Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes

Long-Range Correlated Motion Changes with Protein-Ligand Binding

(2015) Katherine A. Niessen et al.   BIOPHYSICAL JOURNAL

THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

(2014) K. N. Woods   JOURNAL OF BIOLOGICAL PHYSICS

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network of long-range concerted chemical shift displacements upon ligand binding to human angiogenin

(2014) Donald Gagné et al.   PROTEIN SCIENCE

Using THz time-scale infrared spectroscopy to examine the role of collective, thermal fluctuations in the formation of myoglobin allosteric communication pathways and ligand specificity

(2014) K. N. Woods   Soft Matter

The glassy state of crambin and the THz time scale protein-solvent fluctuations possibly related to protein function

(2014) Kristina N Woods   BMC Biophysics

Cytotoxicity of bovine α-lactalbumin: Oleic acid complexes correlates with the disruption of lipid membranes

(2013) Hanzhen Wen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

Protein-fatty acid complexes: biochemistry, biophysics and function

(2013) Christel R. Brinkmann et al.   FEBS Journal

MISTIC: mutual information server to infer coevolution

(2013) Franco L. Simonetti et al.   NUCLEIC ACIDS RESEARCH

Sensitization of Staphylococcus aureus to Methicillin and Other Antibiotics In Vitro and In Vivo in the Presence of HAMLET

(2013) Laura R. Marks et al.   PLoS One

A Complex of Equine Lysozyme and Oleic Acid with Bactericidal Activity against Streptococcus pneumoniae

(2013) Emily A. Clementi et al.   PLoS One

Sequence Evolution Correlates with Structural Dynamics

(2012) Ying Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Human Milk Protein-Lipid Complex HAMLET Sensitizes Bacterial Pathogens to Traditional Antimicrobial Agents

(2012) Laura R. Marks et al.   PLoS One

Low Resolution Solution Structure of HAMLET and the Importance of Its Alpha-Domains in Tumoricidal Activity

(2012) James Ho CS et al.   PLoS One

Recognition Pliability Is Coupled to Structural Heterogeneity: A Calmodulin Intrinsically Disordered Binding Region Complex

(2012) Malini Nagulapalli et al.   STRUCTURE

Far-infrared spectroscopy analysis of linear and cyclic peptides, and lysozyme

(2012) Tao Ding et al.   VIBRATIONAL SPECTROSCOPY

Collective Dynamics Differentiates Functional Divergence in Protein Evolution

(2012) Tyler J. Glembo et al.   PLoS Computational Biology

Low-Frequency Spectroscopic Analysis of Monomeric and Fibrillar Lysozyme

(2011) Hidayatul A. Zakaria et al.   APPLIED SPECTROSCOPY

Evidence of Protein Collective Motions on the Picosecond Timescale

(2011) Yunfen He et al.   BIOPHYSICAL JOURNAL

Evolution of the mammalian lysozyme gene family

(2011) David M Irwin et al.   BMC EVOLUTIONARY BIOLOGY

Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra-molecular communication pathways

(2011) Ruth Nussinov   BRITISH JOURNAL OF PHARMACOLOGY

Hot Spots for Allosteric Regulation on Protein Surfaces

(2011) Kimberly A. Reynolds et al.   CELL

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

(2011) R. Bryn Fenwick et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Fast docking using the CHARMM force field with EADock DSS

(2011) Aurélien Grosdidier et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Characterization of Low-Frequency Modes in Aqueous Peptides Using Far-Infrared Spectroscopy and Molecular Dynamics Simulation

(2011) Tao Ding et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

SwissDock, a protein-small molecule docking web service based on EADock DSS

(2011) A. Grosdidier et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A New Role for an Old Antimicrobial: Lysozyme c-1 Can Function to Protect Malaria Parasites in Anopheles Mosquitoes

(2011) Mayur K. Kajla et al.   PLoS One

Applications of Site-Specific Labeling to Study HAMLET, a Tumoricidal Complex of α-Lactalbumin and Oleic Acid

(2011) Natalia Mercer et al.   PLoS One

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins

(2011) Lidio Meireles et al.   PROTEIN SCIENCE

Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone

(2011) Kateri H. DuBay et al.   PLoS Computational Biology

On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

(2010) Ivet Bahar   JOURNAL OF GENERAL PHYSIOLOGY

Solvent-induced backbone fluctuations and the collective librational dynamics of lysozyme studied by terahertz spectroscopy

(2010) K. N. Woods   PHYSICAL REVIEW E

Structural Relationships in the Lysozyme Superfamily: Significant Evidence for Glycoside Hydrolase Signature Motifs

(2010) Alexandre Wohlkönig et al.   PLoS One

Dissecting the THz spectrum of liquid water from first principles via correlations in time and space

(2010) M. Heyden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information

(2009) C. M. Buslje et al.   BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Protein oligomerization induced by oleic acid at the solid-liquid interface - equine lysozyme cytotoxic complexes

(2009) Kristina Wilhelm et al.   FEBS Journal

α-Lactalbumin, Engineered to be Nonnative and Inactive, Kills Tumor Cells when in Complex with Oleic Acid: A New Biological Function Resulting from Partial Unfolding

(2009) Jenny Pettersson-Kastberg et al.   JOURNAL OF MOLECULAR BIOLOGY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A perturbative view of protein structural variation

(2009) Julián Echave et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Heat-treatment method for producing fatty acid-bound alpha-lactalbumin that induces tumor cell death

(2008) Tatsuro Kamijima et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Hydration Effect on Low-Frequency Protein Dynamics Observed in Simulated Neutron Scattering Spectra

(2008) Yasumasa Joti et al.   BIOPHYSICAL JOURNAL

Direct observation of fast protein conformational switching

(2008) H. Ishikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations

(2002) Buyong Ma et al.   PROTEIN SCIENCE