Mitsuo Tasumi

Bio: Mitsuo Tasumi is an academic researcher from University of Tokyo. The author has contributed to research in topics: Raman spectroscopy & Infrared spectroscopy. The author has an hindex of 50, co-authored 291 publications receiving 19478 citations. Previous affiliations of Mitsuo Tasumi include Saitama University.

The Protein Data Bank. A computer-based archival file for macromolecular structures.

Abstract: The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. alpha-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.

Model calculations on the amide‐I infrared bands of globular proteins

Abstract: Model calculations are performed on the amide‐I infrared (ir) bands of globular proteins by assigning one oscillator with a transition dipole to each peptide group. Coupling between these oscillators is introduced through the transition dipole coupling mechanism. As examples of application of the model, the ir spectra in the amide‐I region of eight representative proteins, viz., carbonmonoxy myoglobin, ribonuclease A, α‐lactalbumin, lysozyme, flavodoxin, carboxypeptidase A, concanavalin A, and β‐trypsin are calculated. Good agreement is obtained between the calculated and observed amide‐I band envelopes. Some structure‐spectrum correlations are discussed on the basis of the model calculations. The presence of bands with significant ir intensities for myoglobin in the region below 1640 cm−1 is consistent with its x‐ray structure having no β sheet. Analysis of the contributions of β sheets to the amide‐I band envelopes shows that parallel, antiparallel, and mixed parallel/antiparallel β sheets give rise to strong ir bands at a similar position in the wave number region below 1650 cm−1, and that no band in the region above 1650 cm−1 can be regarded as a reliable marker of antiparallel β sheets. The contributions of non‐α‐non‐β parts spread over a wide wave number region. The differences in the amide‐I band envelopes between α‐lactalbumin and lysozyme originate most probably from the structural differences between the α‐helical parts near the N termini of these proteins.

Correlation between the Vibrational Frequencies of the Carboxylate Group and the Types of Its Coordination to a Metal Ion: An ab Initio Molecular Orbital Study

Abstract: The structures and vibrational frequencies of the acetate ion interacting with a metal ion (Na+, Mg2+, and Ca2+) in the unidentate, bidentate, bridging, and pseudobridging forms are studied by ab initio molecular orbital calculations. Effects of a water molecule coordinating to either the acetate ion or the metal ion are also examined. The calculations are carried out by using the self-consistent reaction field method at the Hartree−Fock level with the 6-31+G** basis set. For the species interacting with a divalent metal cation, the lengths of the two CO bonds of the acetate ion are nearly equal in the bidentate form but are significantly different in the unidentate form. The frequency of the COO- antisymmetric stretch of the unidentate species is higher than that of the ionic species, which is in turn higher than that of the bidentate species. The reverse is the case for the COO- symmetric stretch. As a result, the frequency separations (Δνa-s) between the COO- antisymmetric and symmetric stretches for t...

The Protein Data Bank

Abstract: 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.

Features and development of Coot.

Abstract: 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.

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

Abstract: 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.

The Pfam protein families database

Abstract: 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/).