Related papers: Topological Solitons and Folded Proteins
Recent advances in computational power and simulation programs finally delivered the first examples of reversible folding for small proteins with an all-atom description. But having at hand the atomistic details of the process did not lead…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
The equivalent nature of 3D coordinates has posed long term challenges in protein structure representation learning, alignment, and generation. Can we create a compact and invariant language that equivalently represents protein structures?…
We offer simple solutions to three kinematic problems that occur in the folding of proteins. We show how to construct suitably local elementary Monte Carlo moves, how to close a loop, and how to fold a loop without breaking the bond that…
In this paper we present a method to study the folding structure of a simple model consisting of two kinds of monomers, hydrophobic and hydrophilic. This method has three main steps: an efficient simulation method to bring an open sequence…
By providing new insights into the distribution of a protein's torsion angles, recent statistical models for this data have pointed the way to more efficient methods for protein structure prediction. Most current approaches have…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
Membrane particles such as proteins and lipids organize into zones that perform unique functions. Here, I introduce a topological and category-theoretic framework to represent particle and zone intra-scale interactions and inter-scale…
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…
We investigate some aspects of the soliton dynamics in an alpha-helical protein macromolecule within the steric Davydov-Scott model. Our main objective is to elucidate the important role of the helical symmetry in the formation, stability…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
We study the thermodynamical properties of a topology-based model proposed by Galzitskaya and Finkelstein for the description of protein folding. We devise and test three different mean-field approaches for the model, that simplify the…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…