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Journal Issue - Volume 18 Issue 9 (September 2009)

  • In this issue

  • Published in Wiley Interscience on Aug 20, 2009
  • DOI: 10.1002/pro.222 (p n/a-n/a)

Abstract The molecular chaperone, Hsp90, is an essential eukaryotic protein that assists in the maturation and activation of client proteins. Hsp90 function depends upon the binding and hydrolysis of ATP, which causes large conformational rearrangements in the chaperone. Hsp90 is highly conserved from bacteria to eukaryotes, and similar nucleotide‐dependent conformations have been demonstrated for the bacterial, yeast, and human...

Abstract Elucidating the structures of membrane proteins is essential to our understanding of disease states and a critical component in the rational design of drugs. Structural characterization of a membrane protein begins with its detergent solubilization from the lipid bilayer and its purification within a functionally stable protein‐detergent complex (PDC). Crystallization of the PDC typically occurs by changing the solution...

Abstract The relation of α‐synuclein (αS) aggregation to Parkinson's disease has long been recognized, but the pathogenic species and its molecular properties have yet to be identified. To obtain insight into the properties of αS in an aggregation‐prone state, we studied the structural properties of αS at acidic pH using NMR spectroscopy and computation. NMR demonstrated that αS remains natively unfolded at lower pH, but secondary...

Abstract 5‐Aminolevulinate synthase (ALAS) controls the rate‐limiting step of heme biosynthesis in mammals by catalyzing the condensation of succinyl‐coenzyme A and glycine to produce 5‐aminolevulinate, coenzyme‐A (CoA), and carbon dioxide. ALAS is a member of the α‐oxoamine synthase family of pyridoxal 5′‐phosphate (PLP)‐dependent enzymes and shares high degree of structural similarity and reaction mechanism with the other members...

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Abstract SecB, a remarkable chaperone involved in protein export, binds diverse ligands rapidly with high affinity and low specificity. Site‐directed spin labeling and electron paramagnetic resonance spectroscopy were used to investigate the surface of interaction on the export chaperone SecB. We examined SecB in complex with the unfolded precursor form of outer membrane protein OmpA as well as with a truncated version of OmpA that...

Abstract Proteolytically activated Protective Antigen (PA) moiety of anthrax toxin self‐associates to form a heptameric ring‐shaped oligomer (the prepore). Acidic pH within the endosome converts the prepore to a pore that serves as a passageway for the toxin's enzymatic moieties to cross the endosomal membrane. Prepore is stable in solution under mildly basic conditions, and lowering the pH promotes a conformational transition to an...

Abstract The Antigen I/II (AgI/II) family of proteins are cell wall anchored adhesins expressed on the surface of oral streptococci. The AgI/II proteins interact with molecules on other bacteria, on the surface of host cells, and with salivary proteins. Streptococcus gordonii is a commensal bacterium, and one of the primary colonizers that initiate the formation of the oral biofilm. S. gordonii expresses two AgI/II proteins, SspA and SspB that are closely...

Abstract Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this...

Abstract The bundling of the N‐terminal, partial domain helix (Helix C′) of human erythroid α‐spectrin (αI) with the C‐terminal, partial domain helices (Helices A′ and B′) of erythroid β‐spectrin (βI) to give a spectrin pseudo structural domain (triple helical bundle A′B′C′) has long been recognized as a crucial step in forming functional spectrin tetramers in erythrocytes. We have used apparent polarity and Stern–Volmer quenching...

Abstract Despite the critical importance of molecular specificity in bimolecular systems, in vitro display technologies have been applied extensively for affinity maturation of peptides and antibodies without explicitly measuring the specificity of the desired interaction. We devised a general strategy to measure, screen, and evolve specificity of protein ligand interactions analogous to widely used affinity maturation strategies. The...

Abstract The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesive protein, TgMIC1, to bind to a wide spectrum of sialyl oligosaccharide ligands. Here, we investigate by further microarray analyses in a dose‐response format the differential binding of...

Abstract Terminal deletions of units from α‐helical repeat proteins have provided insight into the physical origins of their cooperativity. To test if the same principles governing cooperativity apply to β‐sheet‐containing repeat proteins, we have created a series of C‐terminal deletion constructs from a large leucine‐rich repeat (LRR) protein, YopM. We have examined the structure and stability of the resulting deletion constructs...

Abstract Identification and characterization of recurrent supersecondary structural elements is central to understanding the rules governing protein tertiary structure. Here, we describe the GD box, a widespread noncontiguous supersecondary element, which we initially found in a group of topologically distinct but homologous β‐barrels—the cradle‐loop barrels. The GD box is similar both in sequence and structure and comprises two...

Abstract There has been growing interest in polyproline type II (PPII) helices since PPII helices have been found in folded and unfolded proteins and involved in a variety of biological activities. Polyproline can also form type I helices (PPI) which are very different from PPII conformation and only exist in certain organic solvents. Recent studies have shown that stereoelectronic effects play a critical role in stabilizing a PPI...

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