Publications

2022

R.M. Otto, A. Turska-Nowak, P.M. Brown, K.A. Reynolds (2022). A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment. [ bioRxiv ] [ code ]

2021

J.W. McCormick, M.A.X. Russo, S. Thompson, A. Blevins, K.A. Reynolds (2021). Structurally distributed surface sites tune allosteric regulation. Elife (10): e68346. [paper] [ bioRxiv ] [ code ] [ talk ]

K.A. Reynolds, E. Rosa-Molinar, R. Ward, H. Zhang, B. Urbanowicz, M.A. Settles (2021). Accelerated biological insight for understudied genes. Integrative and Comparative Biology , icab029. [ paper ]

2020

A.D. Mathis, R.M. Otto, K.A. Reynolds (2020). A simplified strategy for titrating gene expression reveals new relationships between genotype, environment, and bacterial growth. Nucleic Acids Research , gkaa1073. [ paper ] [ code ]

S. Thompson, Y. Zhang, C. Ingle, K.A. Reynolds, and T. Kortemme (2020). Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme. eLife, 9:e53476. [ paper ] [ code ]

2019

J.W. McCormick, D. Pincus, O. Resnekov, and K.A. Reynolds (2019). Strategies for Engineering and Rewiring Kinase Regulation Trends Biochem Sci, pii:S0968-0004. [ paper ]

A.F. Schober, C. Ingle, J.O. Park, L. Chen, J.D. Rabinowitz, I. Junier, O. Rivoire, and K.A. Reynolds (2019). A two-enzyme adaptive unit in bacterial folate metabolism. Cell Reports, 27:3359-3379. [ paper ] preprint: bioRxiv

Y.T. Tamer, I.K. Gaszek, H. Abdizadeh, T. Batur, K. Reynolds, A.R. Atilgan, C. Atilgan, E. Toprak (2019). High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection. Mol Biol Evol. pii:msz086. [paper] preprint: bioRxiv

2018

D. Pincus, J. Pandey, P. Creixell, O. Resnekov, and K.A. Reynolds (2018). Engineering allosteric regulation in protein kinases. Science Signaling (11):555. [paper][code]. 

C. Rosensweig, K.A. Reynolds, P. Gao, Y. Shan, R. Ranganathan, J.S. Takahashi, C.B Green (2018). An evolutionary hotspot defines functional differences between CRYPTOCHROMES. Nature Communications(9):1138.[paper][code]

2017

D. Pincus, O. Resnekov, K.A. Reynolds (2017). An evolution-based strategy for engineering allosteric regulation. Physical Biology(14):025002. [paper]

C. Narayanan, D. Gagné, K.A. Reynolds, N. Doucet. (2017) Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily. Scientific Reports(7):3207. [paper]

2016

O. Rivoire, K.A. Reynolds, R. Ranganathan. (2016) Evolution-based functional decomposition of proteins. PLoS Comp Biol (12): e1004817. [paper]

2014-2015

K.A. Reynolds (2015). A new test of computational protein design: predicting posttranslational modification specificity for the enzyme SMYD2. Structure (23): 11-12.[paper]

K.A. Reynolds (2014). Finding a common path: predicting gene function using inferred evolutionary trees. Developmental Cell (30): 4-5.[paper]

K. Reynolds – Graduate and Postdoctoral Work:

K.A. Reynolds, W. P. Russ, M. Socolich, R. Ranganathan (2013). Evolution based design of proteins. Methods in Enzymology (523): 213-235. [paper]

K.A. Reynolds, R.N.McLaughlin, R. Ranganathan (2011). Hotspots for allosteric regulation on protein surfaces. Cell (147): 1564-1575. [paper]

M.S. Hanes, K.A. Reynolds, C. McNamara, P. Ghosh, R.A. Bonomo, J.F. Kirsch, T.M. Handel (2011). Specificity and cooperativity at β-lactamase position 104 in TEM-1/BLIP and SHV-1/BLIP interactions. Proteins (73): 1267-1276. [paper]

K.A. Reynolds, V. Katritch, R. Abagyan (2010). Structure and modeling of GPCRs: Implications for drug discovery. Molecular Pharmacology and Drug Targeting: Shifting Paradigms and New Directions, Ed. Annette Gilchrist, Chapter 15.

V. Katritch, K.A. Reynolds, V. Cherezov, M.A. Hanson, C.B. Roth, M. Yeager. R. Abagyan (2009). Analysis of full and partial agonists binding to β2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J. Molecular Recognition (22): 307-318.[PDF]

K.A. Reynolds, V. Katritch, R. Abagyan (2009). Identifying conformational changes of the β2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. Journal of Computer Aided Molecular Design (23): 273-288. [PDF]

K.A. Reynolds, M.S. Hanes, J.M. Thomson, A.J. Antczak, J.M. Berger, R.A. Bonomo, J.F. Kirsch and T.M. Handel (2008). Computational redesign of the SHV-1 β-lactamase/ β-lactamase Inhibitor Protein interface. Journal of Molecular Biology (382): 1265-1275. [paper]

A. Chowdry, K.A. Reynolds, M.S. Hanes, M. Voorhies, N. Pokala, and T.M. Handel (2007). An object-oriented Library for Computational Protein Design. Journal of Computational Chemistry (28): 2378-2388. [paper]

K.A. Reynolds, J.M Thomson, K.D. Corbett, C.R. Bethel, J.M. Berger, J.F. Kirsch, R.A. Bonomo, and T.M. Handel (2006). Structural and Computational Characterization of the SHV-1 β-lactamase/β-lactamase Inhibitor Protein (BLIP) interface. Journal of Biological Chemistry (281): 26745-26753. [PDF]

S. M. Godzina, M. A. Lovato, M. M. Meyer, K. A. Foster, W. K. Wilson, W. Gu, E. L. de Hostos, and S. P. T. Matsuda (2000). Cloning and characterization of the Dictyostelium discoideum cycloartenol synthase cDNA. Lipids (36): 249-255. [paper]