A5014217022- Enzyme Structure and Function
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Enzyme Production and Characterization
- Chemical Synthesis and Analysis
- Crystallography and molecular interactions
- Advanced Chemical Physics Studies
- X-ray Diffraction in Crystallography
- Microbial Applications in Construction Materials
- Computational Drug Discovery Methods
- Glycosylation and Glycoproteins Research
- Advanced Control Systems Optimization
- Porphyrin Metabolism and Disorders
- Bacteriophages and microbial interactions
- Genomics and Chromatin Dynamics
- Quantum, superfluid, helium dynamics
- SARS-CoV-2 and COVID-19 Research
- Fault Detection and Control Systems
- Microbial Metabolic Engineering and Bioproduction
- Hemoglobin structure and function
- Spectroscopy and Quantum Chemical Studies
- Mass Spectrometry Techniques and Applications
- Electron and X-Ray Spectroscopy Techniques
- Advanced X-ray Imaging Techniques
University of Oregon
1992-2024
Oregon State University
2011-2022
Howard Hughes Medical Institute
1993-2012
Institute of Molecular Biology
1987
A package of programs has been developed for efficient restrained least-squares refinement macromolecular crystal structures. The designed to be as flexible and general purpose possible. process is divided into basic units an independent computer program handles each task. Each functional unit communicates with other in the by way files well defined format. To modify or replace any program, user need only understand function that particular element. Stereochemical restraints are a can...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSlow- and fast-binding inhibitors of thermolysin display different modes binding: crystallographic analysis extended phosphonamidate transition-state analogsHazel M. Holden, Dale E. Tronrud, Arthur F. Monzingo, Larry H. Weaver, Brian W. MatthewsCite this: Biochemistry 1987, 26, 8542–8553Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December...
Abstract The unrefined fold of Escherichia coli β‐galactosidase based on a monoclinic crystal form with four independent tetramers has been reported previously. Here, we describe new, orthorhombic one tetramer per asymmetric unit that permitted refinement the structure at 1.7 Å resolution. This high‐resolution analysis confirmed original description and revealed new details. An essential magnesium ion, identified active site in crystals, is also seen form. Additional putative binding sites...
A novel method of function minimization that combines the power diagonal approximation to normal matrix with conjugate directions is described. This approaches closer local minimum than methods are commonly used in macromolecular refinement. The weaknesses current analyzed explain advantage conjugate-direction method.
The mode of binding to thermolysin the ester analog Cbz-GlyP-(O)-Leu-Leu has been determined by x-ray crystallography and shown be virtually identical (maximum difference 0.2 angstrom) with corresponding peptide Cbz-GlyP-(NH)-Leu-Leu. two inhibitors provide a matched pair enzyme-inhibitor complexes that differ 4.1 kilocalories per mole in intrinsic energy but are essentially except for presence or absence specific hydrogen bond.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysisD. R. Holland, D. E. Tronrud, H. W. Pley, K. M. Flaherty, Stark, J. N. Jansonius, B. McKay, MatthewsCite this: Biochemistry 1992, 31, 46, 11310–11316Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November...
The mode of binding to thermolysin the unsubstituted phosphoramidate inhibitor N-phosphoryl-L-leucinamide (P-Leu-NH2) has been determined crystallographically and refined at high resolution (R= 17.9% 0.16-nm resolution). naturally occurring phosphoramidon reported previously [Weaver, L. H., Kester, W. R. Matthews, B. (1977) J. Mol. Biol. 114, 119–132] also confirmed by crystallographic refinement 17.4% 0.23-nm Phosphoramidon binds enzyme with a single oxygen moiety as zinc ligand. Together...
A new type of restraint for the B factors atoms in low- to-moderate resolution models proteins is proposed. This incorporates knowledge that two bonded to each other may be systemically different. In addition, some pairs will more consistent from structure than others. With use B-factor restraints this type, it possible construct whose are with accurately known protein structures, even though only low-resolution crystallographic data available.
Helicobacter mustelae , a gastric pathogen of ferrets, synthesizes distinct iron-dependent urease in addition to its archetypical nickel-containing enzyme. The iron-urease is oxygen-labile, with the inactive protein exhibiting methemerythrin-like electronic spectrum. Significantly, incubation oxidized dithionite under anaerobic conditions leads restoration activity and bleaching Structural analysis species reveals dinuclear iron metallocenter bridged by lysine carbamate, closely resembling...
Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional have shortcomings, it has previously been documented using backbone depend on the conformation helps address these shortcomings and improves performance refinements [Moriarty et al. (2014), FEBS J. 281, 4061-4071]. It is important improvements be made available all in crystallography community. Toward this end, change default geometry library used by...
Abstract It was previously shown that the two replacements Gly 77 ↠ Ala (G77A) and 82 Pro (A82P) increase thermostability of phage T4 lysozyme at pH 6.5. Such are presumed to restrict degrees freedom unfolded protein so decrease entropy unfolding [B. W. Matthews, H. Nicholson, J. Becktel (1987) Proceedings National Academy Science USA Vol. 84, pp. 6663–6667]. To further test this approach, three additional replacements—G113A, K60P A93P— have been constructed. On basis model building, each...
Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement protein crystal structures at all but highest resolutions. The in common use today have been designed on assumption that each type or angle has a single ideal value is independent context. However, recent work shown are, fact, sensitive to local conformation, and, first step towards using such information build more accurate models, ultra-high-resolution derive conformation-dependent...
ADVERTISEMENT RETURN TO ISSUEPREVArticleStructural analysis of the inhibition thermolysin by an active-site-directed irreversible inhibitorM. A. Holmes, D. E. Tronrud, and B. W. MatthewsCite this: Biochemistry 1983, 22, 1, 236–240Publication Date (Print):January 4, 1983Publication History Published online1 May 2002Published inissue 4 January 1983https://doi.org/10.1021/bi00270a034RIGHTS & PERMISSIONSArticle Views158Altmetric-Citations41LEARN ABOUT THESE METRICSArticle Views are...
The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray proteins not consistent with this concept ideality and have been used develop a library main-chain bond lengths angles parameterized by the phi/psi angle residue [Berkholz et al. (2009), Structure, 17, 1316-1325]. Here, it is first shown new conformation-dependent does suffer from...
The process of refinement is such a large problem in function minimization that even the computers today cannot perform calculations to properly fit X-ray diffraction data. Each packages currently under development reduces difficulty this by utilizing unique combination targets, assumptions and optimization methods. This review summarizes basic methods underlying commonly used packages. information can guide selection package best suited for particular project.
To utilize a new conformation-dependent backbone-geometry library (CDL) in protein refinements at atomic resolution, script was written that creates restraint file for the SHELXL refinement program. It found use of this allows models to be created have substantially better fit main-chain bond angles and lengths without degrading their X-ray data even resolutions near 1 Å. For much higher resolution (∼0.7 Å), refined model parts adopting single well occupied positions is largely independent...