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Journal Issue - Volume 16 Issue 11 (November 2007)

Abstract The phenomena of protein reconstitution and three‐dimensional domain swapping reveal that highly similar structures can be obtained whether a protein is comprised of one or more polypeptide chains. In this review, we use protein reconstitution as a lens through which to examine the range of protein tolerance to chain interruptions and the roles of the primary structure in related features of protein structure and folding,...

Abstract Amyloid formation typically follows a time course in which there is a long lag period followed by a rapid formation of fibrils. In this review, I show that the standard mechanisms of polymerization need to be expanded to consider that the monomeric proteins/peptides involved in amyloid formation are intrinsically disordered and exist as an ensemble of disordered‐collapsed states. The review focuses primarily on events which...

Abstract For the first time, 15N solid‐state NMR experiments were conducted on wild‐type phospholamban (WT‐PLB) embedded inside mechanically oriented phospholipid bilayers to investigate the topology of its cytoplasmic and transmembrane domains. 15N solid‐state NMR spectra of site‐specific 15N‐labeled WT‐PLB indicate that the transmembrane domain has a tilt angle of 13° ± 6° with respect to the POPC (1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐phosphocholine) ...

Abstract Periplasmic expression screening is a selection technique used to enrich high‐affinity proteins in Escherichia coli. We report using this screening method to rapidly select a mutated D‐glucose/D‐galactose‐binding protein (GGBP) having low affinity to glucose. Wild‐type GGBP has an equilibrium dissociation constant of 0.2 μM and mediates the transport of glucose within the periplasm of E. coli. The protein undergoes a large...

Abstract The ability to rationally increase the stability and solubility of recombinant proteins has long been a goal of biotechnology and has significant implications for biomedical research. Poorly soluble enzymes, for example, result in the need for larger reaction volumes, longer incubation times, and more restricted reaction conditions, all of which increase the cost and have a negative impact on the feasibility of the process....

Abstract Narrow substrate specificities often limit the use of enzymes in biocatalysis. To further the development of Escherichia coli 2‐keto‐3‐deoxy‐6‐phosphogluconate (KDPG) aldolase as a biocatalyst, the molecular determinants of substrate specificity were probed by mutagenesis. Our data demonstrate that S184 is located in the substrate‐binding pocket and interacts with the phosphate moiety of KDPG, providing biochemical support for the...

Abstract The ability to determine conformational parameters of protein‐folding landscapes is critical for understanding the link between conformation, function, and disease. Monitoring hydrogen exchange (HX) of labile protons at equilibrium enables direct extraction of thermodynamic or kinetic landscape parameters in two limiting extremes. Here, we establish a quantitative framework for relating HX behavior to landscape. We use this...

Abstract The S. typhimurium genome encodes proteins, designated EngA and YhbZ, which have a high sequence identity with the GTPases EngA/Der and ObgE/CgtAE of Escherichia coli. The wild‐type activity of the E. coli proteins is essential for normal ribosome maturation and cell viability. In order to characterize the potential involvement of the Salmonella typhimurium EngA and YhbZ proteins in ribosome biology, we used high stringency affinity chromatography...

Abstract Serpins inhibit serine proteases by mechanically disrupting the protease active site. The protease first reacts with the serpin's reactive center loop (RCL) to form an acylenzyme. Then the RCL inserts into a β‐sheet in the body of the serpin, translocating the attached protease ∼70 Å and deforming the protease active site, thereby trapping the acylenzyme. Loop insertion (∼1 s−1) is an order of magnitude slower than hydrolysis of a...

Abstract Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model...

Abstract The transparency of the eye lens depends on the high solubility and stability of the lens crystallin proteins. The monomeric γ‐crystallins and oligomeric β‐crystallins have paired homologous double Greek key domains, presumably evolved through gene duplication and fusion. Prior investigation of the refolding of human γD‐crystallin revealed that the C‐terminal domain folds first and nucleates the folding of the N‐terminal...

Abstract The Escherichiacoli Cpx envelope stress system is comprised of three proteins; the periplasmic regulatory CpxP, the inner membrane sensor kinase CpxA, and the cytoplasmic transcriptional activator CpxR. Although misfolded envelope proteins activate the Cpx system, the molecular mechanism by which this signal is sensed remains largely unknown. In an attempt to reconstitute the Cpx system from purified proteins, we failed to...

Abstract High‐temperature requirement A (HtrA) and its homologs contain a serine protease domain followed by one or two PDZ domains. Bacterial HtrA proteins and the mitochondrial protein HtrA2/Omi maintain cell function by acting as both molecular chaperones and proteases to manage misfolded proteins. The biological roles of the mammalian family members HtrA1 and HtrA3 are less clear. We report a detailed structural and functional...

Abstract The process of experimental determination of protein structure is marred with a high ratio of failures at many stages. With availability of large quantities of data from high‐throughput structure determination in structural genomics centers, we can now learn to recognize protein features correlated with failures; thus, we can recognize proteins more likely to succeed and eventually learn how to modify those that are less...

Abstract The arsH gene or its homologs are a frequent part of the arsenic resistance system in bacteria and eukaryotes. Although a specific biological function of the gene product is unknown, the ArsH protein was annotated as a member of the NADPH‐dependent FMN reductase family based on a conserved (T/S)XRXXSX(T/S) fingerprint motif common for FMN binding proteins. Presented here are the first crystal structure of an ArsH protein...

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