A5059576369- Protein Structure and Dynamics
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- Retinoids in leukemia and cellular processes
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Alzheimer's disease research and treatments
- Algal biology and biofuel production
- Lipid Membrane Structure and Behavior
- Mass Spectrometry Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Photosynthetic Processes and Mechanisms
- Prion Diseases and Protein Misfolding
- Biotin and Related Studies
- CRISPR and Genetic Engineering
- Protein Interaction Studies and Fluorescence Analysis
- Amyloidosis: Diagnosis, Treatment, Outcomes
- Public Spaces through Art
- Ubiquitin and proteasome pathways
- Folate and B Vitamins Research
- Force Microscopy Techniques and Applications
- Cellular transport and secretion
- Biochemical and Structural Characterization
- Infant Nutrition and Health
- Studies on Chitinases and Chitosanases
Old Dominion University
2010-2023
University of Oxford
2000-2009
University College London
2006-2009
University of Miami
1998-2003
Centre for Human Genetics
2000
Florida State University
1998
We report the latest release (version 3.0) of CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in number structural domains classified CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with increases diverse homologues being determined by genomics initiatives, more sensitive methods have developed for identifying boundaries multi-domain proteins recognising homologues. The classification update is...
We recently have identified an antigen receptor in sharks called NAR ( n ew or urse shark a ntigen r eceptor) that is secreted by splenocytes but does not associate with Ig light (L) chains. The variable (V) region undergoes high levels of somatic mutation and equally divergent from both T cell receptors (TCR). Here we show electron microscopy V regions, unlike those conventional TCR, do form dimers rather are independent, flexible domains. This unusual feature analogous to bona fide camelid...
Chitinases are prevalent in life and found species including archaea, bacteria, fungi, plants, animals. They break down chitin, which is the second most abundant carbohydrate nature after cellulose. Hence, they important for maintaining a balance between carbon nitrogen trapped as insoluble chitin biomass. classified into two families, 18 19 glycoside hydrolases. In addition to catalytic domain, triosephosphate isomerase barrel, many family chitinases contain another module, i.e., chitinase...
The application of the field network science to scientific disciplines structural biology and biochemistry, have yielded important new insights into nature determinants protein structures, function, dynamics folding process. Advancements in further understanding relationships through also reshaped way we view connectivity proteins universe. canonical hierarchical classification can now be visualized for example, as a fold continuum. This review will survey several key advances expanding area...
Abstract Serum retinol binding protein (RBP) is a member of the lipocalin family, proteins with up‐and‐down β‐barrel folds, low levels sequence identity, and diverse functions. Although tryptophan 24 RBP highly conserved among lipocalins, it does not play direct role in activity. To determine if Trp24 other residues have roles stability and/or folding, we investigated effects conservative substitutions for four tryptophans some adjacent on structure, stability, spectroscopic properties...
This paper explores the structural continuum in CATH and extent to which superfamilies adopt distinct folds. Although most are structurally conserved, some of highly populated (4% all superfamilies) there is considerable divergence. While relatives share a similar fold evolutionary conserved core, diverse elaborations this core can result significant differences global structures. Applying protocols examine overlaps occur between different groups, it appears effect confined just few...
Amyloid fibrils are ordered beta-sheet aggregates that associated with a number of neurodegenerative diseases such as Alzheimer and Parkinson. At present, there is no cure for these progressive debilitating diseases. Here we report initial studies indicate low temperature atmospheric pressure plasma can break amyloid into smaller units in vitro. The was generated by the “plasma pencil,” device capable emitting long, plume/jet. This avenue research may facilitate development plasma-based...
α-Lactalbumins and the type-c lysozymes are homologues with similar folds that differ in function stability. To determine if lower stability of α-lactalbumin results from specific substitutions required for its adaptation to a new function, effects lysozyme-based other on thermal were determined. Unblocking upper cleft by replacing Tyr103 Ala, perturbs structure but Pro, which also generates an open cleft, is compatible normal activity. These appear reflect alternative enthalpic entropic...
We systematically identify a group of evolutionarily conserved residues proposed for folding in model β‐barrel superfamily, the lipocalins. The nature conservation at structural level is defined and we show that are involved network interactions form core fold. Exploratory kinetic studies conducted with superfamily member, human serum retinol‐binding protein, to examine their role. present results, coupled key experimental another lipocalin β‐lactoglobulin, suggest regions fold on faster...
The molten globule state is a partially folded conformer of proteins that has been the focus intense study for more than two decades. This non-native fluctuating conformation linked to protein-folding intermediates, biological function, and recently precursors in amyloid fibril formation. human serum retinol-binding protein (RBP) postulated previously be involved mechanism ligand release (Ptitsyn, O. B., et al. (1993) FEBS Lett. 317, 181−184). Conserved residues within RBP have identified...
Retinol‐binding protein transports retinol, and circulates in the plasma as a macromolecular complex with transthyretin. Under acidic conditions retinol‐binding undergoes transition to molten globule state, releases bound retinol ligand. A biased molecular dynamics simulation method has been used generate models for ensemble of conformers populated within this state. Simulation conformers, radius gyration at least 1.1 Å greater than that native contain on average 37%β‐sheet secondary...
Backbone (15)N relaxation parameters and (15)N-(1)H(N) residual dipolar couplings (RDCs) have been measured for a variant of human alpha-lactalbumin (alpha-LA) in 4, 6, 8 10 M urea. In the alpha-LA variant, eight cysteine residues protein replaced by alanines (all-Ala alpha-LA). This is partially folded molten globule at pH 2 has shown previously to unfold stepwise non-cooperative manner on addition R(2) values some regions all-Ala show significant exchange broadening which reduced as urea...
The protein folding process has been studied both computationally and experimentally for over 30 years. To date there is no detailed mechanism to explain the formation of long‐range interactions between transition native states. Long‐range are principle determinants tertiary structure. We present a theoretical model which proposes acquisition these as they form in modified version ‘degrees separation’, that we term ‘levels separation’. It based on integration network science biochemistry.
The B1 domain of protein G (GB1) is a small, 56 amino acid bacterial immunoglobulin-binding with 4β + α fold. Architecturally, it composed two-layer sandwich consisting four-stranded β-sheet that packs against an α-helix. Using several bioinformatics approaches, we investigated which residues may be key determinants this We identified nine structurally conserved acids using conservation analysis and propose they are critical to forming stabilizing the form predominantly hydrophobic nucleus...
Abstract Two proteins within the β‐grasp superfamily, B1‐domain of protein G and small archaeal modifier 1, were investigated to elucidate key determinants structural stability at level individual interactions. These symmetrical both contain two β‐hairpins which form a sheet flanked by central α‐helix. They subjected high temperature molecular dynamics simulations detailed behavior each long‐range interaction was characterized. The results revealed that in GB1 most stable region C‐terminal...