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.

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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.

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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

Polarized 3 He can be used as a spin filter to polarize a broad energy spectrum of neutrons. As a prototype for use on the single-crystal diffractometer (SCD) at the spallation neutron source (SNS), we have built a compact system to continuously polarize a 3 He spin filter by spin-exchange optical pumping. Polarizing in the neutron beam provides a constant neutron polarization and reduces the sensitivity to relaxation mechanisms. The capability to operate in the presence of non-optimal magnetic field homogeneity allowed us to employ a highly compact solenoid only 9.5 cm in diameter and 20 cm long. Using only 7 W of laser light we maintained 44% 3 He polarization in an 11 cm 3 cell, despite an overall cell relaxation time of ≈ 10 h . Results from a test on the SCD at IPNS are discussed.

Continuously operating compact 3He-based neutron spin filter

The structure of quinolinic acid recrystallized from D 2 0 (2,3-pyridinedicarboxylic acid; C 7 H 3 D 2 N 0 4 ) has been refined based on neutron diffraction data measured at four temperatures: 35, 80, 100 and 298 K. The principal temperature dependence in cell constants is observed for the b axis, which is perpendicular to the molecular planes. The refined thermal parameters have been extrapolated by a least-squares procedure, to yield values for T = 0 K which provide estimates of the combined effects of static disorder and zero-point motion. The D atom shifts toward the midpoint of the short intramolecular 0 0 hydrogen bond when the crystal is cooled, just as was found in an earlier study to occur for the H atom in the undeuterated material. At 100 and 298 K, the D atom is displaced significantly further from the bond midpoint than is the H atom at the same temperature. The magnitude of this isotope effect appears to be independent of temperature. The exchangeable protons in the crystal have not been completely replaced by D; refinement of the D * Research carried out at Brookhaven National Laboratory under contract with the US Department of Energy and supported by its Division of Basic Energy Sciences. t To whom correspondence should be addressed. scattering lengths indicates the presence of approximately 2-7% H attached to N(l) and 4-4% H in the short hydrogen bond. The N scattering length has been refined to yield a value of 0-921 (2) x 10"1 1 mm.

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Neutron diffraction study of quinolinic acid recrystallized from D2O: evaluation of temperature and isotope effects in the structure

A study of the charge density in α‐glycylglycine, C4H8N2O3, has been carried out, employing x‐ray and neutron diffraction data measured at a temperature of 82 K. The crystal is monoclinic, space group P21/c, with a cell of the following dimensions a=8.025(2), b=9.543(4), c=7.788(2) A, and β=106.50(2) ° at 82 K. X‐ray data were collected in the sinϑ/λ range 0.00–1.07 A−1, with Nb filtered MoKα radiation. The deformation densities were computed by an X–N method using positional parameters for all atoms from a neutron diffraction study and thermal parameters for nonhydrogen atoms from a high‐order x‐ray refinement. In the case of hydrogen atoms, the neutron thermal parameters were scaled up by 15% as suggested by a comparison of thermal parameters for nonhydrogen atoms from the neutron and the high‐order x‐ray refinements. Well‐defined peaks of deformation charge density are found for all covalent bonds, and polarization of the density towards the more electronegative atom in the bonds can be noticed. The deformation densities in the four N–H⋅⋅⋅O hydrogen bonds are very similar, with excess charge in the N–H bonds and electron deficient regions on the sides of the hydrogen atoms pointing towards the acceptor oxygen atoms. There is also excess electron density close to the oxygen atoms in the direction of each hydrogen bond, but there does not appear to be any systematic correlation between the H...O distance in the hydrogen bonds and the peak heights in the ’’lone‐pair’’ regions around the oxygen atoms.

Deformation electron density of α‐glycylglycine at 82 K. II. The x‐ray diffraction study

The absolute configuration of (+)-neopentyl-1-d alcohol, prepared by the reduction of 2,2-dimethylpropanal-1-d by actively fermenting yeast, has been determined to be S by neutron diffraction The neutron study was carried out on the phthalate half ester of neopentyl-1-d alcohol, crystallized as its strychnine salt The absolute configuration of the (-)-strychninium cation was first determined by an x-ray anomalous dispersion study of its iodide salt The chiral skeleton of strychnine then served as a reference from which the absolute configuration of the -O-CHD-C(CH3)3 group of neopentyl phthalate was determined Difference Fourier maps calculated from the neutron data showed unambiguously that the -O-CHD-C(CH3)3 groups of both independent molecules in the unit cell had the S configuration This work proves conclusively that the yeast system reduces aldehydes by delivering hydrogen to the re face of the carbonyl group Crystallographic details: (-)-strychninium (+)-neopentyl-1-d phthalate, space group P2(1) (monoclinic), a = 18564(6) A, b = 7713(2) A, c = 23361(8) A, beta = 9418(4) degrees, V = 33360(5) A3, Z = 2 (T = 100 K) Final agreement factors are R(F) = 0073 for 2768 reflections collected at room temperature (x-ray analysis) and R(F) = 0144 for 960 reflections collected at 100 K (neutron analysis)

https://www.pnas.org/content/pnas/91/26/12872.full.pdf

Determination of the absolute configuration of (+)-neopentyl-1-d alcohol by neutron and x-ray diffraction analysis.

The structure of the [B2H7]– anion, reported by us earlier in an X-ray structure determination, has been analysed more accurately by neutron diffraction. Data were collected at 80 K on a sample of [N(PPh3)2]+[B2H7]–·CH2Cl2 using the Brookhaven High Flux Beam Reactor. The essential results of the X-ray analysis are confirmed, with more accurate molecular parameters. The [B2H7]– anion has a non-crystallographic Cs symmetry, with a bent geometry [B–H–B 127(2)°] and staggered terminal B–H bonds. Average terminal and bridging B–H bond lengths are 1.18(2) and 1.27(6)A respectively, and the B ⋯ B distance is 2.27(1)A. There is a slight asymmetry of the B–H–B bridge [B(1)–H 1.32(2), B(2)–H 1.21(2)A], which is on the borderline of being significant. [N(PPh3)2]+[B2H7]–·CH2Cl2 crystallizes in the triclinic space group P, with a= 9.633(1), b= 10.513(1), c= 16.938(1)A, α= 90.599(7), β= 93.142(8), γ= 93.744(8)°, and Z= 2 at 80 K. The final R factor is 0.096 for the 1 479 reflections with Fo2 > 3σ(Fo2).

Thomas F. Koetzle

Papers

Continuously operating compact 3He-based neutron spin filter

Neutron diffraction study of quinolinic acid recrystallized from D2O: evaluation of temperature and isotope effects in the structure

Deformation electron density of α‐glycylglycine at 82 K. II. The x‐ray diffraction study

Determination of the absolute configuration of (+)-neopentyl-1-d alcohol by neutron and x-ray diffraction analysis.

A neutron diffraction study of [N(PPh3)2]+[B2H7]–·CH2Cl2 at 80 K