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Journal Issue - Volume 17 Issue 5 (May 2008)

Abstract Antizyme inhibitor (AzI) regulates cellular polyamine homeostasis by binding to the polyamine‐induced protein, Antizyme (Az), with greater affinity than ornithine decarboxylase (ODC). AzI is highly homologous to ODC but is not enzymatically active. In order to understand these specific characteristics of AzI and its differences from ODC, we determined the 3D structure of mouse AzI to 2.05 Å resolution. Both AzI and ODC...

Abstract Bacteriophage Cro proteins bind to target DNA as dimers but do not all dimerize with equal strength, and differ in fold in the region of the dimer interface. We report the structure of the Cro protein from Enterobacteria phage N15 at 1.05 Å resolution. The subunit fold contains five α‐helices and is closely similar to the structure of P22 Cro (1.3 Å backbone room mean square difference over 52 residues), but quite different...

Abstract The small hydrophobic (SH) protein from the human respiratory syncytial virus (hRSV) is a glycoprotein of ∼64 amino acids with one putative α‐helical transmembrane domain. Although SH protein is important for viral infectivity, its exact role during viral infection is not clear. Herein, we have studied the secondary structure, orientation, and oligomerization of the transmembrane domain of SH (SH‐TM) in the presence of...

Abstract Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the...

Abstract Previously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease (SNase) titrate with pKa values shifted by up to 5 pKa units in the direction that promotes the neutral state. In contrast, the internal Lys‐38 in SNase titrates with a normal pKa. The crystal structure of the L38K variant shows that the side chain of Lys‐38 is buried. The ionizable moiety is ∼7 Å from solvent and ion...

Abstract The assembly of FtsZ plays an important role in bacterial cell division. Mycobacterium tuberculosis FtsZ (MtbFtsZ) has a single cysteine residue at position 155. We have investigated the role of the lone cysteine residue in the assembly of MtbFtsZ using different complimentary approaches, namely chemical modification by a thiol‐specific reagent 5,5′‐dithiobis‐(2‐nitrobenzoic acid) (DTNB) or a cysteine‐chelating agent HgCl2, and...

Abstract Mutations in the protein DJ‐1 are associated with familial forms of Parkinson's disease, indicating that DJ‐1 may be involved in pathways related to the etiology of this disorder. Here we have used solution state NMR and circular dichroism spectroscopies to evaluate the extent of structural perturbations associated with five different Parkinson's disease linked DJ‐1mutations: L166P, E64D, M26I, A104T, and D149A. Comparison...

Abstract As a part of the Joint Center for Structural Genomics (JCSG) biological targets, the structures of soluble domains of membrane proteins from Thermotoga maritima were pursued. Here, we report the crystal structure of the soluble domain of TM1634, a putative membrane protein of 128 residues (15.1 kDa) and unknown function. The soluble domain of TM1634 is an α‐helical dimer that contains a single tetratrico peptide repeat...

Abstract C3‐like exoenzymes are ADP‐ribosyltransferases that specifically modify some Rho GTPase proteins, leading to their sequestration in the cytoplasm, and thus inhibiting their regulatory activity on the actin cytoskeleton. This modification process goes through three sequential steps involving NAD‐hydrolysis, Rho recognition, and binding, leading to Rho ADP‐ribosylation. Independently, three distinct residues within the ARTT...

Abstract α‐ and β‐synuclein are closely related proteins, the first of which is associated with deposits formed in neurodegenerative conditions such as Parkinson's disease while the second appears to have no relationship to any such disorders. The aggregation behavior of α‐ and β‐synuclein as well as a series of chimeric variants were compared by exploring the structural transitions that occur in the presence of a widely used lipid...

Abstract Protein oligomerization serves an important function in biological processes, yet solving structures of protein oligomers has always been a challenge. For solution NMR, the challenge arises both from the increased size of these systems and, in the case of homo‐oligomers, from ambiguities in assignment of intra‐ as opposed to intersubunit NOEs. In this study, we present a residual dipolar coupling (RDC)‐assisted method for...

Abstract Miranda is a multidomain adaptor protein involved in neuroblast asymmetric division in Drosophila melanogaster. The central domain of Miranda is necessary for cargo binding of the neural transcription factor Prospero, the Prospero‐mRNA carrier Staufen, and the tumor suppressor Brat. Here, we report the first solution structure of Miranda central “cargo‐binding” domain (residues 460–660) using small‐angle X‐ray scattering. Ab initio...

Abstract Proteins that show similarity in their equilibrium dynamics can be aligned by identifying regions that undergo similar concerted movements. These movements are computed from protein native structures using coarse‐grained elastic network models. We show the existence of common large‐scale movements in enzymes selected from the main functional and structural classes. Alignment via dynamics does not require prior detection of...

Abstract Integrins are α/β heterodimers, but recent in vitro and in vivo experiments also suggest an ability to associate through their transmembrane domains to form homomeric interactions. While the results of some in vitro experiments are consistent with an interaction mediated by a GxxxG‐like motif, homo‐oligomers observed after in vivo cross‐linking are consistent with an almost opposite helix–helix interface. We have shown...

Abstract Cyanovirin (CV‐N) is a small lectin with potent HIV neutralization activity, which could be exploited for a mucosal defense against HIV infection. The wild‐type (wt) protein binds with high affinity to mannose‐rich oligosaccharides on the surface of gp120 through two quasi‐symmetric sites, located in domains A and B. We recently reported on a mutant of CV‐N that contained a single functional mannose‐binding site, domain B,...

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