VMD: Visual molecular dynamics

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

/pdf/the-protein-data-bank-4lbxxcio6v.pdf

The Protein Data Bank

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

/pdf/features-and-development-of-coot-5al5bhwkg1.pdf

Features and development of Coot.

For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

/pdf/the-pfam-protein-families-database-3t3lguk949.pdf

The Pfam protein families database

The structure of [Os([eta][sup 2]-H[sub 2])en[sub 2]CH[sub 3]CO[sub 2]]PF[sub 6] (1) has been studied by X-ray diffraction at 120 K and neutron diffraction at 165 K. Compound 1 belongs to a series of dihydrogen complexes of osmium(II) amines, exhibiting an extensive range in the strength of the H-H interaction as judged by the wide variation in observed J[sub H-D] coupling constants. The ethylenediamine ligands in I have a trans arrangement. The H[sub 2] and the acetate ligands occupy positions on opposite sides of the OsN[sub 4] plane, giving overall approximately octahedral coordination. Consistent with the relatively low J[sub H-D] value (9.0 Hz), the H-H distance in 1.134(2) [angstrom] as determined by neutron diffraction, is unusually long and approaches that of 1.357(7) [angstrom] found in the polyhydride ReH[sub 7][P(p-tolyl)[sub 3]][sub 2]. It is presumed that I may represent an intermediate stage in the oxidative addition of dihydrogen at transition-metal centers. The Os-H distances in 1.1.59(1) [angstrom] and 1.60(2) [angstrom], are shorter than those in the classical osmium polyhydride OsH[sub 4](PMe[sub 2]Ph)[sub 3] (mean Os-H 1.659(3) [angstrom]) lending support to the assertion that the Os([eta][sup 2]-H[sub 2]) interaction is relatively strong. Crystal data are provided. 46 refs., 3 figs., 2 tabs.

Determination of the Structure of [Os(.eta.2-H2)en2CH3CO2]PF6 by X-ray and Neutron Diffraction

Neutron and x-ray diffraction studies of tris(methyldiphenylphosphine)[tetrahydroborato(1-)]copper, Cu[P(C6H5)2CH3]3(BH4). The first accurate characterization of an unsupported metal-hydrogen-boron bridge bond

Pentacoordinate hydrogen atoms were identified by single-crystal neutron diffraction analysis of [N(CH3)4]3[H2Rh13(CO)24]. The hydrogen atoms are located in square pyramidal cavities of the Rh13 cluster, in positions almost coplanar with the Rh4 faces on the surface of the cluster. They are slightly displaced inward, toward the central rhodium atom of the cluster, with average H-Rh(central) and H-Rh(surface) distances of 1.84(2) and 1.97(2) angstroms, respectively. This result shows that hydrogen, which normally forms only one bond, can be attached to five other atoms simultaneously in a large metal cluster.

https://science.sciencemag.org/content/sci/275/5303/1099.full.pdf

Five-Coordinate Hydrogen: Neutron Diffraction Analysis of the Hydrido Cluster Complex [H2Rh13(CO)24]3−

Precision neutron diffraction structure determination of protein and nucleic acid components. II. The crystal and molecular structure of the dipeptide glycylglycine monohydrochloride monohydrate

In contradiction to current bonding paradigms, two terminal Au-oxo molecular complexes have been synthesized by reaction of AuCl3 with metal oxide-cluster ligands that model redox-active metal oxide surfaces. Use of K10[α2-P2W17O61]·20H2O and K2WO4 (forming the [A-PW9O34]9- ligand in situ) produces K15H2[Au(O)(OH2)P2W18O68]·25H2O (1); use of K10[P2W20O70(OH2)2]·22H2O (3) produces K7H2[Au(O)(OH2)P2W20O70(OH2)2]·27H2O (2). Complex 1 crystallizes in orthorhombic Fddd, with a = 28.594(4) A, b = 31.866(4) A, c = 38.241(5) A, V = 34844(7) A3, Z = 16 (final R = 0.0540), and complex 2 crystallizes in hexagonal P6(3)/mmc, with a = 16.1730(9) A, b = 16.1730(9) A, c = 19.7659(15) A, V = 4477.4(5) A3, Z = 2 (final R = 0.0634). The polyanion unit in 1 is disorder-free. Very short (∼1.76 A) Au-oxo distances are established by both X-ray and 30 K neutron diffraction studies, and the latter confirms oxo and trans aqua (H2O) ligands on Au. Seven findings clarify that Au and not W is present in the Au-oxo position in 1 and...

https://pubs.acs.org/doi/pdf/10.1021/ja207909y

Thomas F. Koetzle

Papers

Determination of the Structure of [Os(.eta.2-H2)en2CH3CO2]PF6 by X-ray and Neutron Diffraction

Neutron and x-ray diffraction studies of tris(methyldiphenylphosphine)[tetrahydroborato(1-)]copper, Cu[P(C6H5)2CH3]3(BH4). The first accurate characterization of an unsupported metal-hydrogen-boron bridge bond

Five-Coordinate Hydrogen: Neutron Diffraction Analysis of the Hydrido Cluster Complex [H2Rh13(CO)24]3−

Precision neutron diffraction structure determination of protein and nucleic acid components. II. The crystal and molecular structure of the dipeptide glycylglycine monohydrochloride monohydrate

Terminal gold-oxo complexes.