相关论文: On morphological and functional complexity of prot…
While proteins have been treated as particles with a spherically symmetric interaction, of course in reality the situation is rather more complex. A simple step towards higher complexity is to treat the proteins as non--spherical particles…
Producing food-grade soft particles with controlled structure is of interest to elucidate the structure-properties relationship in soft-particles suspensions. The aim of this work is to evaluate the ability of two elaboration processes to…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
We develop and validate a simulation framework for colloidal gelation. We first reproduce the benchmark results of Santos, Campanella, and Carignano for spherical, gel-forming particles, then extend the methodology to more complex systems…
Proteins and other macromolecules exist not in a single state but as dynamic ensembles of interconverting conformations, which are essential for catalysis, allosteric regulation, and molecular recognition. While AI-based structure…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Microgels are complex macromolecules. These colloid-sized polymer networks possess internal degrees of freedom and, depending on the polymer(s) they are made of, can acquire a responsiveness to variations of the environment (temperature,…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
The quality and ease of proteomics analysis depends on the performance of the analytical tools used, and thus of the performances of the protein separation tools used to deconvolute complex protein samples. Among protein samples, membrane…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
High precision atomic data is indispensable for experiments involving studies of fundamental interactions, astrophysics, atomic clocks, plasma science, and others. We develop new parallel atomic structure codes and explore the difficulties…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…