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Journal Issue - Volume 13 Issue 12 (December 2004)

Abstract Fructose‐1,6‐(bis)phosphate aldolase is a ubiquitous enzyme that catalyzes the reversible aldol cleavage of fructose‐1,6‐(bis)phosphate and fructose 1‐phosphate to dihydroxyacetone phosphate and either glyceral‐dehyde‐3‐phosphate or glyceraldehyde, respectively. Vertebrate aldolases exist as three isozymes with different tissue distributions and kinetics: aldolase A (muscle and red blood cell), aldolase B (liver, kidney,...

Abstract The refolding of barstar from its urea‐unfolded state has been studied extensively using various spectroscopic probes and real‐time NMR, which provide global and residue‐specific information, respectively, about the folding process. Here, a preliminary structural characterization by NMR of barstar in 8 M urea has been carried out at pH 6.5 and 25°C. Complete backbone resonance assignments of the urea‐unfolded protein were...

Abstract Computational conformational searches of putative transition states of the reaction of sucrose with vinyl laurate catalyzed by lipases from Candida antarctica B and Thermomyces lanuginosus have been carried out. The dielectric of the media have been varied to understand the role of protein plasticity in modulating the observed regioselective transesterification. The binding pocket of lipase from Candida adapts to the conformational...

Abstract Infrequent structural fluctuations of a globular protein is seldom detected and studied in detail. One tyrosine ring of HPr from Staphylococcus carnosus, an 88‐residue phosphocarrier protein with no disulfide bonds, undergoes a very slow ring flip, the pressure and temperature dependence of which is studied in detail using the on‐line cell high‐pressure nuclear magnetic resonance technique in the pressure range from 3 MPa...

Abstract The classical Zn finger contains a phenylalanine at the crux of its three architectural elements: a β‐hairpin, an α‐helix, and a Zn2+‐binding site. Surprisingly, phenylalanine is not required for high‐affinity Zn2+ binding, but instead contributes to the specification of a precise DNA‐binding surface. Substitution of phenylalanine by leucine leads to a floppy but native‐like structure whose Zn affinity is maintained by marked...

Abstract NmrA is a negative transcription‐regulating protein that binds to the C‐terminal region of the GATA transcription‐activating protein AreA. The proposed molecular mechanism of action for NmrA is to inhibit AreA binding to its target promoters. In contrast to this proposal, we report that a C‐terminal fragment of AreA can bind individually to GATA‐containing DNA and NmrA and that in the presence of a mixture of...

Abstract α‐Chymotrypsin undergoes a reversible conformational change from an inactive chymotrypsinogen‐like structure at high pH to an active conformation at neutral pH. In order to gain insight into this process on a structural level, we applied molecular dynamics and targeted molecular dynamics simulations in aqueous environment on the activation and inactivation processes of three different types of chymotrypsin. These are the...

Abstract The conformational conversion of the nonpathogenic “cellular” prion isoform into a pathogenic “scrapie” protease‐resistant isoform is a fundamental event in the onset of transmissible spongiform encephalopathies (TSE). During this pathogenic conversion, helix H1 and its two flanking loops of the normal prion protein are thought to undergo a conformational transition into a β‐like structure. A peptide spanning helix H1 and...

Abstract NAD+‐dependent glycerol‐3‐phosphate dehydrogenase (G3PDH) is generally absent in archaea, because archaea, unlike eukaryotes and eubacteria, utilize glycerol‐1‐phosphate instead of glycerol‐3‐phosphate for the biosynthesis of membrane lipids. Surprisingly, the genome of the hyperthermophilic archaeon Archaeoglobus fulgidus comprises a G3PDH ortholog, gpsA, most likely due to horizontal gene transfer from a eubacterial organism....

Abstract Sequence profile and fold recognition methods identified mammalian purple acid phosphatase (PAP), a member of a dimetal‐containing phosphoesterase (DMP) family, as a remote homolog of human acid sphingomyelinase (ASM). A model of the phosphoesterase domain of ASM was built based on its predicted secondary structure and the metal‐coordinating residues of PAP. Due to the low sequence identity between ASM and PAP (∼15%), the...

Abstract The structure of two Thermotoga maritima proteins, a conserved hypothetical protein (TM0160) and a transcriptional regulator (TM1171), have now been determined at 1.9 Å and 2.3 Å resolution, respectively, as part of a large‐scale structural genomics project. Our first efforts to crystallize full‐length versions of these targets were unsuccessful. However, analysis of the recombinant purified proteins using the technique of...

Abstract Family GH16 glycoside hydrolases can be assigned to five subgroups according to their substrate specificities, including xyloglucan transglucosylases/hydrolases (XTHs), (1,3)‐β‐galactanases, (1,4)‐β‐galactanases/κ‐carrageenases, “nonspecific” (1,3/1,3;1,4)‐ β‐d‐glucan endohydrolases, and (1,3;1,4)‐β‐d‐glucan endohydrolases. A structured family GH16 glycoside hydrolase database has been constructed ( ...

Abstract The Escherichia coli heat‐shock protein ClpB reactivates protein aggregates in cooperation with the DnaK chaperone system. The ClpB N‐terminal domain plays an important role in the chaperone activity, but its mechanism remains unknown. In this study, we investigated the effect of the ClpB N‐terminal domain on malate dehydrogenase (MDH) refolding. ClpB reduced the yield of MDH refolding by a strong interaction with the...

Abstract Anti‐DNA antibodies have the potential to be applied in vast fields of fundamental as well as medical research. They are found in autoimmune diseases, such as systemic lupus erythemotosus. In most cases, anti‐dsDNA antibodies do not present sequence specificity and are of low affinity. The dominant role of VH domains in DNA recognition induced us to search for binders based on VH dimers (VHD), previously reported to bind different...

Abstract Prion diseases are a group of neurodegenerative disorders associated with conversion of a normal prion protein, PrPC, into a pathogenic conformation, PrPSc. The PrPSc is thought to promote the conversion of PrPC. The structure and stability of PrPC are well characterized, whereas little is known about the structure of PrPSc, what parts of PrPC undergo conformational transition, or how mutations facilitate this transition. We use a computational...

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