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Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
Protein sequence generation for engineering requires samples that are biophysically plausible and, when targeting a family/domain, remain recognizable members while exploring within-family diversity. Current discrete generative models…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
We present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…