4.5 Article

Early Stages of RNA-Mediated Conversion of Human Prions

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Physics, Fluids & Plasmas

Resolution exchange with tunneling for enhanced sampling of protein landscapes

Fatih Yasar et al.

Summary: Simulations of protein folding and protein association typically take much longer timescales than can be covered in all-atom molecular dynamics simulations. To address this challenge, researchers have introduced a replica-exchange-based multiscale sampling technique that combines the faster sampling in coarse-grained simulations with the potentially higher accuracy of all-atom simulations. By testing the efficiency of this technique in simulations of the Trp-cage protein and comparing the landscapes of wild-type and A2T mutant A beta(1-42) peptides, the researchers found a mechanism by which a small hydrophobic alanine (A) mutation to a bulky polar threonine (T) may interfere with the self-assembly of A beta fibrils.

PHYSICAL REVIEW E (2022)

Article Biochemistry & Molecular Biology

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

David Sehnal et al.

Summary: Large biomolecular structures are being determined experimentally using established techniques such as crystallography and electron microscopy, with performance requirements for visualization and analysis tools increasing rapidly. The Mol* Viewer is an advanced online web-native 3D visualization tool that allows visualization of complex structures, and is the primary tool used by PDBe and RCSB PDB.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

High-resolution structure and strain comparison of infectious mammalian prions

Allison Kraus et al.

Summary: The study reveals the core structure of prions and the templating surface formed by individual monomers at fibril ends. Comparison to another prion strain shows differences in fibril morphology. These findings provide insights into the propagation of prions.

MOLECULAR CELL (2021)

Article Chemistry, Physical

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Physical

Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations

Hoang Linh Nguyen et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

Article Chemistry, Multidisciplinary

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

Adam K. Sieradzan et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)

Article Chemistry, Multidisciplinary

Mutations Alter RNA-Mediated Conversion of Human Prions

Erik J. Alred et al.

ACS OMEGA (2018)

Article Biochemistry & Molecular Biology

Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics

Ana Rojas et al.

ACS CHEMICAL NEUROSCIENCE (2017)

Article Biochemistry & Molecular Biology

Molecular dynamics simulations of early steps in RNA-mediated conversion of prions

Erik J. Alred et al.

PROTEIN SCIENCE (2017)

Review Chemistry, Multidisciplinary

Coarse-Grained Protein Models and Their Applications

Sebastian Kmiecik et al.

CHEMICAL REVIEWS (2016)

Review Biochemistry & Molecular Biology

Mechanisms of prion-induced neurodegeneration

Paula Saa et al.

EXPERT REVIEWS IN MOLECULAR MEDICINE (2016)

Article Chemistry, Physical

Assessing the Current State of Amber Force Field Modifications for DNA

Rodrigo Galindo-Murillo et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Chemistry, Physical

Physics-Based Potentials for Coarse-Grained Modeling of Protein DNA Interactions

Yanping Yin et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Letter Biochemical Research Methods

The I-TASSER Suite: protein structure and function prediction

Jianyi Yang et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions

Adam Liwo et al.

JOURNAL OF MOLECULAR MODELING (2014)

Article Chemistry, Multidisciplinary

Probing the N-Terminal β-Sheet Conversion in the Crystal Structure of the Human Prion Protein Bound to a Nanobody

Romany N. N. Abskharon et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)

Article Multidisciplinary Sciences

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

Rui Zhou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Romelia Salomon-Ferrer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Goetz et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Chemistry, Physical

PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides

Wei Han et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Neurosciences

Axonal prion protein is required for peripheral myelin maintenance

Juliane Bremer et al.

NATURE NEUROSCIENCE (2010)

Article Biochemical Research Methods

I-TASSER: a unified platform for automated protein structure and function prediction

Ambrish Roy et al.

NATURE PROTOCOLS (2010)

Article Multidisciplinary Sciences

Formation of native prions from minimal components in vitro

Nathan R. Deleault et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Chemistry, Physical

Solid-state NMR structural studies of the fibril form of a mutant mouse prion peptide PrP89-143(P101L)

KH Lim et al.

SOLID STATE NUCLEAR MAGNETIC RESONANCE (2006)

Article Multidisciplinary Sciences

NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126

K Kuwata et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Multidisciplinary Sciences

RNA molecules stimulate prion protein conversion

NR Deleault et al.

NATURE (2003)

Article Multidisciplinary Sciences

Simulations of biomolecules: characterization of the early steps in the pH-induced conformational conversion of the hamster, bovine and human forms of the prion protein

DOV Alonso et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2002)