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Modeling of the OX1R–orexin-A complex suggests two alternative binding modes
Springer Science and Business Media LLC - Tập 15 - Trang 1-17 - 2015
Interactions between the orexin peptides and their cognate OX1 and OX2 receptors remain poorly characterized. Site-directed mutagenesis studies on orexin peptides and receptors have indicated amino acids important for ligand binding and receptor activation. However, a better understanding of specific pairwise interactions would benefit small molecule discovery. We constructed a set of three-dimens......
Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method
Springer Science and Business Media LLC - Tập 13 - Trang 1-22 - 2013
Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model ......
Computational identification of residues that modulate voltage sensitivity of voltage-gated potassium channels
Springer Science and Business Media LLC - Tập 5 - Trang 1-17 - 2005
Studies of the structure-function relationship in proteins for which no 3D structure is available are often based on inspection of multiple sequence alignments. Many functionally important residues of proteins can be identified because they are conserved during evolution. However, residues that vary can also be critically important if their variation is responsible for diversity of protein functio......
ProteinShader: illustrative rendering of macromolecules
Springer Science and Business Media LLC - Tập 9 - Trang 1-19 - 2009
Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings. The ProteinShader program, a new tool for macromolecular visualization, uses information from Protein Data Bank files to prod......
Improving consensus structure by eliminating averaging artifacts
Springer Science and Business Media LLC - Tập 9 - Trang 1-9 - 2009
Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, inclu......
Amyloidogenic determinants are usually not buried
Springer Science and Business Media LLC - Tập 9 - Trang 1-9 - 2009
Amyloidoses are a group of usually fatal diseases, probably caused by protein misfolding and subsequent aggregation into amyloid fibrillar deposits. The mechanisms involved in amyloid fibril formation are largely unknown and are the subject of current, intensive research. In an attempt to identify possible amyloidogenic regions in proteins for further experimental investigation, we have developed ......
Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies
Springer Science and Business Media LLC - Tập 7 - Trang 1-14 - 2007
Fungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-N-acetylhexosaminidase. The fungal β-N-acetylhexosamini......
Structural and functional characterisation of the methionine adenosyltransferase from Thermococcus kodakarensis
Springer Science and Business Media LLC - Tập 13 - Trang 1-10 - 2013
Methionine adenosyltransferases catalyse the synthesis of S-adenosylmethionine, a cofactor abundant in all domains of life. In contrast to the enzymes from bacteria and eukarya that show high sequence similarity, methionine adenosyltransferases from archaea diverge on the amino acid sequence level and only few conserved residues are retained. We describe the initial characterisation and the crysta......
Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case study
Springer Science and Business Media LLC - - 2009
Structure-based drug design (SBDD) can provide valuable guidance to drug discovery programs. Robust construct design and expression, protein purification and characterization, protein crystallization, and high-resolution diffraction are all needed for rapid, iterative inhibitor design. We describe here robust methods to support SBDD on an oral anti-cytokine drug target, human MAPKAP kinase 2 (MK2)......
Analysis of the unique structural and physicochemical properties of the DraD/AfaD invasin in the context of its belonging to the family of chaperone/usher type fimbrial subunits
Springer Science and Business Media LLC - Tập 11 Số 1 - Trang 25 - 2011
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