Chapter 10: Advances in Protein Engineering and its Application in Synthetic Biology

Liu, Rongming; Liang, Liya; Lacerda, Maria Priscila; Freed, Emily F.; Eckert, Carrie A.

doi:10.1016/B978-0-12-824469-2.00013-0

Chapter 10: Advances in Protein Engineering and its Application in Synthetic Biology

Book · 14 January 2022

DOI:https://doi.org/10.1016/B978-0-12-824469-2.00013-0· OSTI ID:1983882

Liu, Rongming; Liang, Liya; Lacerda, Maria Priscila; Freed, Emily F.;

Protein engineering has been used successfully in fields ranging from medicine to food science to biofuels. Applications of protein engineering include developing antiviral peptides or other protein therapeutics, antibody engineering, designing protein-based logic circuits, engineering enzymes to be more specific or to function under industrially relevant conditions such as at higher temperatures or high/low pH, modifying cell signaling or regulatory functions, and so on. Advances in recombinant DNA, "omics," and CRISPR-Cas (clustered regularly interspaced short palindromic repeats and its associated proteins) technologies, combined with high-throughput screening facilities, will lead to improved methods for protein engineering, enabling easy modification of more proteins/enzymes for new specific applications. New methods for rational design, directed evolution, and computer-aided protein design will further accelerate the speed of protein evolution and expand the scope for protein engineering. In this chapter we discuss general protein engineering strategies and advances in engineering proteins with desired functions, focusing on the "design" and "build" part of the design-build-test-learn cycle.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office

DOE Contract Number:: AC36-08GO28308

OSTI ID:: 1983882

Report Number(s):: NREL/CH-2700-78847; MainId:32764; UUID:6b5f2aeb-1177-4866-befc-7e38c6920f60; MainAdminID:19185

Country of Publication:: United States

Language:: English

References (97)

Modulation of transglycosylation and improved malto-oligosaccharide synthesis by protein engineering of maltogenic amylase from Bacillus lehensis G1 Abdul Manas, Nor Hasmaliana; Jonet, Mohd Anuar; Abdul Murad, Abdul Munir Process Biochemistry, Vol. 50, Issue 10 https://doi.org/10.1016/j.procbio.2015.06.005	journal	October 2015
Intuitive representation of surface properties of biomolecules using BioBlender Andrei, Raluca Mihaela; Callieri, Marco; Zini, Maria Francesca BMC Bioinformatics, Vol. 13, Issue S4 https://doi.org/10.1186/1471-2105-13-S4-S16	journal	March 2012
Next-generation genetic code expansion Arranz-Gibert, Pol; Vanderschuren, Koen; Isaacs, Farren J. Current Opinion in Chemical Biology, Vol. 46 https://doi.org/10.1016/j.cbpa.2018.07.020	journal	October 2018
Antibody constructs in cancer therapy Beckman, Robert A.; Weiner, Louis M.; Davis, Hugh M. Cancer, Vol. 109, Issue 2 https://doi.org/10.1002/cncr.22402	journal	January 2007
Computational design-based molecular engineering of the glycosyl hydrolase family 11 B. subtilis XynA endoxylanase improves its acid stability Belien, T.; Joye, I. J.; Delcour, J. A. Protein Engineering Design and Selection, Vol. 22, Issue 10 https://doi.org/10.1093/protein/gzp024	journal	June 2009
CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors Butt, Haroon; Eid, Ayman; Momin, Afaque A. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1680-9	journal	April 2019
CRISPR-Based Directed Evolution for Crop Improvement Butt, Haroon; Zaidi, Syed Shan-e-Ali; Hassan, Norhan Trends in Biotechnology, Vol. 38, Issue 3 https://doi.org/10.1016/j.tibtech.2019.08.001	journal	March 2020
Enhancing the stability and solubility of TEV protease using in silico design Cabrita, Lisa D.; Gilis, Dimitri; Robertson, Amy L. Protein Science, Vol. 16, Issue 11 https://doi.org/10.1110/ps.072822507	journal	November 2007
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors Cao, Longxing; Goreshnik, Inna; Coventry, Brian Science, Vol. 370, Issue 6515 https://doi.org/10.1126/science.abd9909	journal	September 2020
Protein engineering approaches to chemical biotechnology Chen, Zhen; Zeng, An-Ping Current Opinion in Biotechnology, Vol. 42 https://doi.org/10.1016/j.copbio.2016.07.007	journal	December 2016
De novo design of protein logic gates Chen, Zibo; Kibler, Ryan D.; Hunt, Andrew Science, Vol. 368, Issue 6486 https://doi.org/10.1126/science.aay2790	journal	April 2020
Applications of Yeast Surface Display for Protein Engineering Cherf, Gerald M.; Cochran, Jennifer R. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-2748-7_8	book	January 2015
Massively parallel de novo protein design for targeted therapeutics Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J. Nature, Vol. 550, Issue 7674 https://doi.org/10.1038/nature23912	journal	September 2017
The relation between the divergence of sequence and structure in proteins. Chothia, C.; Lesk, A. M. The EMBO Journal, Vol. 5, Issue 4 https://doi.org/10.1002/j.1460-2075.1986.tb04288.x	journal	April 1986
From directed evolution to computational enzyme engineering—A review Chowdhury, Ratul; Maranas, Costas D. AIChE Journal, Vol. 66, Issue 3 https://doi.org/10.1002/aic.16847	journal	September 2019
Improved stability and yield of a Fv-toxin fusion protein by computer design and protein engineering of the Fv 1 1Edited by I. Wilson Chowdhury, Partha S.; Vasmatzis, George; Beers, Richard Journal of Molecular Biology, Vol. 281, Issue 5 https://doi.org/10.1006/jmbi.1998.1980	journal	September 1998
Expanding the Plant GSTome Through Directed Evolution: DNA Shuffling for the Generation of New Synthetic Enzymes With Engineered Catalytic and Binding Properties Chronopoulou, Evangelia G.; Papageorgiou, Anastassios C.; Ataya, Farid Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01737	journal	November 2018
Dramatically Increased pH and Temperature Stability of Chymotrypsin Using Dual Block Polymer-Based Protein Engineering Cummings, Chad; Murata, Hironobu; Koepsel, Richard Biomacromolecules, Vol. 15, Issue 3 https://doi.org/10.1021/bm401575k	journal	February 2014
Continuous directed evolution for strain and protein engineering d’Oelsnitz, Simon; Ellington, Andrew Current Opinion in Biotechnology, Vol. 53 https://doi.org/10.1016/j.copbio.2017.12.020	journal	October 2018
Organic solvent-tolerant enzymes Doukyu, Noriyuki; Ogino, Hiroyasu Biochemical Engineering Journal, Vol. 48, Issue 3 https://doi.org/10.1016/j.bej.2009.09.009	journal	February 2010
The imminent role of protein engineering in synthetic biology Foo, Jee Loon; Ching, Chi Bun; Chang, Matthew Wook Biotechnology Advances, Vol. 30, Issue 3 https://doi.org/10.1016/j.biotechadv.2011.09.008	journal	May 2012
Improving catalytic function by ProSAR-driven enzyme evolution Fox, Richard J.; Davis, S. Christopher; Mundorff, Emily C. Nature Biotechnology, Vol. 25, Issue 3 https://doi.org/10.1038/nbt1286	journal	February 2007
Ribosome Subunit Stapling for Orthogonal Translation inE. coli Fried, Stephen D.; Schmied, Wolfgang H.; Uttamapinant, Chayasith Angewandte Chemie, Vol. 127, Issue 43 https://doi.org/10.1002/ange.201506311	journal	August 2015
Yeast surface display for protein engineering and characterization Gai, S. Annie; Wittrup, K. Dane Current Opinion in Structural Biology, Vol. 17, Issue 4 https://doi.org/10.1016/j.sbi.2007.08.012	journal	August 2007
bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming Gao, Jun; Zhang, Qingchen; Liu, Min Journal of Cheminformatics, Vol. 8, Issue 1 https://doi.org/10.1186/s13321-016-0149-z	journal	July 2016
Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering Garst, Andrew D.; Bassalo, Marcelo C.; Pines, Gur Nature Biotechnology, Vol. 35, Issue 1, p. 48-55 https://doi.org/10.1038/nbt.3718	journal	December 2016
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage Gaudelli, Nicole M.; Komor, Alexis C.; Rees, Holly A. Nature, Vol. 551, Issue 7681 https://doi.org/10.1038/nature24644	journal	October 2017
Structural adaptation of enzymes to low temperatures Gianese, Giulio; Argos, Patrick; Pascarella, Stefano Protein Engineering, Design and Selection, Vol. 14, Issue 3 https://doi.org/10.1093/protein/14.3.141	journal	March 2001
Engineered Protein Machines: Emergent Tools for Synthetic Biology Glasscock, Cameron J.; Lucks, Julius B.; DeLisa, Matthew P. Cell Chemical Biology, Vol. 23, Issue 1 https://doi.org/10.1016/j.chembiol.2015.12.004	journal	January 2016
In vitro ribosome synthesis and evolution through ribosome display Hammerling, Michael J.; Fritz, Brian R.; Yoesep, Danielle J. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14705-2	journal	February 2020
Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination Heinzelman, Pete; Komor, Russell; Kanaan, Arvind Protein Engineering, Design and Selection, Vol. 23, Issue 11 https://doi.org/10.1093/protein/gzq063	journal	September 2010
Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response Heler, Robert; Wright, Addison V.; Vucelja, Marija Molecular Cell, Vol. 65, Issue 1 https://doi.org/10.1016/j.molcel.2016.11.031	journal	January 2017
A Robust and All-Inclusive Pipeline for Shuffling of Adeno-Associated Viruses Herrmann, Anne-Kathrin; Bender, Christian; Kienle, Eike ACS Synthetic Biology, Vol. 8, Issue 1 https://doi.org/10.1021/acssynbio.8b00373	journal	December 2018
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins Jayaram, B.; Dhingra, Priyanka; Mishra, Avinash BMC Bioinformatics, Vol. 15, Issue S16 https://doi.org/10.1186/1471-2105-15-S16-S7	journal	December 2014
Protein engineering andde novodesigning of a biocatalyst Kaushik, Mahima; Sinha, Prashant; Jaiswal, Pragya Journal of Molecular Recognition, Vol. 29, Issue 10 https://doi.org/10.1002/jmr.2546	journal	April 2016
Protein structure prediction and analysis using the Robetta server Kim, D. E.; Chivian, D.; Baker, D. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh468	journal	July 2004
Engineered CRISPR-Cas9 nucleases with altered PAM specificities Kleinstiver, Benjamin P.; Prew, Michelle S.; Tsai, Shengdar Q. Nature, Vol. 523, Issue 7561 https://doi.org/10.1038/nature14592	journal	June 2015
Rational and Semirational Protein Design Korendovych, Ivan V. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-7366-8_2	book	October 2017
De novo protein design, a retrospective Korendovych, Ivan V.; DeGrado, William F. Quarterly Reviews of Biophysics, Vol. 53 https://doi.org/10.1017/S0033583519000131	journal	January 2020
Five hard truths for synthetic biology Kwok, Roberta Nature, Vol. 463, Issue 7279 https://doi.org/10.1038/463288a	journal	January 2010
Designed protein logic to target cells with precise combinations of surface antigens Lajoie, Marc J.; Boyken, Scott E.; Salter, Alexander I. Science, Vol. 369, Issue 6511 https://doi.org/10.1126/science.aba6527	journal	September 2020
De novo design of bioactive protein switches Langan, Robert A.; Boyken, Scott E.; Ng, Andrew H. Nature, Vol. 572, Issue 7768 https://doi.org/10.1038/s41586-019-1432-8	journal	July 2019
CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli Liang, Liya; Liu, Rongming; Garst, Andrew D. Metabolic Engineering, Vol. 41 https://doi.org/10.1016/j.ymben.2017.02.009	journal	May 2017
Transcriptional Regulatory Networks Involved in C3–C4 Alcohol Stress Response and Tolerance in Yeast Liang, Liya; Liu, Rongming; Freed, Emily F. ACS Synthetic Biology, Vol. 10, Issue 1 https://doi.org/10.1021/acssynbio.0c00253	journal	December 2020
Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production Liu, Rongming; Liang, Liya; Choudhury, Alaksh Metabolic Engineering, Vol. 47 https://doi.org/10.1016/j.ymben.2018.04.007	journal	May 2018
The state-of-the-art strategies of protein engineering for enzyme stabilization Liu, Qian; Xun, Guanhua; Feng, Yan Biotechnology Advances, Vol. 37, Issue 4 https://doi.org/10.1016/j.biotechadv.2018.10.011	journal	July 2019
Synthetic chimeric nucleases function for efficient genome editing Liu, R. M.; Liang, L. L.; Freed, E. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13500-y	journal	December 2019
Engineering regulatory networks for complex phenotypes in E. coli Liu, Rongming; Liang, Liya; Freed, Emily F. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17721-4	journal	August 2020
Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing Liu, Rongming; Liang, Liya; Freed, Emily F. Trends in Biotechnology, Vol. 39, Issue 3 https://doi.org/10.1016/j.tibtech.2020.07.005	journal	March 2021
Rational Design of Mini-Cas9 for Transcriptional Activation Ma, Dacheng; Peng, Shuguang; Huang, Weiren ACS Synthetic Biology, Vol. 7, Issue 4 https://doi.org/10.1021/acssynbio.7b00404	journal	March 2018
High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis Mason, Derek M.; Weber, Cédric R.; Parola, Cristina Nucleic Acids Research, Vol. 46, Issue 14 https://doi.org/10.1093/nar/gky550	journal	June 2018
Application of modified yeast surface display technologies for non-Antibody protein engineering Mei, Meng; Zhou, Yu; Peng, Wenfang Microbiological Research, Vol. 196 https://doi.org/10.1016/j.micres.2016.12.002	journal	March 2017
Structure-guided SCHEMA recombination of distantly related β-lactamases Meyer, Michelle M.; Hochrein, Lisa; Arnold, Frances H. Protein Engineering, Design and Selection, Vol. 19, Issue 12 https://doi.org/10.1093/protein/gzl045	journal	November 2006
Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering Milligan, John N.; Garry, Daniel J. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-6343-0_3	book	September 2016
Engineering of Enzymes for Selective Catalysis U. Nair, Nikhil; A. Denard, Carl; Zhao, Huimin Current Organic Chemistry, Vol. 14, Issue 17 https://doi.org/10.2174/138527210792927537	journal	October 2010
Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform Oh, Eun Joong; Liu, Rongming; Liang, Liya ACS Synthetic Biology, Vol. 9, Issue 8 https://doi.org/10.1021/acssynbio.0c00159	journal	June 2020
Methods for the directed evolution of proteins Packer, Michael S.; Liu, David R. Nature Reviews Genetics, Vol. 16, Issue 7 https://doi.org/10.1038/nrg3927	journal	June 2015
Applications of DNA shuffling to pharmaceuticals and vaccines Patten, Phillip A.; Howard, Russell J.; Stemmer, Willem PC Current Opinion in Biotechnology, Vol. 8, Issue 6 https://doi.org/10.1016/S0958-1669(97)80127-9	journal	December 1997
ModBase, a database of annotated comparative protein structure models and associated resources Pieper, Ursula; Webb, Benjamin M.; Dong, Guang Qiang Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1144	journal	November 2013
Directed DNA Shuffling of Retrovirus and Retrotransposon Integrase Protein Domains Qi, Xiaojie; Vargas, Edwin; Larsen, Liza PLoS ONE, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pone.0063957	journal	May 2013
Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution Renata, Hans; Wang, Z. Jane; Arnold, Frances H. Angewandte Chemie International Edition, Vol. 54, Issue 11 https://doi.org/10.1002/anie.201409470	journal	February 2015
Exploring protein fitness landscapes by directed evolution Romero, Philip A.; Arnold, Frances H. Nature Reviews Molecular Cell Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nrm2805	journal	December 2009
NGL Viewer: a web application for molecular visualization Rose, Alexander S.; Hildebrand, Peter W. Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv402	journal	April 2015
Molecular dynamics simulation for rational protein engineering: Present and future prospectus Rouhani, Maryam; Khodabakhsh, Farnaz; Norouzian, Dariush Journal of Molecular Graphics and Modelling, Vol. 84 https://doi.org/10.1016/j.jmgm.2018.06.009	journal	September 2018
I-TASSER: a unified platform for automated protein structure and function prediction Roy, Ambrish; Kucukural, Alper; Zhang, Yang Nature Protocols, Vol. 5, Issue 4 https://doi.org/10.1038/nprot.2010.5	journal	March 2010
Synthetic biology in various cellular and molecular fields: applications, limitations, and perspective Safaei, Mohsen; Mobini, Gholam-Reza; Abiri, Ardavan Molecular Biology Reports, Vol. 47, Issue 8 https://doi.org/10.1007/s11033-020-05565-6	journal	June 2020
Chaperone machines for protein folding, unfolding and disaggregation Saibil, Helen Nature Reviews Molecular Cell Biology, Vol. 14, Issue 10 https://doi.org/10.1038/nrm3658	journal	September 2013
Protein structure modeling for structural genomics Sánchez, Roberto; Pieper, Ursula; Melo, Francisco Nature Structural Biology, Vol. 7, p. 986-990 https://doi.org/10.1038/80776	journal	November 2000
BRAGI: A comprehensive protein modeling program system Schomburg, Dietmar; Reichelt, Joachim Journal of Molecular Graphics, Vol. 6, Issue 3 https://doi.org/10.1016/0263-7855(88)80069-9	journal	September 1988
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data Sehnal, David; Deshpande, Mandar; Vařeková, Radka Svobodová Nature Methods, Vol. 14, Issue 12 https://doi.org/10.1038/nmeth.4499	journal	December 2017
Web3DMol: interactive protein structure visualization based on WebGL Shi, Maoxiang; Gao, Juntao; Zhang, Michael Q. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx383	journal	May 2017
Rewiring Cas9 to Target New PAM Sequences Siksnys, Virginijus; Gasiunas, Giedrius Molecular Cell, Vol. 61, Issue 6 https://doi.org/10.1016/j.molcel.2016.03.002	journal	March 2016
Current Trends in Protein Engineering: Updates and Progress Sinha, Rajeshwari; Shukla, Pratyoosh Current Protein & Peptide Science, Vol. 20, Issue 5 https://doi.org/10.2174/1389203720666181119120120	journal	March 2019
Rationally engineered Cas9 nucleases with improved specificity Slaymaker, I. M.; Gao, L.; Zetsche, B. Science, Vol. 351, Issue 6268 https://doi.org/10.1126/science.aad5227	journal	December 2015
Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design Soh, Lemuel M. J.; Mak, Wai Shun; Lin, Paul P. ACS Synthetic Biology, Vol. 6, Issue 4 https://doi.org/10.1021/acssynbio.6b00240	journal	January 2017
Recent Advances in Rational Approaches for Enzyme Engineering Steiner, Kerstin; Schwab, Helmut Computational and Structural Biotechnology Journal, Vol. 2, Issue 3 https://doi.org/10.5936/csbj.201209010	journal	September 2012
Creation of thermostable and alkaline stable xylanase variants by DNA shuffling Stephens, Dawn Elizabeth; Khan, Faez Iqbal; Singh, Parvesh Journal of Biotechnology, Vol. 187 https://doi.org/10.1016/j.jbiotec.2014.07.446	journal	October 2014
A CRISPR-Cas9 Assisted Non-Homologous End-Joining Strategy for One-step Engineering of Bacterial Genome Su, Tianyuan; Liu, Fapeng; Gu, Pengfei Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep37895	journal	November 2016
Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules Sussman, Joel L.; Lin, Dawei; Jiang, Jiansheng Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 6 https://doi.org/10.1107/S0907444998009378	journal	November 1998
Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity Tan, Yuanyan; Chu, Athena H. Y.; Bao, Siyu Proceedings of the National Academy of Sciences, Vol. 116, Issue 42 https://doi.org/10.1073/pnas.1906843116	journal	September 2019
Efficient yeast surface-display of novel complex synthetic cellulosomes Tang, Hongting; Wang, Jiajing; Wang, Shenghuan Microbial Cell Factories, Vol. 17, Issue 1 https://doi.org/10.1186/s12934-018-0971-2	journal	August 2018
Computational design of ligand-binding proteins with high affinity and selectivity Tinberg, Christine E.; Khare, Sagar D.; Dou, Jiayi Nature, Vol. 501, Issue 7466, p. 212-216 https://doi.org/10.1038/nature12443	journal	September 2013
Engineering of Phytase for Improved Activity at Low pH Tomschy, Andrea; Brugger, Roland; Lehmann, Martin Applied and Environmental Microbiology, Vol. 68, Issue 4 https://doi.org/10.1128/AEM.68.4.1907-1913.2002	journal	April 2002
Directed Evolution of Protein Thermal Stability Using Yeast Surface Display Traxlmayr, Michael W.; Shusta, Eric V. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-6857-2_4	book	March 2017
Yeast Surface Displaying Glucose Oxidase as Whole-Cell Biocatalyst: Construction, Characterization, and Its Electrochemical Glucose Sensing Application Wang, Hongwei; Lang, Qiaolin; Li, Liang Analytical Chemistry, Vol. 85, Issue 12 https://doi.org/10.1021/ac400979r	journal	May 2013
Genome Shuffling and Ribosome Engineering of Streptomyces actuosus for High-Yield Nosiheptide Production Wang, Qingling; Zhang, Dong; Li, Yudong Applied Biochemistry and Biotechnology, Vol. 173, Issue 6 https://doi.org/10.1007/s12010-014-0948-5	journal	May 2014
Rational design of a split-Cas9 enzyme complex Wright, Addison V.; Sternberg, Samuel H.; Taylor, David W. Proceedings of the National Academy of Sciences, Vol. 112, Issue 10 https://doi.org/10.1073/pnas.1501698112	journal	February 2015
Improved protein structure prediction using predicted inter-residue orientations Yang, Jianyi; Anishchenko, Ivan; Park, Hahnbeom https://doi.org/10.1101/846279	posted_content	November 2019
UCSF Chimera, MODELLER, and IMP: An integrated modeling system Yang, Zheng; Lasker, Keren; Schneidman-Duhovny, Dina Journal of Structural Biology, Vol. 179, Issue 3 https://doi.org/10.1016/j.jsb.2011.09.006	journal	September 2012
Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment Yang, Jianyi; Roy, Ambrish; Zhang, Yang Bioinformatics, Vol. 29, Issue 20 https://doi.org/10.1093/bioinformatics/btt447	journal	August 2013
Machine-learning-guided directed evolution for protein engineering Yang, Kevin K.; Wu, Zachary; Arnold, Frances H. Nature Methods, Vol. 16, Issue 8 https://doi.org/10.1038/s41592-019-0496-6	journal	July 2019
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere Yu, Jian; Zhou, Yong; Tanaka, Isao Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp599	journal	October 2009
Genome shuffling for improving the activity of alkaline pectinase in Bacillus subtilis FS105 and its molecular mechanism Yu, Ping; Wang, Xinxin; Ren, Qian World Journal of Microbiology and Biotechnology, Vol. 35, Issue 11 https://doi.org/10.1007/s11274-019-2749-z	journal	October 2019
Directed Evolution of Protein Catalysts Zeymer, Cathleen; Hilvert, Donald Annual Review of Biochemistry, Vol. 87, Issue 1 https://doi.org/10.1146/annurev-biochem-062917-012034	journal	June 2018
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction Zhang, Zengming; Li, Yu; Lin, Biaoyang Bioinformatics, Vol. 27, Issue 15 https://doi.org/10.1093/bioinformatics/btr331	journal	June 2011
COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information Zhang, Chengxin; Freddolino, Peter L.; Zhang, Yang Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx366	journal	May 2017
Combining Cell Surface Display and DNA-Shuffling Technology for Directed Evolution of Streptomyces Phospholipase D and Synthesis of Phosphatidylserine Zhang, Haiyang; Chu, Wenqin; Sun, Jianan Journal of Agricultural and Food Chemistry, Vol. 67, Issue 47 https://doi.org/10.1021/acs.jafc.9b05394	journal	November 2019

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