3,844 results found
    1. Structural Biology and Molecular Biophysics

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

    Krystel El Hage et al.
    Simulations of the unliganded human hemoglobin tetramer, which for the first time yield a thermodynamically stable system, cast doubts on the use of standard solvent box sizes for molecular dynamics studies of biological macromolecules.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Krystel El Hage et al.
    We are writing to respond to the comment by Gapsys and de Groot, 2019 on our article about molecular dynamics simulations of human hemoglobin (El Hage et al., 2018).
    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. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation

    Jack Alfred Bryant et al.
    Analysis of the E. coli protein DolP reveals the first dual BON-domain structure and identifies phospholipid binding as a new mechanism for protein localisation to the outer membrane division site.
    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. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    The guide sRNA sequence determines the activity level of box C/D RNPs

    Andrea Graziadei et al.
    Integrative structural biology reveals a conformational equilibrium in the Box C/D methylation enzyme that regulates the extent of site-specific 2'-O-rRNA methylation in dependence of the RNA sequence.
    1. Developmental Biology
    2. Chromosomes and Gene Expression

    A universal vector concept for a direct genotyping of transgenic organisms and a systematic creation of homozygous lines

    Frederic Strobl et al.
    In transgenesis assays involving diploid model organisms, two clearly distinguishable transformation markers embedded in interweaved, but incompatible Lox site pairs allow the systematic creation of homozygous transgenic lines and minimize the number of wasted animals.
    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3

    Ksenia Finogenova et al.
    Nucleosome binding by PRC2 threads H3K27 into its active site via an interaction network set in register by unmodified H3K36.
    1. Epidemiology and Global Health

    Science Forum: Unit of analysis issues in laboratory-based research

    Nick R Parsons et al.
    A simulation study is used to demonstrate how mistakes in identifying the experimental unit and the unit of analysis can lead to incorrect analyses and inappropriate inferences when reporting research studies.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Molecular and topological reorganizations in mitochondrial architecture interplay during Bax-mediated steps of apoptosis

    Nicholas R Ader et al.
    Correlative microscopy and electron cryo-tomography on apoptotic HeLa cells reveal remodeling of outer and inner mitochondrial membranes, Bax cluster ultrastructure and ATP synthase reorganization in ruptured mitochondria.

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