RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB.

New system for archiving integrative structures.

Structures of many complex biological assemblies are increasingly determined using integrative approaches, in which data from multiple experimental methods are combined. A standalone system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. Here, the data standards and software tools that support PDB-Dev are described along with the new and updated components of the PDB-Dev data-collection, processing and archiving infrastructure.

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.

An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells.

Integrative structure and function of the yeast exocyst complex.

Exocyst is an evolutionarily conserved hetero-octameric tethering complex that plays a variety of roles in membrane trafficking, including exocytosis, endocytosis, autophagy, cell polarization, cytokinesis, pathogen invasion, and metastasis. Exocyst serves as a platform for interactions between the Rab, Rho, and Ral small GTPases, SNARE proteins, and Sec1/Munc18 regulators that coordinate spatial and temporal fidelity of membrane fusion. However, its mechanism is poorly described at the molecular level.

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.

Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were localized and shown to occlude transcription factor IIF (TFIIF) and transcription factor IIB (TFIIB) binding by perfect positioning on their Pol II interaction sites. Robust binding of Gdown1 to Pol II is established by cooperative interactions of a strong Pol II binding region and two weaker binding modulatory regions, thus providing a mechanism both for tight Pol II binding and transcription inhibition and for its reversal.

Influence of Monovalent Cation Size on Nanodomain Formation in Anionic-Zwitterionic Mixed Bilayers.

Phosphatidylserine (PS) and phosphatidylcholine (PC) are two of the major anionic and zwitterionic phospholipids in mammalian cell membranes. Ion-PS interaction is hypothesized to play a crucial role in a range of biological events including membrane fusion, lipid phase modulation, membrane protein insertion and translocation. In this study, we characterize lipid nanodomain formation in PC/PS mixed bilayers using coarse-grained simulations.

Correction: Effect of lipid head group interactions on membrane properties and membrane-induced cationic β-hairpin folding.

Correction for 'Effect of lipid head group interactions on membrane properties and membrane-induced cationic β-hairpin folding' by Sai J. Ganesan et al., Phys.

Effect of lipid head group interactions on membrane properties and membrane-induced cationic β-hairpin folding.

Membrane interfaces (mIFs) are ubiquitous components of living cells and are host to many essential biological processes. One key characteristic of mIFs is the dielectric gradient and, subsequently, electrostatic potential that arises from dipolar interactions in the head group region. In this work, we present a coarse-grained (CG) model for anionic and zwitterionic lipids that accounts for dipolar intricacies in the head group region.

Interplay between the hydrophobic effect and dipole interactions in peptide aggregation at interfaces.

Protein misfolding is an intrinsic property of polypeptides, and misfolded conformations have a propensity to aggregate. In the past decade, the development of various coarse-grained models for proteins has provided key insights into the driving forces in folding and aggregation. We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model (WEPPROM) by adding oppositely charged dummy particles inside protein backbone beads.

Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins.

We present a generic solvated coarse-grained protein model that can be used to characterize the driving forces behind protein folding. Each amino acid is coarse-grained with two beads, a backbone, and a side chain. Although the backbone beads are modeled as polar entities, side chains are hydrophobic, polar, or charged, thus allowing the exploration of how sequence patterning determines a protein fold.