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Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.
Masateru Takahashi, Etsuko Takahashi, Luay I Joudeh, Monica Marini, Gobind Das, Mohamed M Elshenawy, Anastassja Akal, Kosuke Sakashita, Intikhab Alam, Muhammad Tehseen, Mohamed A Sobhy, Ulrich Stingl, Jasmeen S Merzaban, Enzo Di Fabrizio, Samir M Hamdan
Nov 05, 2018
The deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study...
DynaMut
Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based...
Linker length affects photostability of protein-targeted sensor of cellular microviscosity.
Markéta Kubánková, Joseph E Chambers, Roland G Huber, Peter J Bond, Stefan J Marciniak, Marina K Kuimova
Sep 26, 2019
Viscosity sensitive fluorophores termed 'molecular rotors' represent a convenient and quantitative tool for measuring intracellular viscosity via Fluorescence Lifetime Imaging Microscopy (FLIM). We compare the FLIM performance...
Decoding Corticotropin-Releasing Factor Receptor Type 1 Crystal Structures.
Andrew S Dore, Andrea Bortolato, Kaspar Hollenstein, Robert KY Cheng, Randy J Read, Fiona H Marshall
Jun 17, 2016
Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells
Quirino Alves de Lima Neto, Francisco Ferreira Duarte Junior, Paulo Sérgio Alves Bueno, Flavio Augusto Vicente Seixas, Madzia Pauline Kowalski, Eyemen Kheir, Torsten Krude, Maria Aparecida Fernandez
Sep 29, 2016
BACKGROUND: The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is...
Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies.
IDP biophysics coupled folding and binding Electrostatics Kinetics phi-value protein dynamic protein electrostatics Protein Folding protein-protein interactions residual structure signaling Apoptosis Regulatory Proteins CREB-Binding Protein Cyclic AMP Response Element-Binding Protein Humans Hydrophobic and Hydrophilic Interactions Intrinsically Disordered Proteins Kinetics Molecular Dynamics Simulation Myeloid Cell Leukemia Sequence 1 Protein Protein Binding Protein Folding Protein Interaction Domains and Motifs Proto-Oncogene Proteins Signal Transduction Static Electricity Thermodynamics
Proposed Allosteric Inhibitors Bind to the ATP Site of CK2α.
CK2α is a ubiquitous, well-studied kinase that is a target for small-molecule inhibition, for treatment of cancers. While many different classes of adenosine 5'-triphosphate (ATP)-competitive inhibitors have been described for...
Adenosine Triphosphate Allosteric Regulation Allosteric Site Binding Competitive Casein Kinase II Crystallography X-Ray Deuterium Exchange Measurement Humans Ligands Molecular Dynamics Simulation Naphthyridines Nuclear Magnetic Resonance Biomolecular Phenazines Protein Binding Protein Kinase Inhibitors Recombinant Proteins
Structural Characterization of Agonist Binding to an A3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments.
Dimitrios Stamatis, Panagiotis Lagarias, Kerry Barkan, Eleni Vrontaki, Graham Ladds, Antonios Kolocouris
Oct 04, 2019
Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.
Alice LB Pyne, Agnes Noy, Kavit HS Main, Victor Velasco-Berrelleza, Michael M Piperakis, Lesley A Mitchenall, Fiorella M Cugliandolo, Joseph G Beton, Clare EM Stevenson, Bart W Hoogenboom, Andrew D Bates, Anthony Maxwell, Sarah A Harris
Feb 16, 2021
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of...
Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.
Stephen E Farr, Esmae J Woods, Jerelle A Joseph, Adiran Garaizar, Rosana Collepardo-Guevara
Mar 24, 2021
Physicochemical-guided design of cathelicidin-derived peptides generates membrane active variants with therapeutic potential.
Nelson GJ Oliveira, Marlon H Cardoso, Nadya Velikova, Marcel Giesbers, Jerry M Wells, Taia MB Rezende, Renko de Vries, Octávio L Franco
Jul 27, 2020
The spread of multi-drug resistance and the slow pace at which antibiotics come onto the market are undermining our ability to treat human infections, leading to high mortality rates. Aiming to overcome this global crisis...
How Detergent Impacts Membrane Proteins
Vilius Kurauskas, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina Weinhäupl, Lionel Imbert, Bernhard Brutscher, Martin S King, Rémy Sounier, Vincenza Dolce, Edmund RS Kunji, Loredana Capobianco, Christophe Chipot, François Dehez, Beate Bersch, Paul Schanda
Apr 18, 2018
Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers...
Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.
Daniel J Cole, Matej Janecek, Jamie E Stokes, Maxim Rossmann, John C Faver, Grahame J McKenzie, Ashok R Venkitaraman, Marko Hyvönen, David R Spring, David J Huggins, William L Jorgensen
Jun 15, 2018
Free energy perturbation theory, in combination with enhanced sampling of protein-ligand binding modes, is evaluated in the context of fragment-based drug design, and used to design two new small-molecule inhibitors of the...
Building a kinetic Monte Carlo model with a chosen accuracy.
The kinetic Monte Carlo (KMC) method is a popular modeling approach for reaching large materials length and time scales. The KMC dynamics is erroneous when atomic processes that are relevant to the dynamics are missing from the...
Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiří Šponer
Feb 15, 2019
G-quadruplexes are the most important noncanonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other...
Targeting Phosphopeptide Recognition by the Human BRCA1 Tandem BRCT Domain to Interrupt BRCA1-Dependent Signaling.
Jayaprakash Periasamy, Vadiraj Kurdekar, Subbarao Jasti, Mamatha B Nijaguna, Sanjana Boggaram, Manjunath A Hurakadli, Dhruv Raina, Lokavya Meenakshi Kurup, Chetan Chintha, Kavyashree Manjunath, Aneesh Goyal, Gayathri Sadasivam, Kavitha Bharatham, Muralidhara Padigaru, Vijay Potluri, Ashok R Venkitaraman
Aug 23, 2018
Intracellular signals triggered by DNA breakage flow through proteins containing BRCT (BRCA1 C-terminal) domains. This family, comprising 23 conserved phosphopeptide-binding modules in man, is inaccessible to small-molecule...
BRCA1 BRCT domain DNA damage response drug-like inhibitor lead discovery Structure-Activity Relationship BRCA1 Protein Cell Survival Cells Cultured Fluorescence Resonance Energy Transfer HEK293 Cells Humans Molecular Dynamics Simulation Molecular Structure Phosphopeptides Protein Domains Signal Transduction Structure-Activity Relationship
Effect of Varying Stiffness and Functionalization on the Interfacial Failure Behavior of Isotactic Polypropylene on Hydroxylated γ-Al2O3 by MD Simulation.
This study focuses on polymer-metal joints consisting of isotactic polypropylene (iPP) or iPP grafted with maleic anhydride (iPP-g-MA) and hydroxylated γ-Al2O3, which is a model for an oxidized aluminum surface, and investigates...
Cardiolipin dynamics and binding to conserved residues in the mitochondrial ADP/ATP carrier.
Cardiolipin in eukaryotes is found in the mitochondrial inner membrane, where it interacts with membrane proteins and, although not essential, is necessary for the optimal activity of a number of proteins. One of them is the...
Adenine nucleotide translocator Adenine nucleotide transporter cardiolipin Mitochondria Molecular Dynamics Simulation Trimethyllysine Amino Acid Sequence Animals Binding Sites Cardiolipins Cattle Conserved Sequence Mitochondria Mitochondrial ADP ATP Translocases Mitochondrial Membranes Models Molecular Molecular Dynamics Simulation Protein Binding Protein Interaction Domains and Motifs Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins
Exposure of the HIV-1 broadly neutralizing antibody 10E8 MPER epitope on the membrane surface by gp41 transmembrane domain scaffolds
Victoria Oakes, Johana Torralba, Edurne Rujas, José L Nieva, Carmen Domene, Beatriz Apellaniz
Jun 01, 2018
The 10E8 antibody achieves near-pan neutralization of HIV-1 by targeting the remarkably conserved gp41 membrane-proximal external region (MPER) and the connected transmembrane domain (TMD) of the HIV-1 envelope glycoprotein...
AIDS Vaccines Amino Acid Sequence Antibodies Neutralizing/immunology Antigen-Antibody Reactions Antigens Surface/chemistry Epitopes/immunology HIV Antibodies/immunology HIV Envelope Protein gp41/chemistry HIV-1/immunology Humans Liposomes Models Molecular Molecular Dynamics Simulation Peptide Fragments/immunology Protein Conformation Protein Domains /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being name=SDG 3 - Good Health and Well-being
Computational Investigation of RNA A-Bulges Related to the Microtubule-Associated Protein Tau Causing Frontotemporal Dementia and Parkinsonism.
Mutations in the human tau gene result in alternative splicing of the tau protein, which causes frontotemporal dementia and Parkinsonism. One disease mechanism is linked to the stability of a hairpin within the...
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