Characterization of the Topological Features of Catalytic Sites in Protein Coevolution Networks *
Xiu-Lian Xu** , Jin-Xuan Shi
School of Physics Science and Technology, Yangzhou University, Yangzhou 225002, China
Abstract ：The knowledge of sequence and structural properties of residues in the catalytic sites of enzymes is important for understanding the physiochemical basis of enzymatic catalysis. We reveal new features of the catalytic sites by analyzing the coevolutionary behavior of amino acid sequences. By performing direct coupling analysis of the sequences of homologous proteins, we construct the coevolution networks at the residue level. Based on the analysis of the topological features of the coevolution networks for a dataset including 20 enzymes, we show that there is significant correlation between the catalytic sites and topological features of protein coevolution networks. Residues at the catalytic center often correspond to the nodes with high values of centralities in the networks as characterized by the degree, betweenness, closeness, and Laplacian centrality. The results of this work provide a possible way to extract key coevolutionary information from the sequences of enzymes, which is useful in the prediction of catalytic sites of enzymes.
收稿日期: 2020-02-06
出版日期: 2020-05-26
PACS:
87.15.-v
(Biomolecules: structure and physical properties)
87.14.E-
(Proteins)
89.75.Fb
(Structures and organization in complex systems)
89.75.-k
(Complex systems)
[1] Finkelstein M B and Ptitsyn O 2002 Protein Physics: A Course of Lectures (London: Academic Press) [2] Segel I H 1993 Enzyme Kinetics (New York: Wiley-Interscience) [3] Ran F A, Hsu P D, Wright J et al 2013 Nat. Protoc. 8 2281 [4] Robertson J G 2005 Biochemistry 44 5561 [5] Benkovic S J, Hammes-Schiffer S 2003 Science 301 1196 [6] Cui Q and Karplus M 2003 Adv. Protein Chem. 66 315 [7] Olsson W H M, Parson W W and Warshel A 2006 Chem. Rev. 106 1737 [8] Warshel A 2003 Ann. Rev. Biophys. Biomol. Struct. 32 425 [9] Li W, Wang J, Zhang J et al 2019 Phys. Rev. Lett. 122 238102 [10] Tong X, Hu R, Li X et al 2018 Chin. Phys. B 27 118705 [11] Yang Z, Hao D, Che Y et al 2018 Chin. Phys. B 27 018704 [12] Kong J Y, Li J C, Lu J J et al 2019 Phys. Rev. E 100 052409 [13] Porter C T, Barlett G J and Thornton J M 2004 Nucl. Acids Res. 32 D129 [14] Lu H P 2014 Chem. Soc. Rev. 43 1118 [15] Pelz B, Žoldák G, Zeller F et al 2016 Nat. Commun. 7 10848 [16] Hanson J A, Duderstadt K, Watkins L P et al 2007 Proc. Natl. Acad. Sci. USA 104 18055 [17] Guo J and Zhou H X 2016 Chem. Rev. 116 6503 [18] Hammes-Schiffer S and Benkovic S J 2006 Annu. Rev. Biochem. 75 519 [19] Ma B and Nussinov R 2010 Curr. Opin. Chem. Biol. 14 652 [20] Henzler-Wildman K A, Lei M, Thai V et al 2007 Nature 450 913 [21] Li W, Wolynes P G and Takada S 2011 Proc. Natl. Acad. Sci. USA 108 3504 [22] Yang L W and Bahar I 2005 Structure 13 893 [23] Fajardo J E and Fiser A 2013 BMC Bioinform. 14 63 [24] Bartlett G T, Porter C T, Borkakoti N et al 2002 J. Mol. Biol. 324 105 [25] Sankararaman S, Sha F, Kirsch J F et al 2010 Bioinformatics 26 617 [26] Yang L W, Liu X, Jursa C J et al 2005 Bioinformatics 21 2978 [27] Lockless S W and Ranganathan R 1999 Science 286 295 [28] Süel G M, Lockless S W, Wall M A et al 2003 Nat. Struct. Biol. 10 59 [29] Marks D S, Hopf T A and Sander C 2012 Nat. Biotechnol. 30 1072 [30] Hopf T A, Morinaga S, Ihara S et al 2015 Nat. Commun. 6 6077 [31] Weigt M, White R A, Szurmant H et al 2009 Proc. Natl. Acad. Sci. USA 106 67 [32] Tian P, Louis J M, Baber J L et al 2018 Angew. Chem. Int. Ed. 57 5674 [33] Collins J J and Carson C C 1998 Nature 393 409 [34] Holliday M J, Camilloni C, Armstrong G S et al 2017 Structure 25 276 [35] Lee Y, Mick J, Furdui C et al 2012 PLOS ONE 7 e38114 [36] Zhu X Y, Liu Z H and Tang M 2007 Chin. Phys. Lett. 24 1118 [37] Zhu X Y and Liu Z H 2007 Chin. Phys. Lett. 24 2142 [38] Zhao Y, Jian Y, Liu Z et al 2017 Sci. Rep. 7 2876 [39] Xu X L, Liu C P and He D R 2016 Chin. Phys. Lett. 33 048901 [40] Newman M E J 2010 Network (New York: Oxford University Press) [41] Finn R D, Clements J and Eddy S R 2011 Nucl. Acids Res. 39 W29 [42] Morcos F, Pagnani A, Lunt B et al 2011 Proc. Natl. Acad. Sci. USA 108 E1293 [43] Sara E G, Mistry J, Bateman A et al 2019 Nucl. Acids Res. 47 D427 [44] Batagelj V and Mrvar A 2003 Graph Drawing Software ed Junger M and Mutzel P (Berlin: Springer) p 77 [45] Jing H, Babu Y S, Moore D et al 1998 J. Mol. Biol. 282 1061 [46] Lindqvist Y, Schneider G and Vihko P 1994 Eur. J. Biochem. 221 139 [47] Pisliakov A V, Cao J, Kamerlin S C et al 2009 Proc. Natl. Acad. Sci. USA 106 17359 [48] Xie J and Lai L 2020 Curr. Opin. Struct. Biol. 62 158 [49] Li W F, Wang W and Takada S 2014 Proc. Natl. Acad. Sci. USA 111 10550
[1]
.
[2]
.
[3]
.
[4]
TIE Zuo-Xiu;QIN Meng**;ZOU Da-Wei;CAO Yi**;WANG Wei
. Photo-Crosslinking Induced Geometric Restriction Controls the Self-Assembly of Diphenylalanine Based Peptides
[5]
PAN Bing-Yi;ZHANG Ling-Yun;DOU Shuo-Xing;WANG Peng-Ye. Effect of Laser Field and Mechanical Force on Deoxyribonucleic Acid Melting
[6]
M. D. Ganji;H. Yazdani. Interaction between B-Doped C60 Fullerene and Glycine Amino Acid from First-Principles Simulation
[7]
ZHANG Ping;WANG Hai-Jun;. Monte Carlo Simulation on Growth of Antibody-Antigen Complexes: the Role of Unequal Reactivity
[8]
WU Zheng-Yi;FENG Jin-Fu;WU Xiao-Shan. Thermal Vibration and Twist Induced Semiconducting Behaviour in Short DNA Wires
[9]
HU Dong-Sheng;ZHU Chen-Ping;ZHANG Long-Qiang;HE Da-Ren;WANG Bing-Hong. Gap Caused by Strong Pairing in the Ladder Model of DNA Molecules
[10]
ZHAO Wei-Jia;WENG Yu-Quan;FU Jing-Li;. Lie Symmetries and Conserved Quantities for Super-Long Elastic Slender Rod
[11]
ZHANG Hong-Yan;LIANG Ru-Qiang;JIN Kui-Juan;Lü Hui-Bin;ZHU Xiang-Dong;ZHOU Yue-Liang;RUAN Kang-Cheng;YANG Guo-Zhen. Applications of Oblique-Incidence Reflectivity Difference Method in Primary Study of Protein Biomolecules
[12]
SONG Fan;MOYNE Christian;BAI Yi-Long. Electrostatic Interactions Between Glycosaminoglycan Molecules
[13]
WANG Ao-Jin;HU Kun-Sheng. Calibration of Membrane Viscosity of the Reconstituted Vesicles by Measurement of Rotational Diffusion of Bacteriorhodopsin
[14]
ZHANG Yi;HU Jun;WU Shi-Ying;AI Xiao-Bai;LI Min-Qian. Experiments and Models of DNA Nano-Catenary Patterns Manipulated by Liquid Flow
[15]
LIU Wenqing;XIA Yuxing;LIU Songhao;R. Ramponi*;R. Cubeddu*. Time-resolved Fluorescence Decay Study of Hematoporphyrin Derivative
2020, Vol. 37 
