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J A Rullmann

Publications and source records attributed to J A Rullmann.

8 recordsLinked to original sources
PubMed1998

Quality assessment of NMR structures: a statistical survey.

A statistical analysis is reported of experimental data and coordinates of a set of 97 NMR structures deposited in the PDB. The aim is to assess the quality of these structures in relation to the amount of experimental information. Experimental restraints were analysed using the program AQUA. Many nomenclature inconsistencies between deposited restraint and coordinate files were observed. The experimental restraint files were found to contain a high proportion of redundant restraints. Procedures for analysing and correcting the inconsistencies and restraint counts are described. The analysis of NOE restraint violations (using AQUA) and of a wide variety of geometrical quality indicators (using PROCHECK-NMR and WHAT IF) provides a reference for other NMR structure determinations. The extent of NOE violations is anti-correlated with the quality of the Ramachandran map. The precision as measured by the circular variance of backbone dihedral angles, does increase with the amount of experimental data, as expected, but is sometimes overestimated. Bond lengths, bond angles and planarity of groups can deviate considerably from ideal values. Outliers appear to cluster per laboratory, indicating that the results depend on particulars of refinement protocols and/or software. We have identified a problem of atom overlap in a number of refined structures.We recommend adhering to the standard nomenclature as put forward by an IUPAC Task Group, to ensure consistency between restraints and coordinates, and to omit redundant restraints from the deposition. The results obtained from this analysis and the AQUA program are available through the World Wide Web.

Databases, Factual↗
PubMed1996

Solution structure of the immunodominant region of protein G of bovine respiratory syncytial virus.

The three-dimensional solution structure of the immunodominant central conserved region of the attachment protein G (BRSV-G) of bovine respiratory syncytial virus has been determined by nuclear magnetic resonance (NMR) spectroscopy. In the 32-residue peptide studied, 19 residues form a small rigid core composed of two short helices, connected by a type I' turn, and linked by two disulfide bridges. This unique fold is among the smallest stable tertiary structures known and could therefore serve as an ideal building block for the design of de novo proteins and as a test case for modeling studies. A characteristic hydrophobic pocket, lined by conserved residues, lies at the surface of the peptide and may play a role in receptor binding. This work provides a structural basis for further peptide vaccine development against the severe diseases associated with the respiratory syncytial viruses in both cattle and man.

Amino Acid Sequence↗
PubMed1993

Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics.

The structure of the complex of lac repressor headpiece and an 11 base-pair lac half-operator has been determined by NMR spectroscopy and restrained Molecular Dynamics calculations. In total 508 distances were derived from two-dimensional nuclear Overhauser enhancement measurements, 260 of which are within the headpiece, 212 within the operator and 36 between operator and headpiece. An equilibrium restrained Molecular Dynamics calculation of the complex in aqueous solution, spanning 85 picoseconds, has been used to analyze the structure. Configuration sampling by an annealing procedure has been undertaken as well in order to estimate the precision of the structure determination. Our data confirm the results of previous two-dimensional NMR studies that the orientation of the recognition helix of lac repressor in the major groove of DNA with respect to the operator dyad axis is opposite to the orientation found in complexes of other DNA binding proteins of the helix-turn-helix class. We find a number of tight contacts between the protein and the operator that are in agreement with the available genetic and biochemical data. The anchoring of lac headpiece on the operator is similar to that of other repressors. Other features are unique for lac headpiece: relative few direct hydrogen bonds between side-chains and bases; extensive apolar contacts; many direct and water-bridged contacts to phosphates from residues in or close to the recognition helix. Overall, an interconnected set of interactions is observed, involving base-specific contacts, phosphate contacts, intra-protein and water-bridged hydrogen bonds. Several of these interactions appear to be dynamic, i.e. fluctuating in time, rather than static.

Amino Acid Sequence↗
PubMed1993

"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.

The structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA) together with distance geometry, distance bound driven dynamics, molecular dynamics, and energy minimization. A new protocol based on an "ensemble" approach is proposed and compared to the more standard initial rate analysis approach and a "single structure" relaxation matrix approach. The effects of fast local motions are included and R-factor calculations are performed on NOE build-ups to describe the quality of agreement between theory and experiment. A new method for stereospecific assignment of prochiral groups, based on a comparison of theoretical and experimental NOE intensities, has been applied. The solution structure of crambin could be determined with a precision (rmsd from the average structure) of 0.7 A on backbone atoms and 1.1 A on all heavy atoms and is largely similar to the crystal structure with a small difference observed in the position of the side chain of Tyr-29 which is determined in solution by both J-coupling and NOE data. Regions of higher structural variability (suggesting higher mobility) are found in the solution structure, in particular for the loop between the two helices (Gly-20 to Pro-22).

Amino Acid Sequence↗
PubMed1990

Two-dimensional NMR study of a protein-DNA complex. lac repressor headpiece-operator interaction.

The interaction of the N-terminal DNA-binding domain (56 amino acid residues) of the lac repressor with lac operator DNA was analyzed using two-dimensional NMR spectroscopy. Both half-operators (11 and 14 bp) and a complete fully symmetric 22 bp operator were studied. Two-dimensional nuclear Overhauser effect (2D NOE) spectra of headpiece-operator complexes were taken in both D2O and H2O solutions. Special attention was given to the problem of 1H resonance assignments. Based on an analysis of the proton-proton NOEs, a model for the headpiece-operator complex could be derived. In this model, most of the protein-DNA contracts occur between amino acid residues in the second helix (recognition helix) of the lac headpiece and DNA bases in the major groove. The orientation of this helix with respect to the dyad axis of the operator is opposite to that found in the X-ray structures of several other repressor-operator complexes.

Base Composition↗
PubMed1989

The active site of papain. All-atom study of interactions with protein matrix and solvent.

The proton transfer between the Cys25 and His159 residues in the active centre of the proteolytic enzyme papain is investigated with the Hartree-Fock SCF direct reaction field method. The active centre is treated quantum mechanically, while the environment is represented by interacting partial charges and polarizabilities. All protein atoms around the active site are included explicitly in the calculations. In this way a complete description is given of both the electrostatic and the dielectric properties of the enzyme. The protein matrix stabilizes the zwitterionic form of Cys-His, which is thought to be the catalytically active state much more than the neutral configuration. The most important contribution to the stabilization comes from the alpha-helix to which Cys25 is attached; more than half of its effect is due to the backbone atoms of Cys25 itself. Other important factors are the Asn175 side-chain and the solvent. Solvent effects are estimated by means of Monte Carlo calculations of crystal water molecules that are located near the active site. The total energies of the neutral and zwitterionic structures are similar, confirming the idea that a zwitterion can exist in the active centre of papain. The energy difference, however, is sensitive to the geometry of the active site, suggesting that the two structures are in thermal equilibrium. Classical analogues of the quantum mechanical interaction energy, employing point charge representations of the active site, are found to be quite useful. The dielectric behaviour of the protein is much more complicated than is implicated in dielectric constant models; force fields that do not include an atomic level representation of electronic polarization are inadequate.

Animals↗
PubMed1988

The interaction of lac repressor headpiece with its operator: an NMR view.

Analysis of nuclear Overhauser enhancements in two-dimensional NMR spectra of the complex of lac repressor headpiece with a 14 base pair lac operator fragment shows that the second helix of the headpiece binds in the major groove of DNA, as has been suggested. The orientation of this helix is approximately 180 degrees different from the proposed models and from that found in the X-ray structure of the 434 repressor-operator complex. The model of the lac headpiece-operator complex provides a good explanation for a large amount of biochemical, genetic and physical data.

Amino Acid Sequence↗