Search Results - "Reynolds, Kimberly A"

Hot Spots for Allosteric Regulation on Protein Surfaces by Reynolds, Kimberly A., McLaughlin, Richard N., Ranganathan, Rama

“…Recent work indicates a general architecture for proteins in which sparse networks of physically contiguous and coevolving amino acids underlie basic aspects…”
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Evolution-Based Functional Decomposition of Proteins by Rivoire, Olivier, Reynolds, Kimberly A, Ranganathan, Rama

“…The essential biological properties of proteins-folding, biochemical activities, and the capacity to adapt-arise from the global pattern of interactions…”
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The genetic landscape of a metabolic interaction by Nguyen, Thuy N., Ingle, Christine, Thompson, Samuel, Reynolds, Kimberly A.

“…While much prior work has explored the constraints on protein sequence and evolution induced by physical protein-protein interactions, the sequence-level…”
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An evolutionary hotspot defines functional differences between CRYPTOCHROMES by Rosensweig, Clark, Reynolds, Kimberly A., Gao, Peng, Laothamatas, Isara, Shan, Yongli, Ranganathan, Rama, Takahashi, Joseph S., Green, Carla B.

“…Mammalian circadian clocks are driven by a transcription/translation feedback loop composed of positive regulators (CLOCK/BMAL1) and repressors (CRYPTOCHROME…”
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Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme by Thompson, Samuel, Zhang, Yang, Ingle, Christine, Reynolds, Kimberly A, Kortemme, Tanja

“…Protein mutational landscapes are shaped by the cellular environment, but key factors and their quantitative effects are often unknown. Here we show that Lon,…”
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Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily by Narayanan, Chitra, Gagné, Donald, Reynolds, Kimberly A., Doucet, Nicolas

“…In this work, we applied the sequence-based statistical coupling analysis approach to characterize conserved amino acid networks important for biochemical…”
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Structurally distributed surface sites tune allosteric regulation by McCormick, James W, Russo, Marielle AX, Thompson, Samuel, Blevins, Aubrie, Reynolds, Kimberly A

“…Our ability to rationally optimize allosteric regulation is limited by incomplete knowledge of the mutations that tune allostery. Are these mutations few or…”
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Finding a Common Path: Predicting Gene Function using Inferred Evolutionary Trees by Reynolds, Kimberly A.

“…Reporting in Cell, Li and colleagues (2014) describe an innovative method to functionally classify genes using evolutionary information. This approach…”
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A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism by Schober, Andrew F, Mathis, Andrew D, Ingle, Christine, Park, Junyoung O, Chen, Li, Rabinowitz, Joshua D, Junier, Ivan, Rivoire, Olivier, Reynolds, Kimberly A

“…Enzyme function and evolution are influenced by the larger context of a metabolic pathway. Deleterious mutations or perturbations in one enzyme can often be…”
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Quantifying the evolvability of allostery at different protein surfaces by Dinan, Jerry C., Reynolds, Kimberly A.

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Strategies for Engineering and Rewiring Kinase Regulation by McCormick, James W., Pincus, David, Resnekov, Orna, Reynolds, Kimberly A.

“…Eukaryotic protein kinases (EPKs) catalyze the transfer of a phosphate group onto another protein in response to appropriate regulatory cues. In doing so, they…”
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High-Order Epistasis in Catalytic Power of Dihydrofolate Reductase Gives Rise to a Rugged Fitness Landscape in the Presence of Trimethoprim Selection by Tamer, Yusuf Talha, Gaszek, Ilona K, Abdizadeh, Haleh, Batur, Tugce Altinusak, Reynolds, Kimberly A, Atilgan, Ali Rana, Atilgan, Canan, Toprak, Erdal

“…Evolutionary fitness landscapes of several antibiotic target proteins have been comprehensively mapped showing strong high-order epistasis between mutations,…”
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A simplified strategy for titrating gene expression reveals new relationships between genotype, environment, and bacterial growth by Mathis, Andrew D, Otto, Ryan M, Reynolds, Kimberly A

“…Abstract A lack of high-throughput techniques for making titrated, gene-specific changes in expression limits our understanding of the relationship between…”
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Determining the mechanisms of the allosteric architecture of DHFR by McCormick, James W., Dinan, Jerry C., Russo, Marielle A., Reynolds, Kimberly A.

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A New Test of Computational Protein Design: Predicting Posttranslational Modification Specificity for the Enzyme SMYD2 by Reynolds, Kimberly A.

“…In this issue of Structure, Lanouette and colleagues use a combination of computation and experiment to define a specificity motif for the lysine…”
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An evolution-based strategy for engineering allosteric regulation by Pincus, David, Resnekov, Orna, Reynolds, Kimberly A

“…Allosteric regulation provides a way to control protein activity at the time scale of milliseconds to seconds inside the cell. An ability to engineer synthetic…”
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Engineering allosteric regulation in protein kinases by Pincus, David, Pandey, Jai P, Feder, Zoë A, Creixell, Pau, Resnekov, Orna, Reynolds, Kimberly A

“…Phosphoregulation, in which the addition of a negatively charged phosphate group modulates protein activity, enables dynamic cellular responses. To understand…”
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Irreversibility in bacterial regulatory networks by Zhao, Yi, Wytock, Thomas P, Reynolds, Kimberly A, Motter, Adilson E

“…Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This property…”
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Accelerating Biological Insight for Understudied Genes by Reynolds, Kimberly A, Rosa-Molinar, Eduardo, Ward, Robert E, Zhang, Hongbin, Urbanowicz, Breeanna R, Settles, A Mark

“…The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with…”
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Identifying conformational changes of the β2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators by Reynolds, Kimberly A., Katritch, Vsevolod, Abagyan, Ruben

“…The new β 2 Adrenoceptor (β 2 AR) crystal structures provide a high-resolution snapshot of receptor interactions with two particular partial inverse agonists,…”
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