Sequence Heterogeneity Accelerates Protein Search for Targets on DNA [PDF]
, 2015 The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity
Alberts B. +5 more
core +2 more sources
Are Protein Shape-Encoded Lowest-Frequency Motions a Key Phenotype Selected by Evolution?
Applied Sciences, 2023 At the very deepest molecular level, the mechanisms of life depend on the operation of proteins, the so-called “workhorses” of the cell. Proteins are nanoscale machines that transform energy into useful cellular work, such as ion or nutrient transport ...
Laura Orellana
doaj +1 more source
Epigenetic mechanisms to propagate histone acetylation by p300/CBP
Nature Communications, 2023 Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which a p300/CREB-binding protein (CBP) multidomain monomer ...
Masaki Kikuchi +8 more
doaj +1 more source
Two domains of Tim50 coordinate translocation of proteins across the two mitochondrial membranes
Life Science Alliance, 2023 Biochemical and genetic experiments identify distinct roles of the two domains of Tim50 in the intermembrane space during translocation of proteins into the mitochondria via the TOM and TIM23 complexes.
Marcel G Genge +7 more
doaj +1 more source
Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis
Nature Communications, 2019 In bacteria, the conserved trans-translation system serves as the primary pathway of ribosome rescue, but many species can also use alternative rescue pathways. Here the authors report that in B. subtilis, the rescue factor BrfA binds to non-stop stalled
Naomi Shimokawa-Chiba +6 more
doaj +1 more source
Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose [PDF]
, 2013 In order to investigate the cryoprotective mechanism of trehalose on proteins, we use molecular dynamics computer simulations to study the microscopic dynamics of water upon cooling in an aqueous solution of lysozyme and trehalose.
Corradini, Dario +3 more
core +1 more source
Substrate-induced conformational dynamics of the dopamine transporter
Nature Communications, 2019 The dopamine transporter is responsible for termination of neurotransmission through Na+-driven reuptake of neurotransmitter from the extracellular space. Here authors use hydrogen-deuterium exchange mass spectrometry to monitor Na+- and dopamine-induced
Anne Kathrine Nielsen +6 more
doaj +1 more source
Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools. [PDF]
, 2016 This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function.
Chang, Chia-En A +3 more
core +2 more sources
COMPARISONS OF PROTEIN FAMILY DYNAMICS [PDF]
Biocomputing 2008, 2007 Similarities between different protein structures have led to the identification of protein families based upon some measure of structural similarity. Using these similarities one can classify proteins into structural families and higher-order groupings from which inferred function can be transferred.
A. J. Radar, Joshua T. Harrell
openaire +3 more sources
Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors. [PDF]
, 2017 Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations.
Gaieb, Zied, Morikis, Dimitrios
core +2 more sources