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A field guide to foldamers
The breadth of structure and function displayed by the molecules of biology is remarkable.
Considering that there are only three major biopolymer backbones (proteins, ribonucleic …
Considering that there are only three major biopolymer backbones (proteins, ribonucleic …
Principles of protein folding—a perspective from simple exact models
General principles of protein structure, stability, and folding kinetics have recently been
explored in computer simulations of simple exact lattice models. These models represent …
explored in computer simulations of simple exact lattice models. These models represent …
Perspective: sign epistasis and genetic costraint on evolutionary trajectories
Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic
background in which it appears. Although epistasis is widely observed in nature, our …
background in which it appears. Although epistasis is widely observed in nature, our …
Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans
Human influenza A (subtype H3N2) is characterized genetically by the limited standing
diversity of its hemagglutinin and antigenically by clusters that emerge and replace each …
diversity of its hemagglutinin and antigenically by clusters that emerge and replace each …
Why are proteins marginally stable?
Most globular proteins are marginally stable regardless of size or activity. The most common
interpretation is that proteins must be marginally stable in order to function, and so marginal …
interpretation is that proteins must be marginally stable in order to function, and so marginal …
Biophysics of protein evolution and evolutionary protein biophysics
The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
Polymer principles and protein folding
This paper surveys the emerging role of statistical mechanics and polymer theory in protein
folding. In the polymer perspective, the folding code is more a solvation code than a code of …
folding. In the polymer perspective, the folding code is more a solvation code than a code of …
Innovation and robustness in complex regulatory gene networks
The history of life involves countless evolutionary innovations, a steady stream of ingenuity
that has been flowing for more than 3 billion years. Very little is known about the principles of …
that has been flowing for more than 3 billion years. Very little is known about the principles of …
Robustness can evolve gradually in complex regulatory gene networks with varying topology
The topology of cellular circuits (the who-interacts-with-whom) is key to understand their
robustness to both mutations and noise. The reason is that many biochemical parameters …
robustness to both mutations and noise. The reason is that many biochemical parameters …
Statistical potentials extracted from protein structures: how accurate are they?
“Statistical potentials” are energies widely used in computer algorithms to fold, dock, or
recognize protein structures. They are derived from:(1) observed pairing frequencies of the …
recognize protein structures. They are derived from:(1) observed pairing frequencies of the …