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10.1002/prot.22160.abs Cystalysin, a dimeric pyridoxal 5′‐phosphate (PLP)‐dependent lyase, is a virulence factor of the human oral pathogen Treponema denticola. Guided by bioinformatic analysis, two interfacial residues (Leu57 and Leu62) and an active site residue (Tyr64*),...
10.1002/prot.22154.abs The use of predicted binding sites (binding sites calculated from the protein structure alone) is evaluated here as a tool to focus the docking of small molecule ligands into protein structures, simulating cases where the real binding sites are unknown. The resulting...
10.1002/prot.22155.abs The mechanism by which proteins fold from an initially random conformation into a functional, native structure remains a major unsolved question in molecular biology. Of particular interest to the protein folding community is the structure that the protein adopts in the...
10.1002/prot.22149.abs A molecular model of the acidic compact state of apomyoglobin (A‐state) from yellowfin tuna was obtained using molecular dynamics simulations (MD) by calculating multiple trajectories. To cause partial unfolding within a reasonable amount of CPU time, both an acidic...
10.1002/prot.22165.abs The N‐terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight‐stranded antiparallel β‐barrel domain that folds into a membrane channel with low conductance. The structure of this protein has been modeled after the...
10.1002/prot.22156.abs Cystatins, a family of structurally related cysteine proteinase inhibitors, have proved to be useful model system to study amyloidogenesis. We have extended previous studies of the kinetics of amyloid‐fibril formation by human stefin B (cystatin B) and some of its...
10.1002/prot.22164.abs We present machine learning approaches for turn prediction from the amino acid sequence. Different turn classes and types were considered based on a novel turn classification scheme. We trained an unsupervised (self‐organizing map) and two kernel‐based classifiers,...
10.1002/prot.22161.abs Studies of protein folding indicate the presence of native contacts in the denatured state, giving rise to folding elements which contribute to the accomplishment of the native state. The possibility of finding molecules which can interact with specific folding elements of...
10.1002/prot.22162.abs The activity and cooperativity of Escherichia coli aspartate transcarbamoylase (ATCase) vary as a function of pH, with a maximum of both parameters at approximately pH 8.3. Here we report the first X‐ray structure of unliganded ATCase at pH 8.5, to establish a structural...
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