Paul A Bates

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Structure of an XRCC1 BRCT domain: a new protein-protein interaction module

Xiaodong Zhang et 10 al.

Nov 2, 1998 in The EMBO Journal
The BRCT domain (BRCA1 C‐terminus), first identified in the breast cancer suppressor protein BRCA1, is an evolutionarily conserved protein–protein interaction region of ∼95 amino acids found in a large number of proteins involved in DNA repair, recombination and cell cycle control. Here we describe the first three‐dimensional structure and fold of a BRCT domain determined by X‐ray crystallography ...

Matrix feedback enables diverse higher-order patterning of the extracellular matrix.

Esther Wershof, Paul A Bates et 5 al.

Oct 28, 2019 in PLoS computational biology
The higher-order patterning of extra-cellular matrix in normal and pathological tissues has profound consequences on tissue function. Whilst studies have documented both how fibroblasts create and maintain individual matrix fibers and how cell migration is altered by the fibers they interact with, a model unifying these two aspects of tissue organization is lacking. Here we use computational model...

Extracellular matrix anisotropy is determined by TFAP2C-dependent regulation of cell collisions.

Danielle Park, Erik Sahai et 8 al.

Oct 28, 2019 in Nature materials
The isotropic or anisotropic organization of biological extracellular matrices has important consequences for tissue function. We study emergent anisotropy using fibroblasts that generate varying degrees of matrix alignment from uniform starting conditions. This reveals that the early migratory paths of fibroblasts are correlated with subsequent matrix organization. Combined experimentation and ad...


Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions.

Melda Tozluoğlu, Erik Sahai et 5 al.

Jun 23, 2013 in Nature cell biology
The molecular requirements and morphology of migrating cells can vary depending on matrix geometry; therefore, predicting the optimal migration strategy or the effect of experimental perturbation is difficult. We present a model of cell motility that encompasses actin-polymerization-based protrusions, actomyosin contractility, variable actin-plasma membrane linkage leading to membrane blebbing, ce...


Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma.

Takuya Kato, Erik Sahai et 11 al.

Mar 9, 2023 in eLife
Cancers, such as squamous cell carcinoma, frequently invade as multicellular units. However, these invading units can be organised in a variety of ways, ranging from thin discontinuous strands to thick 'pushing' collectives. Here we employ an integrated experimental and computational approach to identify the factors that determine the mode of collective cancer cell invasion. We find that matrix pr...

Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.

Shoshana J Wodak, Paul A Bates et 4 al.

Jan 10, 2022 in Annual review of biophysics
Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have over decades emulated this pattern, as monitored by the community-wide blind prediction experiments CASP and CAPRI. However, over the past few years, dra...

Chromosome scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae

Hatim Almutairi et 10 al.

Sep 6, 2021 in Scientific Data
We provide the raw and processed data produced during the genome sequencing of isolates from six species of parasites from the sub-family Leishmaniinae: Leishmania martiniquensis (Thailand), Leishmania orientalis (Thailand), Leishmania enriettii (Brazil), Leishmania sp. Ghana, Leishmania sp. Namibia and Porcisia hertigi (Panama). De novo assembly was performed using Nanopore long reads to construc...

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Marc F. Lensink et 108 al.

Aug 28, 2021 in Proteins: Structure, Function, and Bioinformatics
We present the results for CAPRI Round 50, the 4th joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher‐order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher‐order oligomers). Eight were dif...

LGAAP: Leishmaniinae Genome Assembly and Annotation Pipeline

Hatim Almutairi et 30 al.

Jul 22, 2021 in American Society for Microbiology
Microbiology Resource Announcements, Volume 10, Issue 29, July 2021.

β-diketone interactions

John Emsley et 4 al.

Aug 1, 1988 in Journal of Molecular Structure
A new derivative of pentane-2,4-dione has been made, 3-(4′-biphenyl)pentane-2,4-dione, which exists predominantly (98.5%) as the enol tautomer in CDCl 3 solution and in the solid state. An X-ray crystal structure reveals a very short hydrogen bond whose vibrations are characterized as broad bands at 1600, 1380 and 960 (± 20) cm −1 in the infrared. The hydrogen bond energy of this bond probably ex...