4.7 Article

Equilibrium Dynamics of a Biomolecular Complex Analyzed at Single-amino Acid Resolution by Cryo-electron Microscopy

Related references

Note: Only part of the references are listed.
Article Biophysics

Antiviral compounds modulate elasticity, strength and material fatigue of a virus capsid framework

Santos Dominguez-Zotes et al.

Summary: This study investigates the effects of organic compounds binding to different sites in the HIV capsid on the mechanical properties of the capsid protein lattice. The results show that different compounds have different effects on the elasticity, breathing, strength, and fatigue resistance of the capsid lattice. The study provides insights into the biophysical action of capsid-binding antiviral agents by examining the mechanical properties of the viral capsid material.

BIOPHYSICAL JOURNAL (2022)

Article Multidisciplinary Sciences

Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment

Jennifer Ross et al.

Summary: In this study, the structural relationship between the encapsulin shell and its protein cargo was investigated using cryo-electron microscopy and hydrogen/deuterium exchange mass spectrometry. The study revealed the arrangement of encapsulated ferritin decamers within the encapsulin nanocompartment and the dynamic behavior of the encapsulin shell pore.

SCIENCE ADVANCES (2022)

Review Biochemistry & Molecular Biology

Comparison of CryoEM and X-ray structures of dimethylformamidase

Kutti R. Vinothkumar et al.

Summary: Dimethylformamidase (DMFase) catalyzes the hydrolysis of dimethylformamide, and recent studies have determined its tetrameric structure with a mononuclear iron at the active site. Isolated from Paracoccus sp. in India, this enzyme shows maximal activity at 54 degrees C and is halotolerant. Comparison of structures determined by electron cryo microscopy and X-ray crystallography reveals conserved water molecules which may play a structural role in the enzyme's mechanism.

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2021)

Review Chemistry, Analytical

Mass Spectrometry-Based Structural Virology

Tobias P. Worner et al.

ANALYTICAL CHEMISTRY (2021)

Article Virology

Cryo EM Analysis Reveals Inherent Flexibility of Authentic Murine Papillomavirus Capsids

Samantha R. Hartmann et al.

Summary: HPV is a significant health burden and a leading cause of virus-induced cancers, but studies have been hindered by restricted tropism. Alternative methods such as VLPs have been developed to overcome this issue, but structural studies have been limited by heterogeneity, fragility, and stability. By studying MmuPV1, a framework for continuing biochemical, genetic, and biophysical research for papillomaviruses has been provided.

VIRUSES-BASEL (2021)

Review Biochemistry & Molecular Biology

Bridging protein structure, dynamics, and function using hydrogen/deuterium-exchange mass spectrometry

Edgar A. Hodge et al.

PROTEIN SCIENCE (2020)

Article Biochemistry & Molecular Biology

Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo-electron microscopy

Mao Oide et al.

FEBS JOURNAL (2020)

Review Biochemistry & Molecular Biology

Cryo-electron microscopy for the study of virus assembly

Daniel Luque et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Chemistry, Multidisciplinary

A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

Chetan Kumar Arya et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Review Chemistry, Physical

Enzyme Dynamics: Looking Beyond a Single Structure

Pratul K. Agarwal et al.

CHEMCATCHEM (2020)

Article Biochemical Research Methods

Time-resolved cryo-EM using Spotiton

Venkata P. Dandey et al.

NATURE METHODS (2020)

Review Biochemistry & Molecular Biology

Local resolution estimates of cryoEM reconstructions

J. L. Vilas et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

Review Virology

The Dynamic Life of Virus Capsids

Michael B. Sherman et al.

VIRUSES-BASEL (2020)

Article Multidisciplinary Sciences

Atomic-resolution protein structure determination by cryo-EM

Ka Man Yip et al.

NATURE (2020)

Article Biophysics

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

Massimiliano Bonomi et al.

BIOPHYSICAL JOURNAL (2018)

Article Chemistry, Multidisciplinary

Mechanical stiffening of human rhinovirus by cavity-filling antiviral drugs

Alejandro Valbuena et al.

NANOSCALE (2018)

Article Multidisciplinary Sciences

Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant

Yong Zi Tan et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Time-resolved cryo-electron microscopy: Recent progress

Joachim Frank

JOURNAL OF STRUCTURAL BIOLOGY (2017)

Letter Biochemical Research Methods

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

Shawn Q. Zheng et al.

NATURE METHODS (2017)

Article Virology

Electron Cryomicroscopy of Viruses at Near-Atomic Resolutions

Jason T. Kaelber et al.

Annual Review of Virology (2017)

Article Biophysics

Structural Analysis of a Temperature-Induced Transition in a Viral Capsid Probed by HDX-MS

Michiel van de Waterbeemd et al.

BIOPHYSICAL JOURNAL (2017)

Article Biochemistry & Molecular Biology

EMDataBank unified data resource for 3DEM

Catherine L. Lawson et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

J. M. de la Rosa-Trevin et al.

JOURNAL OF STRUCTURAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

2.9 Å Resolution Cryo-EM 3D Reconstruction of Close-Packed Virus Particles

Zheng Liu et al.

STRUCTURE (2016)

Article Virology

Virus particle dynamics derived from CryoEM studies

Peter C. Doerschuk et al.

CURRENT OPINION IN VIROLOGY (2016)

Review Chemistry, Multidisciplinary

Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation

Kateri H. DuBay et al.

ACCOUNTS OF CHEMICAL RESEARCH (2015)

Article Biochemistry & Molecular Biology

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

Alexis Rohou et al.

JOURNAL OF STRUCTURAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Dynamic and geometric analyses of Nudaurelia capensis. virus maturation reveal the energy landscape of particle transitions

Jinghua Tang et al.

JOURNAL OF MOLECULAR RECOGNITION (2014)

Article Virology

Parvoviruses: Small Does Not Mean Simple

Susan F. Cotmore et al.

ANNUAL REVIEW OF VIROLOGY, VOL 1 (2014)

Review Biochemistry & Molecular Biology

Assembly, stability and dynamics of virus capsids

Mauricio G. Mateu

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2013)

Article Biochemistry & Molecular Biology

Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps

Qiu Wang et al.

JOURNAL OF STRUCTURAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Xmipp 3.0: An improved software suite for image processing in electron microscopy

J. M. de la Rosa-Trevin et al.

JOURNAL OF STRUCTURAL BIOLOGY (2013)

Review Biophysics

Virus Maturation

David Veesler et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)

Article Biochemistry & Molecular Biology

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

Sjors H. W. Scheres

JOURNAL OF STRUCTURAL BIOLOGY (2012)

Article Multidisciplinary Sciences

Mechanical elasticity as a physical signature of conformational dynamics in a virus particle

Milagros Castellanos et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Identifying Conformational States of Macromolecules by Eigen-Analysis of Resampled Cryo-EM Images

Pawel A. Penczek et al.

STRUCTURE (2011)

Article Biochemical Research Methods

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemical Research Methods

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Paul D. Adams et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemistry & Molecular Biology

The universal mechanism for iron translocation to the ferroxidase site in ferritin, which is mediated by the well conserved transit site

Taro Masuda et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2010)

Review Chemistry, Physical

Structure, dynamics, and assembly of filamentous bacteriophages by nuclear magnetic resonance spectroscopy

Stanley J. Opella et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2008)

Article Chemistry, Multidisciplinary

Solution NMR studies of the maturation intermediates of a 13 MDa viral capsid

Blair R. Szymczyna et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Instruments & Instrumentation

WSXM: A software for scanning probe microscopy and a tool for nanotechnology

I. Horcas et al.

REVIEW OF SCIENTIFIC INSTRUMENTS (2007)

Article Biochemistry & Molecular Biology

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

PL Freddolino et al.

STRUCTURE (2006)

Article Biochemistry & Molecular Biology

Capsid structure and dynamics of a human rhinovirus probed by hydrogen exchange mass spectrometry

LT Wang et al.

PROTEIN SCIENCE (2005)

Article Multidisciplinary Sciences

Role of interfacial amino acid residues in assembly, stability, and conformation of a spherical virus capsid

J Reguera et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemical Research Methods

Coot:: model-building tools for molecular graphics

P Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

Article Multidisciplinary Sciences

Bacteriophage capsids: Tough nanoshells with complex elastic properties

IL Ivanovska et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Multidisciplinary Sciences

Topologically linked protein rings in the bacteriophage HK97 capsid

WR Wikoff et al.

SCIENCE (2000)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)