Impact of In Vivo Protein Folding Probability on Local Fitness Landscapes

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

(2019) Alexander Mayorov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Principles of Protein Stability and Their Application in Computational Design

(2018) Adi Goldenzweig et al.   Annual Review of Biochemistry

Codon usage influences fitness through RNA toxicity

(2018) Pragya Mittal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating the contribution of folding stability to non-specific epistasis in protein evolution

(2018) Pouria Dasmeh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme

(2018) JohnCarlo Kristofich et al.   PLoS Genetics

Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit

(2018) Justin R Klesmith et al.   BIOINFORMATICS

Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

(2018) Haoran Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics

(2018) Haoran Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stability-Mediated Epistasis Restricts Accessible Mutational Pathways in the Functional Evolution of Avian Hemoglobin

(2017) Amit Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

(2017) Justin R. Klesmith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

(2017) Emily E. Wrenbeck et al.   Nature Communications

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

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

(2016) Eleanor Campbell et al.   Nature Chemical Biology

Plasmid-based one-pot saturation mutagenesis

(2016) Emily E Wrenbeck et al.   NATURE METHODS

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

(2016) Benjamin R. Jack et al.   PLOS BIOLOGY

Direct Observation of Multimer Stabilization in the Mechanical Unfolding Pathway of a Protein Undergoing Oligomerization

(2015) Zackary N. Scholl et al.   ACS Nano

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Rigidity versus flexibility: the dilemma of understanding protein thermal stability

(2015) Andrey Karshikoff et al.   FEBS Journal

Identification of cis-suppression of human disease mutations by comparative genomics

(2015) Daniel M. Jordan et al.   NATURE

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme

(2015) Luciano A. Abriata et al.   PLoS One

Contingency and entrenchment in protein evolution under purifying selection

(2015) Premal Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli

(2015) Justin R. Klesmith et al.   ACS Synthetic Biology

High-Resolution Sequence-Function Mapping of Full-Length Proteins

(2015) Caitlin A. Kowalsky et al.   PLoS One

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate

(2014) Matthew S. Bienick et al.   PLoS One

Contribution of Selection for Protein Folding Stability in Shaping the Patterns of Polymorphisms in Coding Regions

(2013) Adrian W.R. Serohijos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutational effects on stability are largely conserved during protein evolution

(2013) O. Ashenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Hidden Codes That Shape Protein Evolution

(2013) R. J. Weatheritt et al.   SCIENCE

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

A biophysical protein folding model accounts for most mutational fitness effects in viruses

(2011) C. S. Wylie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The population genetics of beneficial mutations

(2010) H. A. Orr   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Chaperonin overexpression promotes genetic variation and enzyme evolution

(2009) Nobuhiko Tokuriki et al.   NATURE

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology

Contributions of folding cores to the thermostabilities of two ribonucleases H

(2002) Srebrenka Robic et al.   PROTEIN SCIENCE