Cited by 190Protein Structure and DynamicsEvolution and Genetic DynamicsRNA and protein synthesis mechanisms

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The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution

Campitelli, Paul, Modi, Tushar, Kumar, Sudhir, Ozkan, S. Banu·2020·Annual Review of Biophysics

DOI 10.1146/annurev-biophys-052118-115517

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Abstract

Advances in sequencing techniques and statistical methods have made it possible not only to predict sequences of ancestral proteins but also to identify thousands of mutations in the human exome, some of which are disease associated. These developments have motivated numerous theories and raised many questions regarding the fundamental principles behind protein evolution, which have been traditionally investigated horizontally using the tip of the phylogenetic tree through comparative studies of extant proteins within a family. In this article, we review a vertical comparison of the modern and resurrected ancestral proteins. We focus mainly on the dynamical properties responsible for a protein's ability to adapt new functions in response to environmental changes. Using the Dynamic Flexibility Index and the Dynamic Coupling Index to quantify the relative flexibility and dynamic coupling at a site-specific, single-amino-acid level, we provide evidence that the migration of hinges, which are often functionally critical rigid sites, is a mechanism through which proteins can rapidly evolve. Additionally, we show that disease-associated mutations in proteins often result in flexibility changes even at positions distal from mutational sites, particularly in the modulation of active site dynamics.

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Molecular Evolution and Phylogenetics
Nei, M., & Kumar, S. (2000) · doi:10.1093/oso/9780195135848.001.0001 · Cited by 8,012
Self-citation
Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations
Guerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728 · cited 1×
“It is known that disease-associated variants alter the stability of a protein (3, 27, 111).”
Background
Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins
Weinreich, D. M., Delaney, N. F., DePristo, M. A., & Hartl, D. L. (2006) · Science · doi:10.1126/science.1123539 · Cited by 1,418
Enzyme promiscuity: A mechanistic and evolutionary perspective
Tawfik, O. K. A. D. S. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-030409-143718 · Cited by 1,355
Walking the Interactome for Prioritization of Candidate Disease Genes
Köhler, S., Bauer, S., Horn, D., & Robinson, P. N. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.02.013 · Cited by 1,268
Protein stability promotes evolvability
Bloom, J. D., Labthavikul, S. T., Otey, C. R., & Arnold, F. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510098103 · Cited by 1,221
Protein Dynamism and Evolvability
Tokuriki, N., & Tawfik, D. S. (2009) · Science · doi:10.1126/science.1169375 · Cited by 932
Genetic drift, selection and the evolution of the mutation rate
Lynch, M., Ackerman, M. S., Gout, J.-F., Long, H., Sung, W., Thomas, W. K., & Foster, P. L. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.104 · Cited by 911
Stability effects of mutations and protein evolvability
Tokuriki, N., & Tawfik, D. S. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.08.003 · Cited by 836
Allostery in Disease and in Drug Discovery
Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 769
Allostery without conformational change
Cooper, A., & Dryden, D. T. F. (1984) · European Biophysics Journal · doi:10.1007/bf00276625 · Cited by 740
Protein Sectors: Evolutionary Units of Three-Dimensional Structure
Halabi, N. M., Rivoire, O., Leibler, S., & Ranganathan, R. (2009) · Cell · doi:10.1016/j.cell.2009.07.038 · Cited by 697
Enzyme promiscuity: evolutionary and mechanistic aspects
Khersonsky, O., Roodveldt, C., & Tawfik, D. S. (2006) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2006.08.011 · Cited by 641
Widespread macromolecular interaction perturbations in human genetic disorders
Sahni, N., Yi, S., Taipale, M., Fuxman Bass, J. I., Coulombe-Huntington, J., Yang, F., Peng, J., Weile, J., Karras, G. I., Wang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.013 · Cited by 594
Loss of Protein Structure Stability as a Major Causative Factor in Monogenic Disease
Yue, P., Li, Z. A., & Moult, J. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.08.020 · Cited by 529
Protein Allostery and Conformational Dynamics
Guo, J., & Zhou, H.-X. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00590 · Cited by 484 · cited 1×
“Rather than forming a new structure, a ligand binding to a remote site promotes a shift in the dynamics of all residues in the protein, changing the distribution of accessible conformational states in the ensemble and, thus, promoting easier access to certain conformers for allosteric regulations while restricting oth…”
Background
Improving enzyme properties: when are closer mutations better?
Morley, K. L., & Kazlauskas, R. J. (2005) · Trends in biotechnology · doi:10.1016/j.tibtech.2005.03.005 · Cited by 447
Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability
Bahar, İ., Atılgan, A. R., Demirel, M. C., & Erman, B. (1998) · Physical Review Letters · doi:10.1103/physrevlett.80.2733 · Cited by 442
Evolutionary information for specifying a protein fold
Socolich, M., Lockless, S. W., Russ, W. P., Lee, H. J., Gardner, K. H., & Ranganathan, R. (2005) · Nature · doi:10.1038/nature03991 · Cited by 437
Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436
Allostery in Its Many Disguises: From Theory to Applications
Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure · doi:10.1016/j.str.2019.01.003 · Cited by 404
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
Wang, X., Wei, X., Thijssen, B., Das, J., Lipkin, S. M., & Yu, H. (2012) · Nature Biotechnology · doi:10.1038/nbt.2106 · Cited by 385
The power of protein interaction networks for associating genes with diseases
Navlakha, S., & Kingsford, C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq076 · Cited by 355
Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life.
Pauling, L. C., Zuckerkandl, E., Henriksen, T., & Løvstad, R. A. (1963) · Acta chemica Scandinavica/Acta chemica Scandinavica. B, Organic chemistry and biochemistry/Acta chemica Scandinavica. A, Physical and inorganic chemistry/Acta chemica Scandinavica. Series B. Organic chemistry and biochemistry/Acta chemica Scandinavica. Series A, Physical and inorganic chemistry · doi:10.3891/acta.chem.scand.17s-0009 · Cited by 313
The role of protein dynamics in the evolution of new enzyme function
Campbell, E., Kaltenbach, M., Correy, G. J., Carr, P. D., Porebski, B. T., Livingstone, E. K., Afriat-Jurnou, L., Buckle, A. M., Weik, M., Hollfelder, F., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2175 · Cited by 311
MUTATIONAL EFFECTS ON PROTEIN STABILITY
Alber, T. (1989) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.58.070189.004001 · Cited by 309
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
Zheng, W., Brooks, B. R., & Thirumalai, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510426103 · Cited by 261
Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy
Tunçbağ, N., Gürsoy, A., & Keskin, Ö. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp240 · Cited by 259
Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian β-Lactamases
Risso, V. A., Gavira, J. A., Mejia-Carmona, D. F., Gaucher, E. A., & Sánchez‐Ruiz, J. M. (2013) · Journal of the American Chemical Society · doi:10.1021/ja311630a · Cited by 258
Structure of acid β-glucosidase with pharmacological chaperone provides insight into Gaucher disease
Lieberman, R. L., Wustman, B. A., Huertas, P. E., Powe, A. C., Pine, C. W., Khanna, R., Schlossmacher, M. G., Ringe, D., & Petsko, G. A. (2006) · Nature Chemical Biology · doi:10.1038/nchembio850 · Cited by 254
The interface of protein structure, protein biophysics, and molecular evolution
Liberles, D. A., Teichmann, S. A., Bahar, İ., Bastolla, U., Bloom, J. D., Bornberg‐Bauer, E., Colwell, L. J., de Koning, A. P. J., Dokholyan, N. V., Echave, J., et al. (2012) · Protein Science · doi:10.1002/pro.2071 · Cited by 224
Evolution of increased complexity in a molecular machine
Finnigan, G. C., Hanson-Smith, V., Stevens, T. H., & Thornton, J. W. (2012) · Nature · doi:10.1038/nature10724 · Cited by 219
The role of distant mutations and allosteric regulation on LovD active site dynamics
Jiménez‐Osés, G., Osuna, S., Gao, X., Sawaya, M. R., Gilson, L., Collier, S. J., Huisman, G. W., Yeates, T. O., Tang, Y., & Houk, K. N. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1503 · Cited by 211
Dynamic allostery can drive cold adaptation in enzymes
Saavedra, H. G., Wrabl, J. O., Anderson, J. A., Li, J., & Hilser, V. J. (2018) · Nature · doi:10.1038/s41586-018-0183-2 · Cited by 210
Single-molecule paleoenzymology probes the chemistry of resurrected enzymes
Pérez‐Jiménez, R., Inglés‐Prieto, Á., Zhao, Z., Sánchez-Romero, I., Alegre‐Cebollada, J., Kosuri, P., Garcia-Manyes, S., Kappock, T. J., Tanokura, M., Holmgren, A., et al. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2020 · Cited by 202
Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning
Gerek, Z. N., & Ozkan, S. B. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002154 · Cited by 181
Self-citation
Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series
Khersonsky, O., Röthlisberger, D., Dym, O., Albeck, S., Jackson, C. J., Baker, D. A., & Tawfik, D. S. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.12.031 · Cited by 178
Divergent evolution of protein conformational dynamics in dihydrofolate reductase
Bhabha, G., Ekiert, D. C., Jennewein, M. F., Zmasek, C. M., Tuttle, L. M., Kroon, G. J. A., Dyson, H. J., Godzik, A., Wilson, I. A., & Wright, P. E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2676 · Cited by 172
Measuring and comparing structural fluctuation patterns in large protein datasets
Fuglebakk, E., Echave, J., & Reuter, N. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts445 · Cited by 160
Sequence Evolution Correlates with Structural Dynamics
Liu, Y., & Bahar, İ. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss097 · Cited by 158
Principles of Allosteric Interactions in Cell Signaling
Nussinov, R., Tsai, C.-J., & Liu, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510028c · Cited by 154
Evolution of Conformational Dynamics Determines the Conversion of a Promiscuous Generalist into a Specialist Enzyme
Zou, T., Risso, V. A., Gavira, J. A., Sánchez‐Ruiz, J. M., & Ozkan, S. B. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu281 · Cited by 146
Self-citation
Manipulation of Conformational Change in Proteins by Single-Residue Perturbations
Atılgan, C., Gerek, Z. N., Ozkan, S. B., & Atılgan, A. R. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.05.020 · Cited by 143
Self-citation
An Ensemble View of Allostery
Hilser, V. J. (2010) · Science · doi:10.1126/science.1186121 · Cited by 141
Conservation of Protein Structure over Four Billion Years
Inglés‐Prieto, Á., Ibarra‐Molero, B., Delgado-Delgado, A., Pérez‐Jiménez, R., Fernández, J. M., Gaucher, E. A., Sánchez‐Ruiz, J. M., & Gavira, J. A. (2013) · Structure · doi:10.1016/j.str.2013.06.020 · Cited by 141
Rescue of conformational dynamics in enzyme catalysis by directed evolution
Otten, R., Liu, L., Kenner, L. R., Clarkson, M. W., Mavor, D., Tawfik, D. S., Kern, D., & Fraser, J. S. (2018) · Nature Communications · doi:10.1038/s41467-018-03562-9 · Cited by 130
Adaptability of protein structures to enable functional interactions and evolutionary implications
Haliloǧlu, T., & Bahar, İ. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.07.007 · Cited by 128
The CATH database
Knudsen, M., & Wiuf, C. (2010) · Human Genomics · doi:10.1186/1479-7364-4-3-207 · Cited by 122
Network of Dynamically Important Residues in the Open/Closed Transition in Polymerases Is Strongly Conserved
Zheng, W., Brooks, B. R., Doniach, S., & Thirumalai, D. (2005) · Structure · doi:10.1016/j.str.2005.01.017 · Cited by 121
Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines
Thirumalai, D., Hyeon, C., Zhuravlev, P. I., & Lorimer, G. H. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00760 · Cited by 108
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
Geng, C., Xue, L. C., Roel‐Touris, J., & Bonvin, A. M. J. J. (2019) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1410 · Cited by 104
Structural dynamics flexibility informs function and evolution at a proteome scale
Gerek, Z. N., Kumar, S., & Ozkan, S. B. (2013) · Evolutionary Applications · doi:10.1111/eva.12052 · Cited by 103
Self-citation
Evolutionary conservation of protein vibrational dynamics
Maguid, S., Fernández-Alberti, S., & Echave, J. (2008) · Gene · doi:10.1016/j.gene.2008.06.002 · Cited by 94
On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus
Hobbs, J. K., Shepherd, C., Saul, D. J., Demetras, N. J., Haaning, S., Monk, C. R., Daniel, R. M., & Arcus, V. L. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr253 · Cited by 92
Structural dynamics is a determinant of the functional significance of missense variants
Ponzoni, L., & Bahar, İ. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1715896115 · Cited by 91
Protein engineering: the potential of remote mutations
Wilding, M., Hong, N., Spence, M. A., Buckle, A. M., & Jackson, C. J. (2019) · Biochemical Society Transactions · doi:10.1042/bst20180614 · Cited by 87
Hidden randomness between fitness landscapes limits reverse evolution.
Tan, L.-Z., Serene, S., Chao, H.-X., & Gore, J. (2011) · Physical Review Letters · doi:10.1103/physrevlett.106.198102 · Cited by 86
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications
Liang, Z. T., Verkhivker, G. M., & Hu, G. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz029 · Cited by 85
Biotechnological and protein-engineering implications of ancestral protein resurrection
Risso, V. A., Sánchez‐Ruiz, J. M., & Ozkan, S. B. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.02.007 · Cited by 84
Self-citation
Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations
Kumar, S., Dudley, J. T., Filipski, A., & Liu, L. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.06.004 · Cited by 81
Self-citation
A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins
Kim, H., Zou, T., Modi, C. K., Dörner, K., Grunkemeyer, T. J., Chen, L., Fromme, R., Matz, M. V., Ozkan, S. B., & Wachter, R. M. (2015) · Structure · doi:10.1016/j.str.2014.11.011 · Cited by 80
Self-citation
Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History
Risso, V. A., Manssour-Triedo, F., Delgado-Delgado, A., Arco, R., Jesus, A. B.-D., Inglés‐Prieto, Á., Godoy‐Ruiz, R., Gavira, J. A., Gaucher, E. A., Ibarra‐Molero, B., et al. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu312 · Cited by 79
Reverse evolution leads to genotypic incompatibility despite functional and active site convergence
Kaltenbach, M., Jackson, C. J., Campbell, E. C., Hollfelder, F., & Tokuriki, N. (2015) · eLife · doi:10.7554/elife.06492 · Cited by 78
Evolutionary Conservation of Protein Backbone Flexibility
Maguid, S., Fernández-Alberti, S., Parisi, G. D., & Echave, J. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0209-x · Cited by 76
Limits of multifunctionality in tunable networks
Rocks, J. W., Ronellenfitsch, H., Liu, A. J., Nagel, S. R., & Katifori, E. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1806790116 · Cited by 76
Allostery without conformation change: modelling protein dynamics at multiple scales
McLeish, T. C. B., Rodgers, T. L., & Wilson, M. R. (2013) · Physical Biology · doi:10.1088/1478-3975/10/5/056004 · Cited by 72
Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs
Liu, Y., Gierasch, L. M., & Bahar, İ. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000931 · Cited by 71
Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome
Subramanian, S., & Kumar, S. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-306 · Cited by 70
Self-citation
Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions
Bahar, İ., Cheng, M. H., Lee, J. Y., Kaya, C., & Zhang, S. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.06.004 · Cited by 67
Coarse-Grained Model Of Entropic Allostery
Hawkins, R. J., & McLeish, T. C. B. (2004) · Physical Review Letters · doi:10.1103/physrevlett.93.098104 · Cited by 67
Perturbation–Response Scanning Reveals Key Residues for Allosteric Control in Hsp70
Penkler, D. L., Şensoy, Ö., Atılgan, C., & Bishop, Ö. T. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00775 · Cited by 65
Ancient thioredoxins evolved to modern-day stability–function requirement by altering native state ensemble
Modi, T., Huihui, J., Ghosh, K., & Ozkan, S. B. (2018) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2017.0184 · Cited by 64
Self-citation
Protein evolution speed depends on its stability and abundance and on chaperone concentrations
Agozzino, L., & Dill, K. A. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810194115 · Cited by 64
The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin
Kumar, A., Glembo, T. J., & Ozkan, S. B. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.06.060 · Cited by 61
Self-citation
E pluribus unum, no more: from one crystal, many conformations
Woldeyes, R. A., Sivak, D. A., & Fraser, J. S. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.07.005 · Cited by 59
Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutationsPreprint
Kumar, S., Suleski, M., Markov, G. J., Lawrence, S., Marco, A. D., & Filipski, A. J. (2009) · Genome Research · doi:10.1101/gr.091991.109 · Cited by 58
Self-citation
Structural plasticity of an aminoacyl-tRNA synthetase active site
Turner, J. M., Graziano, J. J., Spraggon, G., & Schultz, P. G. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601756103 · Cited by 55
Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity
Zhang, S., Li, H., Krieger, J., & Bahar, İ. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz102 · Cited by 55
Exploitation of Latent Allostery Enables the Evolution of New Modes of MAP Kinase Regulation
Coyle, S. M., Flores, J. A., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.07.019 · Cited by 54
Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics
Mishra, S. K., & Jernigan, R. L. (2018) · PLoS ONE · doi:10.1371/journal.pone.0199225 · Cited by 54
Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes
Baier, F., Hong, N., Yang, G., Pabis, A., Miton, C. M., Barrozo, A. H., Carr, P. D., Kamerlin, S. C. L., Jackson, C. J., & Tokuriki, N. (2019) · eLife · doi:10.7554/elife.40789 · Cited by 54
A flexible docking scheme to explore the binding selectivity of PDZ domains
Gerek, Z. N., & Ozkan, S. B. (2010) · Protein Science · doi:10.1002/pro.366 · Cited by 49
Self-citation
Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects
Yang, G., Hong, N., Baier, F., Jackson, C. J., & Tokuriki, N. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00561 · Cited by 49
Computational predictors fail to identify amino acid substitution effects at rheostat positions
Miller, M. J., Bromberg, Y., & Swint‐Kruse, L. (2017) · Scientific Reports · doi:10.1038/srep41329 · Cited by 49
Mutations Utilize Dynamic Allostery to Confer Resistance in TEM-1 β-lactamase
Modi, T., & Ozkan, S. B. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19123808 · Cited by 48
Self-citation
Using Evolution to Guide Protein Engineering: The Devil IS in the Details
Swint‐Kruse, L. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.05.030 · Cited by 42
Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity
Larrimore, K. E., Kazan, I. C., Kannan, L., Kendle, R., Jamal, T., Barcus, M., Bolia, A., Brimijoin, S., Zhan, C., Ozkan, S. B., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10571-z · Cited by 40
Self-citation
Evolutionary profiles from the QR factorization of multiple sequence alignments
Sethi, A., O’Donoghue, P., & Luthey-Schulten, Z. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409715102 · Cited by 39
Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members
Mikulska‐Ruminska, K., Shrivastava, I. H., Krieger, J., Zhang, S., Li, H., Bayır, H., Wenzel, S. E., VanDemark, A. P., Kagan, V. E., & Bahar, İ. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00006 · Cited by 38
Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association
Butler, B. M., Gerek, Z. N., Kumar, S., & Ozkan, S. B. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24748 · Cited by 36
Self-citation
Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes
Abrusán, G., & Marsh, J. A. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz093 · Cited by 35
The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein
Townsend, P. D., Rodgers, T. L., Glover, L. C., Korhonen, H. J., Richards, S. A., Colwell, L. J., Pohl, E., Wilson, M. R., Hodgson, D. R. W., McLeish, T. C. B., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.669267 · Cited by 34
Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites
Mishra, S. K., Kandoi, G., & Jernigan, R. L. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25749 · Cited by 33
Engineering ancestral protein hyperstability
Romero, M. L. R., Risso, V. A., Martínez‐Rodríguez, S., Ibarra‐Molero, B., & Sánchez‐Ruiz, J. M. (2016) · Biochemical Journal · doi:10.1042/bcj20160532 · Cited by 30
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Kumar, A., Butler, B. M., Kumar, S., & Ozkan, S. B. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.11.002 · Cited by 29
Self-citation
Comparative Modeling in Structural Genomics
Moult, J. (2008) · Structure · doi:10.1016/j.str.2007.12.001 · Cited by 28
Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization
Ponzoni, L., Zhang, S., Cheng, M. H., & Bahar, İ. (2018) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2017.0177 · Cited by 28
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Self-citation
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Copp, J. N., Anderson, D. W., Akiva, E., Babbitt, P. C., & Tokuriki, N. (2019) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2019.03.015 · Cited by 26
Revealing evolutionary constraints on proteins through sequence analysis
Wang, S., Bitbol, A., & Wingreen, N. S. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007010 · Cited by 25
The binding affinities of proteins interacting with the PDZ domain of PICK1
Bolia, A., Gerek, Z. N., Keskin, Ö., Ozkan, S. B., & Dev, K. K. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24034 · Cited by 24
Self-citation
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Gobeil, S., Ebert, M. C. C. J. C., Park, J., Gagné, D., Doucet, N., Berghuis, A. M., Pleiss, J., & Pelletier, J. N. (2019) · Scientific Reports · doi:10.1038/s41598-019-42866-8 · Cited by 23
Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores
Ben-David, M., Huang, H., Sun, M., Corbi‐Verge, C., Petsalaki, E., Liu, K., Gfeller, D., Garg, P., Tempel, W., Sochirca, I., et al. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.11.018 · Cited by 22
The CHAIN program: forging evolutionary links to underlying mechanisms
Neuwald, A. F. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.08.009 · Cited by 19
Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs
Butler, B. M., Kazan, I. C., Kumar, A., & Ozkan, S. B. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006626 · Cited by 19
Self-citation
The ‘allosteron’ model for entropic allostery of self-assembly
McLeish, T. C. B., Schaefer, C., & von der Heydt, A. (2018) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2017.0186 · Cited by 18
Directed evolution of the substrate specificity of dialkylglycine decarboxylase
Taylor, J. L., Price, J. E., & Toney, M. D. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2014.12.003 · Cited by 17
Resurrected Ancestral Proteins as Scaffolds for Protein Engineering
Risso, V. A., & Sánchez‐Ruiz, J. M. (2017) · Springer eBooks · doi:10.1007/978-3-319-50413-1_9 · Cited by 16
Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction
Liu, X., Golden, L. C., Lopez, J. A., Shepherd, T. R., Yu, L. P., & Fuentes, E. J. (2019) · Biophysical Journal · doi:10.1016/j.bpj.2019.05.008 · Cited by 13
A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs
Li, Z., Bolia, A., Maxwell, J. D., Bobkov, A. A., Ghirlanda, G., Ozkan, S. B., & Margulis, C. J. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00635 · Cited by 12
Self-citation
Adaptive Landscape of Protein Variation in Human Exomes
Patel, R., Scheinfeldt, L., Sanderford, M. D., Lanham, T. R., Tamura, K., Platt, A., Glicksberg, B. S., Xu, K., Dudley, J. T., & Kumar, S. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy107 · Cited by 11
Self-citation
Molecular Dynamics Simulations on Aspergillus niger Monoamine Oxidase: Conformational Dynamics and Inter‐monomer Communication Essential for Its Efficient Catalysis
Curado-Carballada, C., Feixas, F., & Osuna, S. (2019) · Advanced Synthesis and Catalysis · doi:10.1002/adsc.201900158 · Cited by 7

Research works printed but not linked: 3

Keskin O, 2000, Anticancer Drug Des, 15, 79
Kimura M., 1991, Idengaku Zasshi, 66, 367
Knies JL, 2017, Mol. Biol. Evol., 34, 1040

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Authors: Campitelli, P., Modi, T., Kumar, S., & Ozkan, S. B.
Affiliations: Arizona State University (US)
King Abdulaziz University (SA)
ORCID: Campitelli, Paul
Modi, Tushar
Kumar, Sudhir
Ozkan, S. Banu
Venue: Annual Review of Biophysics
Publisher: Annual Reviews
Published: 2020-05-06
Volume: 49
Issue: 1
Pages: 267-288
ISSN: 1936-122X (ISSN-L)
1936-1238
DOI: 10.1146/annurev-biophys-052118-115517
OpenAlex: W3007324177
Cited by: 190
References: 112
Citations by year: 2026: 17 · 2025: 40 · 2024: 31 · 2023: 31 · 2022: 28 · 2021: 32 · 2020: 11
FWCI: 2.43
Type: journal article
Language: en
Open access: closed
Locations: Annual Review of Biophysics (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: protein evolution, conformational dynamics, allosteric regulation, ancestral proteins, disease-associated mutations, active site dynamics, protein flexibility, functional adaptation
MeSH terms: Allosteric Regulation, Humans, Mutation, Protein Conformation, Proteins, Evolution, Molecular

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The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution

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