Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

[HTML][HTML] Permeability across lipid membranes

W Shinoda - Biochimica et Biophysica Acta (BBA)-Biomembranes, 2016 - Elsevier
Molecular permeation through lipid membranes is a fundamental biological process that is
important for small neutral molecules and drug molecules. Precise characterization of free …

Revolutionizing peptide‐based drug discovery: Advances in the post‐AlphaFold era

L Chang, A Mondal, B Singh… - Wiley …, 2024 - Wiley Online Library
Peptide‐based drugs offer high specificity, potency, and selectivity. However, their inherent
flexibility and differences in conformational preferences between their free and bound states …

Arginine residues modulate the membrane interactions of pHLIP peptides

TFD Silva, H Visca, C Klumpp… - Journal of Chemical …, 2023 - ACS Publications
Most processes at the water–membrane interface often involve protonation events in
proteins or peptides that trigger important biological functions and events. This is the …

Energy-representation theory of solutions: Its formulation and application to soft, molecular aggregates

N Matubayasi - Bulletin of the Chemical Society of Japan, 2019 - academic.oup.com
The energy-representation theory of solutions is developed to address the dissolution of a
molecule in homogeneous fluid as well as the partitioning into such nanoscale structures as …

Computational compound screening of biomolecules and soft materials by molecular simulations

T Bereau - Modelling and Simulation in Materials Science and …, 2021 - iopscience.iop.org
Decades of hardware, methodological, and algorithmic development have propelled
molecular dynamics (MD) simulations to the forefront of materials-modeling techniques …

Modes of interaction of pleckstrin homology domains with membranes: toward a computational biochemistry of membrane recognition

FB Naughton, AC Kalli, MSP Sansom - Journal of molecular biology, 2018 - Elsevier
Pleckstrin homology (PH) domains mediate protein–membrane interactions by binding to
phosphatidylinositol phosphate (PIP) molecules. The structural and energetic basis of …

Ultra-coarse-graining of homopolymers in inhomogeneous systems

F Berressem, C Scherer, D Andrienko… - Journal of Physics …, 2021 - iopscience.iop.org
We develop coarse-grained (CG) models for simulating homopolymers in inhomogeneous
systems, focusing on polymer films and droplets. If the CG polymers interact solely through …

Engineering proteins at interfaces: from complementary characterization to material surfaces with designed functions

S Morsbach, G Gonella, V Mailänder… - Angewandte Chemie …, 2018 - Wiley Online Library
Once materials come into contact with a biological fluid containing proteins, proteins are
generally—whether desired or not—attracted by the material's surface and adsorb onto it …

Unraveling the Phase Behavior, Mechanical Stability, and Protein Reconstitution Properties of Polymer–Lipid Hybrid Vesicles

WA Müller, PA Beales, AR Muniz… - …, 2023 - ACS Publications
Hybrid vesicles consisting of natural phospholipids and synthetic amphiphilic copolymers
have shown remarkable material properties and potential for biotechnology, combining the …