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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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