Publications

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2021

  1. Modi T, Campitelli P. Kazan I K and Ozkan SB* “Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective” (2021) Current Opinion in Structural Biology, 66:207-215

  2. Ozkan SB “Can sequence specific and dynamics-based metric representing the conformational ensemble allow us to decipher the encoded function in IDP sequences?” 2021, Biophysical Journal in press

  3. Modi T,.Risso V.A., Martinez-Rodriguez S., Gavira J. A., Mebrat M.D., Van Horn W.D., Sanchez-Ruiz J.M. and Ozkan S.B. “Hinge-Shift Mechanism: A Protein design principle for the evolution from substrate promiscuity to specificity” 2021 Nature Communications

  4. Zou T, Woodrum BW, Campitelli P, Ghirlanda G, Ozkan SB*. “Local interactions that contribute minimal frustration determine foldability” (2021) Journal of Physical Chemistry


2020

  1. Campitelli P, Kruse-Swint L, and Ozkan SB* “Substitutions on non-conserved sites modulate protein dynamics” (2020) Molecular Biology and Evolution, 38:201-214

  2. Campitelli P, Modi T and Ozkan SB* “The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution” (2020) Annual Reviews in Biophysics, 49:267-288

  3. Campitelli P and Ozkan SB* “Dynamic allostery modulates epistasis in protein evolution” (2020) Entropy 22:667

  4. Modi T and Ozkan S.B* and Presse S* “Information propagation in time through allosteric signaling” (2020) Physical Review Research


2019

  1. Paul Campitelli, and Ozkan SB* “Allostery and Structural Dynamics in Protein Evolution” (2019) Evolution, Origin of Life, Concepts and Methods, 179-194.

2018

  1. Modi T and Ozkan S.B* “Allostery and conformational flexibility modulates resistance in beta-lactamases (2018) International Journal of Molecular Science 19:3808
  2. Butler BM, Kumar A, Modi T, Kumar S and Ozkan SB* “Dynamic allosteric residue coupling (DARC spots) reveals disease mechanism for Gaucher disease and nSNVs across the proteome” (2018) Under revision
  3. Butler BM, Kazan IC, Kumar A and Ozkan SB* “Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs” (2018) Plos Computational Biology 14 (11), e1006626
  4. Risso VA , Sanchez-Ruiz J and Ozkan SB* “Biotechnological and protein-engineering implications of ancestral protein resurrection” (2018) Current Opinion In Structural Biology,51:106-115
  5. Modi T, Hui Hui J, Ghosh K and Ozkan SB* “Thioredoxins evolved to modern day stability-function requirement by altering Native State ensemble” (2018) Philosophical Transactions of The Royal Society B 373:20170184
  6. Dutta P, Dargahi L,O’ Connell KE, Bolia A, Ozkan SB, Sailer AW and Dev KK “ A novel modelling mechanism of PAEL receptor and GABARAPL2 interaction involved in Parkinson’s disease” (2018) Neuroscience Letters, 673:12-18

2017

  1. 16. Campitelli P, Guo J, Zhou HX, Ozkan SB* “A Hinge-shift Mechanism Modulates Allosteric Regulations in Human Pin1” (2017) J. Phys Chem B DOI: 10.1021/acs.jpcb.7b11971
  2. Larrimore KEm Kazan IC, Bolia A LKannan L, R Kendle RP,Jamal T, Barcus M, , Stephen Brimijoin S, Gao Y, Zhan CG, Ozkan SB, and Moore TS, “Enhanced nerve agent bioscavenging of cocaine hydrolase mutants of butyrylcholinesterase expressed in plants” (2017),Nature Scientific Reports 7:10419.

2016

  1. Bolia A and Ozkan SB* “Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility” (2016) J. Chem Inf. Model 56:734-746

2015

  1. Kumar A, Campitelli P, Thorpe MF and Ozkan SB* “ Partial Unfolding and Refolding for Structure Refinement: A Unified Approach of Geometric Simulations and Molecular Dynamics” (2015) Proteins 83: 2279-2292
  2. Li Z, Bolia A, Maxwell JD, Bobkow AA Ghirlanda G*, Ozkan SB* and Margulis CM* “A Rigid Hinge Region is Necessary for High Affinity Binding of Dimannose to Cyanovirin and Associated Constructs” (2015) Biochemistry 54 :6951-6960
  3. Kumar A, Butler BM, Kumar S and Ozkan SB* “Integration of Structural Dynamics and Evolution to Protein Interaction Networks: A New Era in Genomic Medicine” (2015) Current Opinion in Structural Biology 35:135-142
  4. Butler MA, Gerek ZN, Kumar S and Ozkan SB* “Dynamically critical sites at protein interface are more prone to disease” (2015) Proteins, 83:428-435
  5. Zou T, Risso VA, Gavira JA, Sanchez-Ruiz JM, Ozkan SB* “Evolution of Conformational Dynamics Determines the Conversion of a Promiscuous Generalist into a Specialist Enzyme”. (2015) Mol Biol. Evol. 32:132-143.
  6. Kim H, Zou T, Modi C, Dorner K, Grunkmeyer TJ, Chen L, Fromme R, Matz MV, Ozkan SB*, Wachter RM,* “A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins”. (2015) Structure , 23:34-43

2014

  1. Zou T, Williams N, Ozkan SB, Ghosh K. “Proteome folding kinetics is limited by protein half-life.” (2014) PLoS One, 9(11):e112701
  2. Dutta B, Ozkan SB, Sailer A and Dev KK “PICK1 interacts with and protects against PAEL receptor induced cell death.” (2014) J. Neurochemistry. 130:360-73
  3. Mielke C, Cordova J, Border AW, Ozkan SB, Wayne W and Mandarino LW, “Acetylation of Adenine Nucleotide Translocase in Vivo in Human Muscle May Decrease Affinity for ADP and Alter Mitochondrial Function” (2014) Biochemistry 53:3817-29
  4. Bolia A, Woodrum B, Cerada A, Ruben MA, Wang X, Ozkan SB* and Ghirlanda GH* “Dissecting the determinants for dimannose binding in cyanovirin “ (2014) Biophysical J 10:1142-51
  5. Bolia, A., Gerek Z.N and Ozkan SB* “BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures.” (2014) J. Chem. Inf Model. 54(3):913-25.

2013

  1. Woodrum BW, Maxwell JD, Bolia A, Ozkan SB*, Ghirlanda G*. “The antiviral lectin cyanovirin-N: probing multivalency and glycan recognition through experimental and computational approaches.” (2013) Biochem Soc. 5:1170-1176.
  2. Gerek ZN, Kumar S and Ozkan SB* Structural dynamics flexibility informs function and evolution at a proteome scale” (2013) Evol Appl. 6:4223-4332. doi: 10.1111/eva.12052
  3. Culviner PH, Anders M. Knight AM, Kurt N, Zhou T, Ozkan SB* and Cavagnero S Electrostatic Effects of the Ribosomal Surface on Nascent Protein Dynamics (2013) ACS Chem Biol. 6: 1195–1204.

2012

  1. Glembo, TJ, Farrell DW, Thorpe MF and Ozkan SB* “Collective dynamics differentiates functional divergence in protein evolution” (2012) Plos Comp. Biol. 8(3):e100242
  2. Martin DR, Ozkan SB and Matyushov DV “Dissipative electro-elastic network model of protein electrostatic” (2012) Phys Biol. 9(3):036004.

2011

  1. Kumar A, Glembo, TJ, Ozkan SB* “Mechanism of Protein Evolution: The Role of Conformational Dynamics and Allostery in Disease Development ” (2011) Biophysical Journal 109:1273-1281
  2. Gerek ZN and Ozkan SB* “ (2011) “Change in allosteric network affects binding affinities of PDZ Domains: Analysis through Perturbation Response Scanning PLoS Comp Biol. 10: e1002154.
  3. Zou T and Ozkan SB* “Native local topology shows important features of denatured basin” (2011) Phys. Biol. 8(6):06601.

2010

  1. Glembo, TJ and Ozkan SB* “Union of geometric constrained based simulations with molecular dynamics for protein structure prediction” (2010) Biophysical J. 98:1046-1054
  2. Gerek ZN and Ozkan SB* “ A Flexible docking scheme to explore PDZ Domain’s binding selectivity” (2010) Protein Science 19:914-928.
  3. Atilgan C, Gerek ZN, Ozkan SB*, Atilgan AR* “Manipulation of conformational change in proteins by single residue perturbation” (2010) Biophysical J. 99:933-943

2009

  1. Gerek ZN, Keskin O and Ozkan SB* “Identification of specificity and promiscuity in PDZ domain interactions through their dynamics behavior” (2009) Proteins. 77: 796-811.
  2. Shell MS, Ozkan SB, Voelz V, Wu AGH and Dill KA “Blind test of physics-bases prediction of protein structures “ (2009) Biophysical. J. 96:917-924.

2008

  1. Engen, JR, Wales TR, Hochrein JM, Meyn MA, Ozkan SB, Bahar I, and Smithgall TE, “ Structure and dynamic regulation of Src-Famy Kinases (2008) Cell. Mol. Life Sci 65: 3058-3073
  2. Dill KA, Ozkan SB, Shell MS, Weikl TR “The Protein Folding Problem” (2008) Annu. Rev. Biopyhs. Biomol. Struct. 37: 289-316

2007

  1. Dill KA, Ozkan SB, Wiekl TR, Chodera JD, Voelz VA, "The protein folding problem: when will it be solved?" (2007) Curr. Opin. Struct. Biol. 17: 342-346.
  2. Ozkan SB, Wu AGH , Chodera JD, Dill KA “Protein Folding by Zipping and Assembly” (2007) Proc. Natl. Acad. Sci. USA 104:11987-11992
  3. Ghosh K, Ozkan SB, Dill KA “The Ultimate Speed Limit of Protein Folding is Conformational Searching“ (2007) J. Amer. Chem. Soc. 129:11920 -11927.

2004

  1. Ozkan SB and Meirovitch H “Conformation Search of Peptides and Proteins: The Monte Carlo Minimization with Adaptive Bias Applied to Hepta-Peptide Deltorphin”, (2004) J. Comp Chem. 25:565-572.
  2. Ozkan SB, Kirca S and Haliloglu T “Unfolding Events of Chymotrypsin Inhibitor 2 Revealed by off-lattice Monte Carlo Simulations and their Consistency from Structure-Based Analysis of Conformations”, Polymers (2004) 45 :581-595

2003

  1. Ozkan SB and Meirovitch H, “Efficient Conformational Search Method for Peptides and Proteins: Monte Carlo Minimization with an Adaptive Bias", (2003) J. Phys Chem. 107: 9128-9131
  2. Ozkan SB, Dill KA and Bahar I, “Computing the Transition State Populations in Simple Protein Models”, (2003) Biopolymers 68: 35-46

2002

  1. Ozkan SB, Dill KA and Bahar I, “Fast-Folding Protein Kinetics, Hidden Intermediates and the Sequential Stabilization Model”, (2002) Protein Science 11:1958-1970.

2001

  1. Ozkan SB, Bahar I and Dill KA, “Nonclassical Phi-values in Protein Folding Kinetics", Nature Structural Biology (2001) 98: 765-767.

1998

  1. Ozkan B and Bahar I, “ Recognition of Native Structure from a Complete Enumeration of Low Resolution Conformation with Constraints” Proteins (1998) 32: 211-222.