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Title: Algorithm‐based coevolution network identification reveals key functional residues of the α/β hydrolase subfamilies

Authors:
 [1];  [1];  [1];  [2];  [1]
  1. State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai China
  2. State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai China, Shanghai Center for Bioinformation Technology Shanghai China
Publication Date:
Sponsoring Org.:
USDOE Office of Electricity Delivery and Energy Reliability (OE), Power Systems Engineering Research and Development (R&D) (OE-10)
OSTI Identifier:
1580205
Grant/Contract Number:  
2017YFE0103300; 31770771; 31620103901; YG2017MS08
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
FASEB Journal
Additional Journal Information:
Journal Name: FASEB Journal Journal Volume: 34 Journal Issue: 2; Journal ID: ISSN 0892-6638
Publisher:
FASEB
Country of Publication:
United States
Language:
English

Citation Formats

Wu, Zhiyun, Liu, Hao, Xu, Lishi, Chen, Hai‐Feng, and Feng, Yan. Algorithm‐based coevolution network identification reveals key functional residues of the α/β hydrolase subfamilies. United States: N. p., 2019. Web. doi:10.1096/fj.201900948RR.
Wu, Zhiyun, Liu, Hao, Xu, Lishi, Chen, Hai‐Feng, & Feng, Yan. Algorithm‐based coevolution network identification reveals key functional residues of the α/β hydrolase subfamilies. United States. doi:10.1096/fj.201900948RR.
Wu, Zhiyun, Liu, Hao, Xu, Lishi, Chen, Hai‐Feng, and Feng, Yan. Wed . "Algorithm‐based coevolution network identification reveals key functional residues of the α/β hydrolase subfamilies". United States. doi:10.1096/fj.201900948RR.
@article{osti_1580205,
title = {Algorithm‐based coevolution network identification reveals key functional residues of the α/β hydrolase subfamilies},
author = {Wu, Zhiyun and Liu, Hao and Xu, Lishi and Chen, Hai‐Feng and Feng, Yan},
abstractNote = {},
doi = {10.1096/fj.201900948RR},
journal = {FASEB Journal},
number = 2,
volume = 34,
place = {United States},
year = {2019},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on December 22, 2020
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Works referenced in this record:

Improving tolerance of Candida antarctica lipase B towards irreversible thermal inactivation through directed evolution
journal, August 2003

  • Zhang, N.; Suen, W. -C.; Windsor, W.
  • Protein Engineering Design and Selection, Vol. 16, Issue 8
  • DOI: 10.1093/protein/gzg074

Clustal Omega for making accurate alignments of many protein sequences: Clustal Omega for Many Protein Sequences
journal, October 2017

  • Sievers, Fabian; Higgins, Desmond G.
  • Protein Science, Vol. 27, Issue 1
  • DOI: 10.1002/pro.3290

Mutated variant of Candida antarcticalipase B in (S)-selective dynamic kinetic resolution of secondary alcohols
journal, January 2011

  • Engström, Karin; Vallin, Michaela; Syrén, Per-Olof
  • Org. Biomol. Chem., Vol. 9, Issue 1
  • DOI: 10.1039/C0OB00748J

Improved Enantioselectivity of a Lipase by Rational Protein Engineering
journal, October 2001


Direct-coupling analysis of residue coevolution captures native contacts across many protein families
journal, November 2011

  • Morcos, F.; Pagnani, A.; Lunt, B.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 49
  • DOI: 10.1073/pnas.1111471108

The spatial architecture of protein function and adaptation
journal, October 2012

  • McLaughlin Jr, Richard N.; Poelwijk, Frank J.; Raman, Arjun
  • Nature, Vol. 491, Issue 7422
  • DOI: 10.1038/nature11500

Algorithm 97: Shortest path
journal, June 1962


Surface Sites for Engineering Allosteric Control in Proteins
journal, October 2008


Introduction of glycine and proline residues onto protein surface increases the thermostability of endoglucanase CelA from Clostridium thermocellum
journal, February 2011


Rational Design of Pseudozyma antarctica Lipase B Yielding a General Esterification Catalyst
journal, March 2010


Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
journal, March 1977

  • Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
  • Journal of Computational Physics, Vol. 23, Issue 3
  • DOI: 10.1016/0021-9991(77)90098-5

Automatic atom type and bond type perception in molecular mechanical calculations
journal, October 2006

  • Wang, Junmei; Wang, Wei; Kollman, Peter A.
  • Journal of Molecular Graphics and Modelling, Vol. 25, Issue 2
  • DOI: 10.1016/j.jmgm.2005.12.005

Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site
journal, January 2014

  • Xie, Yuan; An, Jiao; Yang, Guangyu
  • Journal of Biological Chemistry, Vol. 289, Issue 11
  • DOI: 10.1074/jbc.M113.536045

Cell-free synthesis and multifold screening of Candida antarctica lipase B (CalB) variants after combinatorial mutagenesis of hot spots
journal, December 2010

  • Park, Chang-Gil; Kwon, Min-A.; Song, Jae-Kwang
  • Biotechnology Progress, Vol. 27, Issue 1
  • DOI: 10.1002/btpr.532

Protein Sectors: Evolutionary Units of Three-Dimensional Structure
journal, August 2009


The α/β-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein Engineering
journal, June 2010

  • Kourist, Robert; Jochens, Helge; Bartsch, Sebastian
  • ChemBioChem, Vol. 11, Issue 12
  • DOI: 10.1002/cbic.201000213

Rational engineering of Candida antarctica lipase B for selective monoacylation of diols
journal, January 2012

  • Hamberg, Anders; Maurer, Steffen; Hult, Karl
  • Chemical Communications, Vol. 48, Issue 80
  • DOI: 10.1039/c2cc34684b

Activity Enhancement of Candida antarctica Lipase B by Flexibility Modulation in Helix Region Surrounding the Active Site
journal, April 2013


The development of a thermostable CiP ( Coprinus cinereus peroxidase) through in silico design
journal, January 2010

  • Kim, Su Jin; Lee, Jeong Ah; Joo, Jeong Chan
  • Biotechnology Progress
  • DOI: 10.1002/btpr.408

Coevolution-based inference of amino acid interactions underlying protein function
journal, July 2018


Development of thermostable Candida antarctica lipase B through novel in silico design of disulfide bridge
journal, November 2011

  • Le, Quang Anh Tuan; Joo, Jeong Chan; Yoo, Young Je
  • Biotechnology and Bioengineering, Vol. 109, Issue 4
  • DOI: 10.1002/bit.24371

Computational design of a lipase for catalysis of the Diels-Alder reaction
journal, June 2010

  • Linder, Mats; Hermansson, Anders; Liebeschuetz, John
  • Journal of Molecular Modeling, Vol. 17, Issue 4
  • DOI: 10.1007/s00894-010-0775-8

The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica
journal, April 1994


Dynamic Coupling between the SH2 and SH3 Domains of c-Src and Hck Underlies Their Inactivation by C-Terminal Tyrosine Phosphorylation
journal, April 2001


3DM: Systematic analysis of heterogeneous superfamily data to discover protein functionalities
journal, January 2010

  • Kuipers, Remko K.; Joosten, Henk-Jan; van Berkel, Willem J. H.
  • Proteins: Structure, Function, and Bioinformatics
  • DOI: 10.1002/prot.22725

Protein Model Discrimination Using Mutational Sensitivity Derived from Deep Sequencing
journal, February 2012


Improved Thermostability of Lipase B from Candida antarctica by Directed Evolution and Display on Yeast Surface
journal, November 2012


Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
journal, November 1991

  • Ichiye, Toshiko; Karplus, Martin
  • Proteins: Structure, Function, and Genetics, Vol. 11, Issue 3
  • DOI: 10.1002/prot.340110305

Hot Spots for Allosteric Regulation on Protein Surfaces
journal, December 2011


High-resolution mapping of protein sequence-function relationships
journal, August 2010

  • Fowler, Douglas M.; Araya, Carlos L.; Fleishman, Sarel J.
  • Nature Methods, Vol. 7, Issue 9
  • DOI: 10.1038/nmeth.1492

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993

  • Darden, Tom; York, Darrin; Pedersen, Lee
  • The Journal of Chemical Physics, Vol. 98, Issue 12
  • DOI: 10.1063/1.464397

Specificity in lipases: A computational study of transesterification of sucrose
journal, December 2004

  • Fuentes, Gloria; Ballesteros, Anthonio; Verma, Chandra S.
  • Protein Science, Vol. 13, Issue 12
  • DOI: 10.1110/ps.04724504

Mutant Lipase-Catalyzed Kinetic Resolution of Bulky Phenyl Alkyl sec -Alcohols: A Thermodynamic Analysis of Enantioselectivity
journal, February 2010


Emerging methods in protein co-evolution
journal, March 2013

  • de Juan, David; Pazos, Florencio; Valencia, Alfonso
  • Nature Reviews Genetics, Vol. 14, Issue 4
  • DOI: 10.1038/nrg3414

Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields
journal, April 2010


Statistical coevolution analysis and molecular dynamics: Identification of amino acid pairs essential for catalysis
journal, January 2005

  • Estabrook, R. A.; Luo, J.; Purdy, M. M.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 4
  • DOI: 10.1073/pnas.0409128102

Development of yeast cells displaying Candida antarctica lipase B and their application to ester synthesis reaction
journal, April 2007

  • Tanino, Takanori; Ohno, Takumi; Aoki, Tohru
  • Applied Microbiology and Biotechnology, Vol. 75, Issue 6
  • DOI: 10.1007/s00253-007-0959-z

Analysis of a 10-ns Molecular Dynamics Simulation of Mouse Acetylcholinesterase
journal, August 2001


Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations
journal, September 1995

  • Hünenberger, P. H.; Mark, A. E.; van Gunsteren, W. F.
  • Journal of Molecular Biology, Vol. 252, Issue 4
  • DOI: 10.1006/jmbi.1995.0514

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003


Evolutionary information for specifying a protein fold
journal, September 2005

  • Socolich, Michael; Lockless, Steve W.; Russ, William P.
  • Nature, Vol. 437, Issue 7058
  • DOI: 10.1038/nature03991

Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis
journal, November 2016

  • Bai, Fang; Morcos, Faruck; Cheng, Ryan R.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 50
  • DOI: 10.1073/pnas.1615932113

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011

  • Sievers, Fabian; Wilm, Andreas; Dineen, David
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.75

Amino Acid Oxidation of Candida antarctica Lipase B Studied by Molecular Dynamics Simulations and Site-Directed Mutagenesis
journal, February 2013

  • Irani, Mehdi; Törnvall, Ulrika; Genheden, Samuel
  • Biochemistry, Vol. 52, Issue 7
  • DOI: 10.1021/bi301298m

Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis
journal, April 2016

  • Liu, Ying; Yan, Zhihui; Lu, Xiaoyun
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep24117

Dynamical networks in tRNA:protein complexes
journal, April 2009

  • Sethi, A.; Eargle, J.; Black, A. A.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 16
  • DOI: 10.1073/pnas.0810961106

Laboratory Evolution of Enantiocomplementary Candida antarctica Lipase B Mutants with Broad Substrate Scope
journal, January 2013

  • Wu, Qi; Soni, Pankaj; Reetz, Manfred T.
  • Journal of the American Chemical Society, Vol. 135, Issue 5
  • DOI: 10.1021/ja310455t

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
journal, September 2009

  • van Opijnen, Tim; Bodi, Kip L.; Camilli, Andrew
  • Nature Methods, Vol. 6, Issue 10
  • DOI: 10.1038/nmeth.1377

Engineering of Candida antarctica lipase B for hydrolysis of bulky carboxylic acid esters
journal, December 2010


Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent
journal, February 2013


Origins of coevolution between residues distant in protein 3D structures
journal, August 2017

  • Anishchenko, Ivan; Ovchinnikov, Sergey; Kamisetty, Hetunandan
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 34
  • DOI: 10.1073/pnas.1702664114

Improving the expression yield of Candida antarctica lipase B in Escherichia coli by mutagenesis
journal, November 2007