415 results found
    1. Structural Biology and Molecular Biophysics

    On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

    Vytautas Gapsys, Bert L de Groot
    The use of adequate statistics is demonstrated to be an essential prerequisite to derive conclusions on thermodynamics and kinetics from molecular simulations.
    1. Physics of Living Systems

    Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility

    Elizabeth Eck et al.
    Confronting different models of chromatin accessibility with temporally resolved transcription profiles favors a scenario where transcription factors actively, rather than passively, drive chromatin from the inaccessible to the accessible state.
    1. Biochemistry and Chemical Biology

    Thermodynamic evidence for a dual transport mechanism in a POT peptide transporter

    Joanne L Parker et al.
    Two thermodynamically distinct transport mechanisms operating within the same binding site explains the remarkable promiscuity of POT family transporters towards peptide and drug ligands.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

    Ekaterina Morgunova et al.
    The epistasis observed in TF-DNA binding preferences can be explained by the presence of two optima of very similar Gibbs energy that are located relatively far from each other in sequence space.
    1. Structural Biology and Molecular Biophysics

    Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Vytautas Gapsys, Bert L de Groot
    We are writing to comment on the article by El Hage et al., 2018 about molecular dynamics simulations of human hemoglobin.
    1. Physics of Living Systems
    2. Structural Biology and Molecular Biophysics

    Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

    Salvatore Assenza et al.
    A multiscale modeling approach reveals how the energy from ATP hydrolysis is used by Hsp70 chaperones to remodel the conformation of their substrates through a novel force-generating mechanism.
    1. Genetics and Genomics

    On the mechanistic nature of epistasis in a canonical cis-regulatory element

    Mato Lagator et al.
    Thermodynamic framework accurately predicts the sign of epistasis and its environment dependence for a canonical cis-regulatory element.
    1. Computational and Systems Biology

    The genetic landscape of a physical interaction

    Guillaume Diss, Ben Lehner
    First comprehensive analysis of how many different mutations combine within and between two genes to alter a molecular phenotype.
    1. Neuroscience

    Mechanistic insights into a TIMP3-sensitive pathway constitutively engaged in the regulation of cerebral hemodynamics

    Carmen Capone et al.
    Extracellular matrix signaling constitutively regulates cerebral blood flow in both physiological and pathological settings.
    1. Developmental Biology

    Hemodynamic-mediated endocardial signaling controls in vivo myocardial reprogramming

    Manuel Gálvez-Santisteban et al.
    The heart is able to sense and adaptively respond to environmental changes due to cardiac injury through flow-mediated mechanisms that regulate cardiomyocyte reprogramming and regeneration.

Refine your results by:

Type
Research categories