4.3 Article

Guide for determination of protein structural ensembles by combining cryo-EM data with metadynamics

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes

Halina Mikolajek et al.

Summary: This study generated nanobodies with different affinities using the receptor binding domain (RBD) of SARS-CoV-2 spike protein and a naive library. By analyzing the structure-activity relationship, it was found that higher conformational entropy losses were associated with tighter binding. Structural ensembles and conformational fluctuations were investigated to enhance the affinity of nanobodies.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Chemistry, Multidisciplinary

A Structural Ensemble of a Tau-Microtubule Complex Reveals Regulatory Tau Phosphorylation and Acetylation Mechanisms

Z. Faidon Brotzakis et al.

Summary: By studying the structure and dynamics of the tau-microtubule complex, we identified the ground state and excited states of the complex, as well as important positions for stability. This analysis revealed the destabilizing effects of phosphorylation and acetylation events on the complex, showcasing how determining ground and excited states can uncover functional and regulatory mechanisms of macromolecular complexes.

ACS CENTRAL SCIENCE (2021)

Article Materials Science, Multidisciplinary

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Mrinal Shekhar et al.

Summary: The study introduces a new pipeline, CryoFold, which uses molecular dynamics simulations to determine protein structure ensembles by integrating density data, sequence information, and topological knowledge. This method is effective for folding proteins of various sizes and types. With data-driven approach, CryoFold can discover common low-energy models and rare low-probability structures, leading to experimentally validated conformations and relevant functional insights.

MATTER (2021)

Article Chemistry, Multidisciplinary

Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy

Z. Faidon Brotzakis et al.

Summary: Research using cryo-electron microscopy has identified the process of SARS-CoV-2 spike transitioning from closed to open state, revealing a cryptic pocket that could be targeted for therapeutic interventions. This study emphasizes the importance of understanding transient intermediate states of proteins for developing effective treatments against invisible binding sites.

CHEMICAL SCIENCE (2021)

Review Biochemistry & Molecular Biology

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

Yihang Wang et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils

Christine Roeder et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Article Multidisciplinary Sciences

Retrieving functional pathways of biomolecules from single-particle snapshots

Ali Dashti et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Effects of α-tubulin acetylation on microtubule structure and stability

Lisa Eshun-Wilson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Determination of protein structural ensembles using cryo-electron microscopy

Massimiliano Bonomi et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2019)

Editorial Material Biochemical Research Methods

Promoting transparency and reproducibility in enhanced molecular simulations

Massimiliano Bonomi et al.

NATURE METHODS (2019)

Article Biophysics

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

Massimiliano Bonomi et al.

BIOPHYSICAL JOURNAL (2018)

Article Multidisciplinary Sciences

Reversible inhibition of the ClpP protease via an N-terminal conformational switch

Siavash Vahidi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

Metainference: A Bayesian inference method for heterogeneous systems

Massimiliano Bonomi et al.

SCIENCE ADVANCES (2016)

Article Biophysics

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Robert T. McGibbon et al.

BIOPHYSICAL JOURNAL (2015)

Article Chemistry, Physical

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

Jim Pfaendtner et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Computer Science, Interdisciplinary Applications

PLUMED 2: New feathers for an old bird

Gareth A. Tribello et al.

COMPUTER PHYSICS COMMUNICATIONS (2014)

Article Biochemical Research Methods

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Sander Pronk et al.

BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

The fuzzy coat of pathological human Tau fibrils is a two-layered polyelectrolyte brush

Susanne Wegmann et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

High-Resolution Comparative Modeling with RosettaCM

Yifan Song et al.

STRUCTURE (2013)

Article Biochemistry & Molecular Biology

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Kresten Lindorff-Larsen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics

Leonardo G. Trabuco et al.

STRUCTURE (2008)

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

P Raiteri et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)