. Biotechnol., 2007, 75(4), 801-811.
[] [PMID: 17347819]
Nel, A.J.; Tuffin, I.M.; Sewell, B.T.; Cowan, D.A. Unique aliphatic amidase from a psychrotrophic and haloalkaliphilic nesterenkonia isolate. Appl. Environ. Microbiol., 2011, 77(11), 3696-3702.
[] [PMID: 21498772]
Ko, H.J.; Lee, E.W.; Bang, W.G.; Lee, C.K.; Kim, K.H.; Choi, I.G. Molecular characterization of a novel bacterial aryl acylamidase belonging to the amidase signature enzyme family. Mol. Cells, 2010, 29(5), 485-492.
[] [PMID: 20396964]
Lee, S.; Park, E.H.; Ko, H.J.; Bang, W.G.; Kim, H.Y.; Kim, K.H.; Choi, I.G. Crystal structure analysis of a bacterial aryl acylamidase belonging to the amidase signature enzyme family. Biochem. Biophys. Res. Commun., 2015, 467(2), 268-274.
[] [PMID: 26454172]
Bhalla, T.C.; Kumar, J.; Kumar, H.; Agrawal, H.O. Amidase production by Rhodococcus sp. NHB-2. Natl. Acad. Sci. Lett., 1997, 20, 139-142.
Cai, G.; Zhu, S.; Wang, X.; Jiang, W. Cloning, sequence analysis and expression of the gene encoding a novel wide-spectrum amidase belonging to the amidase signature superfamily from Achromobacter xylosoxidans. FEMS Microbiol. Lett., 2005, 249(1), 15-21.
[] [PMID: 16002239]
Sonke, T.; Ernste, S.; Tandler, R.F.; Kaptein, B.; Peeters, W.P.; van Assema, F.B.; Wubbolts, M.G.; Schoemaker, H.E. L-selective amidase with extremely broad substrate specificity from Ochrobactrum anthropi NCIMB 40321. Appl. Environ. Microbiol., 2005, 71(12), 7961-7973.
[] [PMID: 16332774]
Cavicchioli, R.; Charlton, T.; Ertan, H.; Mohd Omar, S.; Siddiqui, K.S.; Williams, T.J. Biotechnological uses of enzymes from psychrophiles. Microb. Biotechnol., 2011, 4(4), 449-460.
[] [PMID: 21733127]
Adrio, J.L.; Demain, A.L. Microbial enzymes: tools for biotechnological processes. Biomolecules, 2014, 4(1), 117-139.
[] [PMID: 24970208]
Sarmiento, F.; Peralta, R.; Blamey, J.M. Cold and hot extremozymes: industrial relevance and current trends. Front. Bioeng. Biotechnol., 2015, 3, 148.
[] [PMID: 26539430]
Dumorné, K.; Córdova, D.C.; Astorga-Eló, M.; Renganathan, P. Extremozymes: a potential source for industrial applications. J. Microbiol. Biotechnol., 2017, 27(4), 649-659.
[] [PMID: 28104900]
Yennamalli, R.M.; Rader, A.J.; Wolt, J.D.; Sen, T.Z. Thermostability in endoglucanases is fold-specific. BMC Struct. Biol., 2011, 11, 10.
[] [PMID: 21291533]
Yennamalli, R.M.; Rader, A.J.; Kenny, A.J.; Wolt, J.D.; Sen, T.Z. Endoglucanases: insights into thermostability for biofuel applications. Biotechnol. Biofuels, 2013, 6(1), 136.
[] [PMID: 24070146]
Charlesworth, J.; Burns, B.P. Extremophilic adaptations and biotechnological applications in diverse environments. AIMS. Microbiol., 2016, 2, 251-261.
Kumar, A.; Alam, A.; Tripathi, D.; Rani, M.; Khatoon, H.; Pandey, S.; Ehtesham, N.Z.; Hasnain, S.E. Protein adaptations in extremophiles: an insight into extremophilic connection of mycobacterial proteome. Semin. Cell Dev. Biol., 2018, 84, 147-157.
[] [PMID: 29331642]
Hult, K.; Berglund, P. Engineered enzymes for improved organic synthesis. Curr. Opin. Biotechnol., 2003, 14(4), 395-400.
[] [PMID: 12943848]
Sharma, N.; Kushwaha, R.; Sodhi, J.S.; Bhalla, T.C. In silico analysis of amino acid sequences in relation to specificity and physiochemical properties of some microbial nitrilases. J. Proteomics Bioinform., 2009, 2, 185-192.
Devi, S.; Sharma, N. Comparative analysis of amino acid sequences from mesophiles and thermophiles in respective of carbonnitrogen hydrolase family. 3 Biotech.,, 2013, 3, 491-507.
Gopal, K.; Sharma, N.; Bhalla, T.C. In silico analysis of some microbial amidases for their amino acid and physiochemical parameters. Int. J. Bioassays, 2013, 2, 630-636.
Sharma, N.; Thakur, N.; Raj, T. Savitri; Bhalla, T.C. Mining of microbial genomes for the novel sources of nitrilases. BioMed Res. Int., 2017, 2017(70), 39245.
[] [PMID: 28497061]
Kyte, J.; Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 1982, 157(1), 105-132.
[] [PMID: 7108955]
Bjellqvist, B.; Hughes, G.J.; Pasquali, C.; Paquet, N.; Ravier, F.; Sanchez, J.C.; Frutiger, S.; Hochstrasser, D. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 1993, 14(10), 1023-1031.
[] [PMID: 8125050]
Gill, S.C.; von Hippel, P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem., 1989, 182(2), 319-326.
[] [PMID: 2610349]
Wilkins, M.R.; Gasteiger, E.; Bairoch, A.; Sanchez, J.C.; Williams, K.L.; Appel, R.D.; Hochstrasser, D.F. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol., 1999, 112, 531-552.
[PMID: 10027275]
Guruprasad, K.; Reddy, B.V.; Pandit, M.W. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng., 1990, 4(2), 155-161.
[] [PMID: 2075190]
Anderson, I.; Chertkov, O.; Chen, A.; Saunders, E.; Lapidus, A.; Nolan, M.; Lucas, S.; Hammon, N.; Deshpande, S.; Cheng, J.F.; Han, C.; Tapia, R.; Goodwin, L.A.; Pitluck, S.; Liolios, K.; Pagani, I.; Ivanova, N.; Mikhailova, N.; Pati, A.; Palaniappan, K.; Land, M.; Pan, C.; Rohde, M.; Pukall, R.; Göker, M.; Detter, J.C.; Woyke, T.; Bristow, J.; Eisen, J.A.; Markowitz, V.; Hugenholtz, P.; Kyrpides, N.C.; Klenk, H.P.; Mavromatis, K. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand. Genomic Sci., 2012, 6(3), 1-13.
[] [PMID: 23407703]
Küsel, K.; Dorsch, T.; Acker, G.; Stackebrandt, E. Microbial reduction of Fe(III) in acidic sediments: isolation of Acidiphilium cryptum JF-5 capable of coupling the reduction of Fe(III) to the oxidation of glucose. Appl. Environ. Microbiol., 1999, 65(8), 3633-3640.
[PMID: 10427060]
Deepika, G.; Karunakaran, E.; Hurley, C.R.; Biggs, C.A.; Charalampopoulos, D. Influence of fermentation conditions on the surface properties and adhesion of Lactobacillus rhamnosus GG. Microb. Cell Fact., 2012, 11, 116.
[] [PMID: 22931558]
Männistö, M.; Rawat, S.; Starovoytov, V.; Haggblom, M.M. Granulicella arctica sp. nov., Granulicella mallensis sp. nov., Granulicella sapmiensis sp. nov. and Granulicella tundricola sp. nov., novel acidobacteria from tundra soil. Int. J. Syst. Evol. Microbiol., 2012, 62, 2097-2106.
[] [PMID: 22058325]
Clum, A.; Nolan, M.; Lang, E.; Glavina Del Rio, T.; Tice, H.; Copeland, A.; Cheng, J.F.; Lucas, S.; Chen, F.; Bruce, D.; Goodwin, L.; Pitluck, S.; Ivanova, N.; Mavrommatis, K.; Mikhailova, N.; Pati, A.; Chen, A.; Palaniappan, K.; Göker, M.; Spring, S.; Land, M.; Hauser, L.; Chang, Y.J.; Jeffries, C.C.; Chain, P.; Bristow, J.; Eisen, J.A.; Markowitz, V.; Hugenholtz, P.; Kyrpides, N.C.; Klenk, H.P.; Lapidus, A. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP). Stand. Genomic Sci., 2009, 1(1), 38-45.
[] [PMID: 21304635]
Wang, L.; Zhao, B.; Li, F.; Xu, K.; Ma, C.; Tao, F.; Li, Q.; Xu, P. Highly efficient production of D-lactate by Sporolactobacillus sp. CASD with simultaneous enzymatic hydrolysis of peanut meal. Appl. Microbiol. Biotechnol., 2011, 89(4), 1009-1017.
[] [PMID: 21042797]
Kobayashi, M.; Komeda, H.; Nagasawa, T.; Nishiyama, M.; Horinouchi, S.; Beppu, T.; Yamada, H.; Shimizu, S. Amidase coupled with low-molecular-mass nitrile hydratase from Rhodococcus rhodochrous J1. Sequencing and expression of the gene and purification and characterization of the gene product. Eur. J. Biochem., 1993, 217(1), 327-336.
[] [PMID: 7916690]
Kallimanis, A.; Karabika, E.; Mavromatis, K.; Lapidus, A.; Labutti, K.M.; Liolios, K.; Ivanova, N.; Goodwin, L.; Woyke, T.; Velentzas, A.D.; Perisynakis, A.; Ouzounis, C.C.; Kyrpides, N.C.; Koukkou, A.I.; Drainas, C. Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1. Stand. Genomic Sci., 2011, 5(1), 144-153.
[] [PMID: 22180818]
Geszvain, K.; Tebo, B.M. Identification of a two-component regulatory pathway essential for Mn(II) oxidation in Pseudomonas putida GB-1. Appl. Environ. Microbiol., 2010, 76(4), 1224-1231.
[] [PMID: 20038702]
So, C.M.; Phelps, C.D.; Young, L.Y. Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3. Appl. Environ. Microbiol., 2003, 69(7), 3892-3900.
[] [PMID: 12839758]
Kim, Y.O.; Kim, W.J.; Choi, S.H.; Kim, D.S.; Kim, D.W.; Lee, J.S.; Kong, H.J.; Nam, B.H.; Kim, B.S.; Lee, S.J.; Park, H.S.; Chae, S.H. Genome sequence of Acinetobacter sp. strain P8-3-8, isolated from Fistularia commersonii in Vietnam. J. Bacteriol., 2011, 193(16), 4288-4289.
[] [PMID: 21685286]
Huu, N.B.; Denner, E.B.; Ha, D.T.; Wanner, G.; Stan-Lotter, H. Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well. Int. J. Syst. Bacteriol., 1999, 49(Pt 2), 367-375.
[] [PMID: 10319457]
Muyzer, G.; Sorokin, D.Y.; Mavromatis, K.; Lapidus, A.; Foster, B.; Sun, H.; Ivanova, N.; Pati, A.; D’haeseleer, P.; Woyke, T.; Kyrpides, N.C. Complete genome sequence of Thioalkalivibrio sp. K90mix. Stand. Genomic Sci., 2011, 5(3), 341-355.
[] [PMID: 22675584]
Cai, M.; Chen, W.M.; Nie, Y.; Chi, C.Q.; Wang, Y.N.; Tang, Y.Q.; Li, G.Y.; Wu, X.L. Complete genome sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil. J. Bacteriol., 2011, 193(17), 4538-4539.
[] [PMID: 21725023]
Hoeft, S.E.; Blum, J.S.; Stolz, J.F.; Tabita, F.R.; Witte, B.; King, G.M.; Santini, J.M.; Oremland, R.S. Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor. Int. J. Syst. Evol. Microbiol., 2007, 57(Pt 3), 504-512.
[] [PMID: 17329775]
Horikoshi, K. Alkaliphiles: some applications of their products for biotechnology. Microbiol. Mol. Biol. Rev., 1999, 63(4), 735-750.
[PMID: 10585964]
Procópio, L.; Alvarez, V.M.; Jurelevicius, D.A.; Hansen, L.; Sørensen, S.J.; Cardoso, J.S.; Pádula, M.; Leitão, A.C.; Seldin, L.; van Elsas, J.D. Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential. Antonie van Leeuwenhoek, 2012, 101(2), 289-302.
[] [PMID: 21901521]
Cho, J.C.; Giovannoni, S.J. Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol., 2006, 56(Pt 4), 855-859.
[] [PMID: 16585706]
Fang, Y.; Middaugh, C.R.; Fang, J. In silico classification of proteins from acidic and neutral cytoplasms. PLoS One, 2012, 7(9)e45585
[] [PMID: 23049817]
Fütterer, O.; Angelov, A.; Liesegang, H.; Gottschalk, G.; Schleper, C.; Schepers, B.; Dock, C.; Antranikian, G.; Liebl, W. Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc. Natl. Acad. Sci. USA, 2004, 101(24), 9091-9096.
[] [PMID: 15184674]
Baker-Austin, C.; Dopson, M. Life in acid: pH homeostasis in acidophiles. Trends Microbiol., 2007, 15(4), 165-171.
[] [PMID: 17331729]
Huang, Y.; Krauss, G.; Cottaz, S.; Driguez, H.; Lipps, G. A highly acid-stable and thermostable endo-beta-glucanase from the thermoacidophilic archaeon Sulfolobus solfataricus. Biochem. J., 2005, 385(Pt 2), 581-588.
[] [PMID: 15456402]
Bönisch, H.; Schmidt, C.L.; Schäfer, G.; Ladenstein, R. The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution. J. Mol. Biol., 2002, 319(3), 791-805.
[] [PMID: 12054871]
Beliën, T.; Joye, I.J.; Delcour, J.A.; Courtin, C.M. Computational design-based molecular engineering of the glycosyl hydrolase family 11 B. subtilis XynA endoxylanase improves its acid stability. Protein Eng. Des. Sel., 2009, 22(10), 587-596.
[] [PMID: 19531602]
Shirai, T.; Suzuki, A.; Yamane, T.; Ashida, T.; Kobayashi, T.; Hitomi, J.; Ito, S. High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism. Protein Eng., 1997, 10(6), 627-634.
[] [PMID: 9278275]
Fushinobu, S.; Ito, K.; Konno, M.; Wakagi, T.; Matsuzawa, H. 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., 1998, 11(12), 1121-1128.
[] [PMID: 9930661]
Wang, J.; Gambhir, A.; McLaughlin, S.; Murray, D. A computational model for the electrostatic sequestration of PI (4,5)P2 by membrane-adsorbed basic peptides. Biophys. J., 2004, 86(4), 1969-1986.
[] [PMID: 15041641]
Suplatov, D.; Panin, N.; Kirilin, E.; Shcherbakova, T.; Kudryavtsev, P.; Svedas, V. Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase’s adaptation to alkaline conditions. PLoS One, 2014, 9(6)e100643
[] [PMID: 24959852]
Robinson, N.E. Protein deamidation. Proc. Natl. Acad. Sci. USA, 2002, 99(8), 5283-5288.
[] [PMID: 11959979]
Gülich, S.; Linhult, M.; Ståhl, S.; Hober, S. Engineering streptococcal protein G for increased alkaline stability. Protein Eng., 2002, 15(10), 835-842.
[] [PMID: 12468718]
Palmer, B.; Angus, K.; Taylor, L.; Warwicker, J.; Derrick, J.P. Design of stability at extreme alkaline pH in streptococcal protein G. J. Biotechnol., 2008, 134(3-4), 222-230.
[] [PMID: 18304667]
Gibrat, J.F.; Garnier, J.; Robson, B. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J. Mol. Biol., 1987, 198(3), 425-443.
[] [PMID: 3430614]
Zhang, G.; Li, H.; Fang, B. Discriminating acidic and alkaline enzymes using a random forest model with secondary structure amino acid composition. Process Biochem., 2009, 44, 654-660.
Bonneté, F.; Madern, D.; Zaccaï, G. Stability against denaturation mechanisms in halophilic malate dehydrogenase “adapt” to solvent conditions. J. Mol. Biol., 1994, 244(4), 436-447.
[] [PMID: 7990132]
Oren, A.; Mana, L. Amino acid composition of bulk protein and salt relationships of selected enzymes of Salinibacter ruber, an extremely halophilic bacterium. Extremophiles, 2002, 6(3), 217-223.
[] [PMID: 12072957]
Vieille, C.; Zeikus, G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev., 2001, 65(1), 1-43.
[] [PMID: 11238984]
Kumar, S.; Tsai, C.J.; Nussinov, R. Factors enhancing protein thermostability. Protein Eng., 2000, 13(3), 179-191.
[] [PMID: 10775659]
Kumar, V.; Sharma, N.; Bhalla, T.C. In silico analysis of β-galactosidases primary and secondary structure in relation to temperature adaptation. J. Amino Acids, 2014, 2014475839
[] [PMID: 24790757]

Rights & PermissionsPrintExport Cite as

Article Details

Year: 2020
Published on: 30 January, 2020
Page: [95 - 106]
Pages: 12
DOI: 10.2174/1570164616666190718150627
Price: $25

Article Metrics

PDF: 15
PRC: 1