Related papers: How Do Proteins Fold?
The Levinthal paradox exposes many critical questions on the protein folding problem, among which we could point out why proteins can reach their native state in a biologically reasonable time. A proper answer to this question is of…
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
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…
Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein…
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…
Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Nonetheless, given the success of generative models across…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein…
The remarkable success of AlphaFold2 in providing accurate atomic-level prediction of protein structures from their amino acid sequence has transformed approaches to the protein folding problem. However, its core paradigm of mapping one…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. To date, many theories for the prevalence of two-state kinetics have been…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…
Emergence of new protein structures has proved difficult to trace in nature and engineer in the laboratory. However, one aspect of structure evolution has proved immensely helpful for determining the three-dimensional structure of proteins…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…
Learning how proteins fold will hardly have any impact in the way conventional -- active site centered -- drugs are designed. On the other hand, this knowledge is proving instrumental in defining a new paradigm for the identification of…