201
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Salamanca Viloria J, Allega MF, Lambrughi M, Papaleo E. An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass. Sci Rep 2017; 7:2838. [PMID: 28588190 PMCID: PMC5460117 DOI: 10.1038/s41598-017-01498-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/28/2017] [Indexed: 02/05/2023] Open
Abstract
Proteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Structure Networks (PSNs). Despite their broad applicability, few efforts have been devoted to benchmarking PSN methods and to provide the community with best practices. In many applications, it is convenient to use the centers of mass of the side chains as nodes. It becomes thus critical to evaluate the minimal distance cutoff between the centers of mass which will provide stable network properties. Moreover, when the PSN is derived from a structural ensemble collected by molecular dynamics (MD), the impact of the MD force field has to be evaluated. We selected a dataset of proteins with different fold and size and assessed the two fundamental properties of the PSN, i.e. hubs and connected components. We identified an optimal cutoff of 5 Å that is robust to changes in the force field and the proteins. Our study builds solid foundations for the harmonization and standardization of the PSN approach.
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Affiliation(s)
- Juan Salamanca Viloria
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Maria Francesca Allega
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.
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202
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Bayer CD, van Loo B, Hollfelder F. Specificity Effects of Amino Acid Substitutions in Promiscuous Hydrolases: Context-Dependence of Catalytic Residue Contributions to Local Fitness Landscapes in Nearby Sequence Space. Chembiochem 2017; 18:1001-1015. [PMID: 28464395 PMCID: PMC5488252 DOI: 10.1002/cbic.201600657] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 12/18/2022]
Abstract
Catalytic promiscuity can facilitate evolution of enzyme functions-a multifunctional catalyst may act as a springboard for efficient functional adaptation. We test the effect of single mutations on multiple activities in two groups of promiscuous AP superfamily members to probe this hypothesis. We quantify the effect of site-saturating mutagenesis of an analogous, nucleophile-flanking residue in two superfamily members: an arylsulfatase (AS) and a phosphonate monoester hydrolase (PMH). Statistical analysis suggests that no one physicochemical characteristic alone explains the mutational effects. Instead, these effects appear to be dominated by their structural context. Likewise, the effect of changing the catalytic nucleophile itself is not reaction-type-specific. Mapping of "fitness landscapes" of four activities onto the possible variation of a chosen sequence position revealed tremendous potential for respecialization of AP superfamily members through single-point mutations, highlighting catalytic promiscuity as a powerful predictor of adaptive potential.
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Affiliation(s)
- Christopher D. Bayer
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
- Present address: c-LEcta GmbHPerlickstrasse 504103LeipzigGermany
| | - Bert van Loo
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
- Present address: Institute for Evolution and BiodiversityUniversity of MünsterHüfferstrasse 148149MünsterGermany
| | - Florian Hollfelder
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
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203
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Li W, Xu S, Zhang B, Zhu Y, Hua Y, Kong X, Sun L, Hong J. Directed evolution to improve the catalytic efficiency of urate oxidase from Bacillus subtilis. PLoS One 2017; 12:e0177877. [PMID: 28531234 PMCID: PMC5439685 DOI: 10.1371/journal.pone.0177877] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/04/2017] [Indexed: 12/02/2022] Open
Abstract
Urate oxidase is a key enzyme in purine metabolism and catalyzes the oxidation of uric acid to allantoin. It is used to treat hyperuricemia and gout, and also in a diagnostic kit. In this study, error-prone polymerase chain reaction and staggered extension process was used to generate a mutant urate oxidase with improved enzyme activity from Bacillus subtilis. After several rounds of mutagenesis and screening, two mutants 6E9 and 8E279 were obtained which exhibited 2.99 and 3.43 times higher catalytic efficiency, respectively. They also exhibited lower optimal reaction temperature and higher thermo-stability. D44V, Q268R and K285Q were identified as the three most beneficial amino acid substitutions introduced by site-directed mutagenesis. D44V/Q268R, which was obtained through random combination of the three mutants, displayed the highest catalytic activity. The Km,kcat/Km and enzyme activity of D44V/Q268R increased by 68%, 83% and 129% respectively, compared with that of wild-type urate oxidase. Structural modeling indicated that mutations far from the active site can have significant effects on activity. For many of them, the underlying mechanisms are still difficult to explain from the static structural model. We also compared the effects of the same set of single point mutations on the wild type and on the final mutant. The results indicate strong effects of epistasis, which may imply that the mutations affect catalysis through influences on protein dynamics besides equilibrium structures.
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Affiliation(s)
- Wenjie Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Shouteng Xu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Biao Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Yelin Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Yan Hua
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Xin Kong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Lianhong Sun
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
- * E-mail:
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204
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Structural and functional innovations in the real-time evolution of new (βα) 8 barrel enzymes. Proc Natl Acad Sci U S A 2017; 114:4727-4732. [PMID: 28416687 DOI: 10.1073/pnas.1618552114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
New genes can arise by duplication and divergence, but there is a fundamental gap in our understanding of the relationship between these genes, the evolving proteins they encode, and the fitness of the organism. Here we used crystallography, NMR dynamics, kinetics, and mass spectrometry to explain the molecular innovations that arose during a previous real-time evolution experiment. In that experiment, the (βα)8 barrel enzyme HisA was under selection for two functions (HisA and TrpF), resulting in duplication and divergence of the hisA gene to encode TrpF specialists, HisA specialists, and bifunctional generalists. We found that selection affects enzyme structure and dynamics, and thus substrate preference, simultaneously and sequentially. Bifunctionality is associated with two distinct sets of loop conformations, each essential for one function. We observed two mechanisms for functional specialization: structural stabilization of each loop conformation and substrate-specific adaptation of the active site. Intracellular enzyme performance, calculated as the product of catalytic efficiency and relative expression level, was not linearly related to fitness. Instead, we observed thresholds for each activity above which further improvements in catalytic efficiency had little if any effect on growth rate. Overall, we have shown how beneficial substitutions selected during real-time evolution can lead to manifold changes in enzyme function and bacterial fitness. This work emphasizes the speed at which adaptive evolution can yield enzymes with sufficiently high activities such that they no longer limit the growth of their host organism, and confirms the (βα)8 barrel as an inherently evolvable protein scaffold.
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205
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Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Structure 2017; 25:739-749.e3. [PMID: 28416112 DOI: 10.1016/j.str.2017.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/20/2017] [Accepted: 03/13/2017] [Indexed: 11/22/2022]
Abstract
Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently sample nonfunctional conformations. To test this idea, we exploited advances in multiconformer modeling of room-temperature X-ray data collection on redesigned ubiquitin variants selected for increasing binding affinity to the deubiquitinase USP7. Initial core mutations disrupt natural packing and lead to increased flexibility. Additional, experimentally selected mutations quenched conformational heterogeneity through new stabilizing interactions. Stabilizing interactions, such as cation-pi stacking and ordered waters, which are not included in standard protein design energy functions, can create specific interactions that have long-range effects on flexibility across the protein. Our results suggest that increasing flexibility may be a useful strategy to escape local minima during initial directed evolution and protein design steps when creating new functions.
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206
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Pinheiro S, Soteras I, Gelpí JL, Dehez F, Chipot C, Luque FJ, Curutchet C. Structural and energetic study of cation–π–cation interactions in proteins. Phys Chem Chem Phys 2017; 19:9849-9861. [DOI: 10.1039/c6cp08448f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Statistical and energetic analysis of cation–π–cation motifs in protein structures suggests a potential stabilizing role in the protein fold.
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Affiliation(s)
- Silvana Pinheiro
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Barcelona
- Spain
| | - Ignacio Soteras
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Santa Coloma de Gramenet
- Spain
| | - Josep Lluis Gelpí
- Departament de Bioquímica i Biomedicina Molecular
- Facultat de Biologia
- Universitat de Barcelona
- Spain
| | - François Dehez
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana – Champaign
- Unité Mixte de Recherche No. 7565
- Université de Lorraine
- Vandoeuvre-lès-Nancy cedex
- France
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana – Champaign
- Unité Mixte de Recherche No. 7565
- Université de Lorraine
- Vandoeuvre-lès-Nancy cedex
- France
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Santa Coloma de Gramenet
- Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Barcelona
- Spain
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207
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Sugrue E, Scott C, Jackson CJ. Constrained evolution of a bispecific enzyme: lessons for biocatalyst design. Org Biomol Chem 2017; 15:937-946. [DOI: 10.1039/c6ob02355j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of the natural evolution of bispecificity in triazine hydrolase highlights the importance of epistasis in protein engineering and evolution.
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Affiliation(s)
- E. Sugrue
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - C. Scott
- Commonwealth Scientific and Industrial Research Organisation
- Canberra
- Australia
| | - C. J. Jackson
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
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208
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Liu W, Huang B, Kuang Y, Liu G. Molecular dynamics simulations elucidate conformational selection and induced fit mechanisms in the binding of PD-1 and PD-L1. MOLECULAR BIOSYSTEMS 2017; 13:892-900. [DOI: 10.1039/c7mb00036g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PD-L1 binds PD-1 through a complex mechanism including both the conformational selection and induced fit pathways.
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Affiliation(s)
- Wenping Liu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
- Division of Birth Cohort Study
| | - Bing Huang
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
| | - Yashu Kuang
- Division of Birth Cohort Study
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou 510623
- China
| | - Guangjian Liu
- Division of Birth Cohort Study
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou 510623
- China
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209
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Levsh O, Chiang YC, Tung CF, Noel JP, Wang Y, Weng JK. Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase. Biochemistry 2016; 55:6314-6326. [PMID: 27805809 PMCID: PMC6276119 DOI: 10.1021/acs.biochem.6b00887] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment by cellular metabolites that qualify as non-native substrates? Here, we combine X-ray crystallography and molecular dynamics to reveal distinct dynamic modes of HCT under native and non-native catalysis. We find that essential electrostatic and hydrogen-bonding interactions between the ligand and active site residues, permitted by active site plasticity, are elicited more effectively by shikimate than by other non-native substrates. This work provides a structural basis for how dynamic conformational states of HCT favor native over non-native catalysis by reducing the number of futile encounters between the enzyme and shikimate.
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Affiliation(s)
- Olesya Levsh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ying-Chih Chiang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun Fai Tung
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, La Jolla, CA
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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210
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Abstract
The mechanisms by which proteins evolve new functions can be slow and mysterious. Comprehensive structural analysis of enzyme variants reveal how gradual enrichments of pre-existing populations with the right productive dynamics for new functions can accomplish this aim.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., and the Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., and the Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
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211
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Kaltenbach M, Emond S, Hollfelder F, Tokuriki N. Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity. PLoS Genet 2016; 12:e1006305. [PMID: 27716796 PMCID: PMC5065130 DOI: 10.1371/journal.pgen.1006305] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022] Open
Abstract
The extent to which an emerging new function trades off with the original function is a key characteristic of the dynamics of enzyme evolution. Various cases of laboratory evolution have unveiled a characteristic trend; a large increase in a new, promiscuous activity is often accompanied by only a mild reduction of the native, original activity. A model that associates weak trade-offs with “evolvability” was put forward, which proposed that enzymes possess mutational robustness in the native activity and plasticity in promiscuous activities. This would enable the acquisition of a new function without compromising the original one, reducing the benefit of early gene duplication and therefore the selection pressure thereon. Yet, to date, no experimental study has examined this hypothesis directly. Here, we investigate the causes of weak trade-offs by systematically characterizing adaptive mutations that occurred in two cases of evolutionary transitions in enzyme function: (1) from phosphotriesterase to arylesterase, and (2) from atrazine chlorohydrolase to melamine deaminase. Mutational analyses in various genetic backgrounds revealed that, in contrast to the prevailing model, the native activity is less robust to mutations than the promiscuous activity. For example, in phosphotriesterase, the deleterious effect of individual mutations on the native phosphotriesterase activity is much larger than their positive effect on the promiscuous arylesterase activity. Our observations suggest a revision of the established model: weak trade-offs are not caused by an intrinsic robustness of the native activity and plasticity of the promiscuous activity. We propose that upon strong adaptive pressure for the new activity without selection against the original one, selected mutations will lead to the largest possible increases in the new function, but whether and to what extent they decrease the old function is irrelevant, creating a bias towards initially weak trade-offs and the emergence of generalist enzymes. Understanding how enzymes evolve is a fundamental question that can help us decipher not only the mechanisms of evolution on a higher level, i.e., whole organisms, but also advances our knowledge of sequence-structure-function relationships as a guide to artificial evolution in the test tube. An important yet unexplained phenomenon occurs during the evolution of a new enzymatic function; it has been observed that new and ancestral functions often trade-off only weakly, meaning the original native activity is initially maintained at a high level despite drastic improvement of the new promiscuous activity. It has previously been proposed that weak trade-offs occur because the native activity is robust to mutations while the promiscuous activity is not. However, the present work contradicts this hypothesis, based on the detailed characterization of mutational effects on both activities in two examples of enzyme evolution. We propose an alternative explanation: the weak activity trade-off is consistent with being a by-product of strong selection for the new activity rather than an intrinsic property of the native activity.
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Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- * E-mail:
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