The role of protein dynamics in the evolution of new enzyme function

Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme's Conformational Freedom and Disorder

(2015) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

On the Challenge of Exploring the Evolutionary Trajectory from Phosphotriesterase to Arylesterase Using Computer Simulations

(2015) Ram Prasad Bora et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

Reverse evolution leads to genotypic incompatibility despite functional and active site convergence

(2015) Miriam Kaltenbach et al.   eLife

Maintenance of Native-like Protein Dynamics May Not Be Required for Engineering Functional Proteins

(2014) Sophie M.C. Gobeil et al.   CHEMISTRY & BIOLOGY

Evolutionary Aspects of Enzyme Dynamics

(2014) Judith P. Klinman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis

(2014) Adam T. Van Wart et al.   Journal of Chemical Theory and Computation

Dynamics and hydration explain failed functional transformation in dehalogenase design

(2014) Jan Sykora et al.   Nature Chemical Biology

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

(2014) N. Preiswerk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Conformational Populations and Functionally Relevant Substates

(2013) Arvind Ramanathan et al.   ACCOUNTS OF CHEMICAL RESEARCH

Evolution of a designed retro-aldolase leads to complete active site remodeling

(2013) Lars Giger et al.   Nature Chemical Biology

Automated identification of functional dynamic contact networks from X-ray crystallography

(2013) Henry van den Bedem et al.   NATURE METHODS

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

(2013) Gira Bhabha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The universality of enzymatic rate–temperature dependency

(2013) Mikael Elias et al.   TRENDS IN BIOCHEMICAL SCIENCES

Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions

(2012) J.-P. Colletier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure and dynamics of a primordial catalytic fold generated by in vitro evolution

(2012) Fa-An Chao et al.   Nature Chemical Biology

Taking Ockham's razor to enzyme dynamics and catalysis

(2012) David R. Glowacki et al.   Nature Chemistry

Topological analysis and interactive visualization of biological networks and protein structures

(2012) Nadezhda T Doncheva et al.   Nature Protocols

Linking Crystallographic Model and Data Quality

(2012) P. A. Karplus et al.   SCIENCE

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme

(2011) R. G. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

(2011) G. Bhabha et al.   SCIENCE

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Mining electron density for functionally relevant protein polysterism in crystal structures

(2010) James S. Fraser et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Hitting a moving target?—Understanding how conformational diversity impacts enzymatic catalysis

(2010) Patrick J. O’Brien et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Enzyme dynamics point to stepwise conformational selection in catalysis

(2010) Buyong Ma et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

(2009) Henry van den Bedem et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase

(2009) C. J. Jackson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

In Crystallo Capture of a Michaelis Complex and Product-binding Modes of a Bacterial Phosphotriesterase

(2007) Colin J. Jackson et al.   JOURNAL OF MOLECULAR BIOLOGY