Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction

Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity

(2020) Farzaneh Tondnevis et al.   Scientific Reports

Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate

(2020) Xue Fei et al.   eLife

A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery

(2020) Zev A Ripstein et al.   eLife

Covalent modifications of bacteriophage genome confer a degree of resistance to bacterial CRISPR systems

(2020) Yuepeng Liu et al.   JOURNAL OF VIROLOGY

Structure of the human clamp loader reveals an autoinhibited conformation of a substrate-bound AAA+ switch

(2020) Christl Gaubitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and functional characterization of G protein-coupled receptors with deep mutational scanning

(2020) Eric M Jones et al.   eLife

On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment

(2020) Liam M Longo et al.   eLife

Simulating Water Exchange to Buried Binding Sites

(2019) Ido Y. Ben-Shalom et al.   Journal of Chemical Theory and Computation

A structural view of bacterial DNA replication

(2019) Aaron J. Oakley   PROTEIN SCIENCE

CRISPR Cpf1 proteins: structure, function and implications for genome editing

(2019) Fatemeh Safari et al.   Cell and Bioscience

Stairway to translocation: AAA+ motor structures reveal the mechanisms of ATP‐dependent substrate translocation

(2019) Stephanie N. Gates et al.   PROTEIN SCIENCE

Pivotal roles of PCNA loading and unloading in heterochromatin function

(2018) Ryan Janke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolution-based inference of amino acid interactions underlying protein function

(2018) Victor H Salinas et al.   eLife

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation

(2018) Neel H. Shah et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Understanding DNA replication by the bacteriophage T4 replisome

(2017) Stephen J. Benkovic et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Linchpin DNA-binding residues serve as go/no-go controls in the replication factor C-catalyzed clamp-loading mechanism

(2017) Juan Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanism of opening a sliding clamp

(2017) Lauren G. Douma et al.   NUCLEIC ACIDS RESEARCH

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

(2017) Marnix Vlot et al.   NUCLEIC ACIDS RESEARCH

Structural basis of human PCNA sliding on DNA

(2017) Matteo De March et al.   Nature Communications

Engineering of Bacteriophage T4 Genome Using CRISPR-Cas9

(2017) Pan Tao et al.   ACS Synthetic Biology

Review: Structure and mechanism of the dynein motor ATPase

(2016) Helgo Schmidt et al.   BIOPOLYMERS

Review: The lord of the rings: Structure and mechanism of the sliding clamp loader

(2016) Brian A. Kelch   BIOPOLYMERS

Origins of Allostery and Evolvability in Proteins: A Case Study

(2016) Arjun S. Raman et al.   CELL

Solution structure of an “open” E. coli Pol III clamp loader sliding clamp complex

(2016) Farzaneh Tondnevis et al.   JOURNAL OF STRUCTURAL BIOLOGY

Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

(2016) Jeffrey I. Boucher et al.   PROTEIN SCIENCE

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

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

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

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9

(2015) Alexandra L. Bryson et al.   mBio

Viewing Protein Fitness Landscapes Through a Next-Gen Lens

(2014) J. I. Boucher et al.   GENETICS

The ATP Sites of AAA+ Clamp Loaders Work Together as a Switch to Assemble Clamps on DNA

(2014) Melissa R. Marzahn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Replication Clamps and Clamp Loaders

(2013) M. Hedglin et al.   Cold Spring Harbor Perspectives in Biology

A Novel Function for the Conserved Glutamate Residue in the Walker B Motif of Replication Factor C

(2013) Ankita Chiraniya et al.   Genes

Clamp loader ATPases and the evolution of DNA replication machinery

(2012) Brian A Kelch et al.   BMC BIOLOGY

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the AAA+ nucleotide binding pocket

(2011) Petra Wendler et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

DNA stretching by bacterial initiators promotes replication origin opening

(2011) Karl E. Duderstadt et al.   NATURE

How a DNA Polymerase Clamp Loader Opens a Sliding Clamp

(2011) B. A. Kelch et al.   SCIENCE

On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture

(2010) Catherine L Worth et al.   BMC EVOLUTIONARY BIOLOGY

Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase for Remodeling Bacterial RNA Polymerase

(2010) Baoyu Chen et al.   STRUCTURE

Analysis of the role of PCNA-DNA contacts during clamp loading

(2010) Randall McNally et al.   BMC STRUCTURAL BIOLOGY

The Mechanism of ATP-Dependent Primer-Template Recognition by a Clamp Loader Complex

(2009) Kyle R. Simonetta et al.   CELL

Multiple ATP Binding Is Required to Stabilize the “Activated” (Clamp Open) Clamp Loader of the T4 DNA Replication Complex

(2008) Paola Pietroni et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures

(2008) Zhucheng Chen et al.   NATURE