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Protein Structure, Secondary (1):
Recent article
Protein Structure, Secondary
Abstract
We determined the crystal structure of the catalytic domain of MMP-2 in complex with APP-IP. We found that APP-IP in the complex is indeed embedded into the substrate-binding cleft of the catalytic domain in the N to C direction opposite that of substrate. With the crystal structure, it was first cl...
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PMID: 21813640
PDF is available here.
PDF is available here.
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Abstract
We report that, although glycosome-resident enzyme T. brucei hexokinase 1 (TbHK1) protein levels are maintained during pexophagy, acidification inactivates the activity. Glycerol 3-phosphate, which is produced in vivo by a glycosome-resident glycerol kinase, mitigated acid inactivation of lysate-der...
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PMID: 21813651
PDF is available here.
PDF is available here.
Abstract
We have investigated which portion of Tg is engaged in this late stage of its maturation. First, we demonstrate that this event is linked to oxidation involving region I. Introduction of the Tg-C1245R mutation in the hinge (identical to that causing human goitrous hypothyroidism) inhibits this matur...
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PMID: 21816825
PDF is available here.
PDF is available here.
Abstract
We report the 1.5 Å resolution crystal structure of the human USP15 N-terminal domains revealing a 80 Å elongated arrangement with the DU domains aligned in tandem. This architecture is generated through formation of a defined interface that is dominated by an intervening β-hairpin structure (DU...
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PMID: 21848306
PDF is available here.
PDF is available here.
Abstract
Cobalamin (Cbl) is a complex cofactor produced only by bacteria but used by all animals and humans. Cyanocobalamin (vitamin B(12), CNCbl) is one commonly isolated form of cobalamin. B(12) belongs to a large group of corrinoids, which are characterized by a distinct red color conferred by the system o...
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PMID: 21851077
PDF is available here.
PDF is available here.
Abstract
We now report the design and characterization of three single-site mutants of CD4D12 (G6A, L51I, and V86L) and one multisite mutant of CD4D1 (G6A/L51I/L5K/F98T). G6A, L51I, and V86L are cavity-filling mutations while L5K and F98T are surface mutations which were introduced to minimize the aggregatio...
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PMID: 21827143
PDF is available here.
PDF is available here.
Abstract
Myeloperoxidase (MPO) is the most abundant neutrophil enzyme and catalyzes predominantly the two-electron oxidation of ubiquitous chloride to generate the potent bleaching hypochlorous acid, thus contributing to pathogen killing as well as inflammatory diseases. Its catalytic properties are closely r...
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PMID: 21854003
PDF is available here.
PDF is available here.
Abstract
We investigated whether prolines in or near the transmembrane helices are essential for BCRP function. Six proline residues were substituted with alanine individually, and the mutants were stably expressed in Flp-In(TM)-293 cells at levels comparable to that of wild-type BCRP and predominantly local...
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PMID: 21854076
PDF is available here.
PDF is available here.
Abstract
We review evidence that the lipid-exposed surfaces of membrane proteins have generally evolved to maintain correct structure and function in the face of major changes in lipid composition. Such tolerance has allowed evolution to extensively remodel membrane lipid compositions during the emergence of...
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PMID: 21848311
PDF is available here.
PDF is available here.
Abstract
We show that Rrn7, a subunit of the yeast Pol I core factor, and its human ortholog TAF1B are TFIIB-like factors. Although distantly related, Rrn7 shares many activities associated with TFIIB-like factors. Domain swaps between TFIIB-related factors show that Rrn7 is most closely related to the Pol I...
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PMID: 21921198
PDF is available here.
PDF is available here.
Abstract
We obtained an all-atom model structure for the high-affinity form of MTBD bound to MT by an anisotropic network model, protein-protein docking, and molecular dynamics simulations. We observe that the magnitude of the coiled-coil helix sliding is dramatically reduced near the two prolines that form...
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PMID: 21809817
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
We investigated antibacterial effects of Rev-NIS and suggested the role of positively charged amino acids on membrane pore forming activity of the peptide in bacterial cells, by synthesizing two analogs, Anal R and Anal S. Based on the amphipathic property of Rev-NIS, Anal R and Anal S were designed...
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PMID: 21762675
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)9 2011
Abstract
GuHCl-induced denaturation of human plasma apoA-I, apoA-II, apoA-IV, apoE3 and three recombinant apoE isoforms in solution and discoidal complexes with phosphatidylcholine (only plasma proteins) was studied. The protein conformational stability (ΔG(H(2)O)) and a slope of linear depe...
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PMID: 21600318
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)9 2011
Abstract
We designed a novel VLR protein (called dVLR) containing six LRR repeats based on a sea lamprey receptor sequence. The designed protein was expressed in Escherichia coli in a soluble, native form and showed very favorable biophysical properties. Recombinant dVLR is monomeric in solution and preserve...
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PMID: 21621013
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
We perform an EPR study on the role played by the membrane composition in tuning the interaction between lipid bilayers and two peptides, gH626-644 and gB632-650, that are highly fusogenic fragments of the gH and gB glycoproteins of herpes simplex virus. Our results show that both peptides interact...
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PMID: 21798233
PDF is available here.
PDF is available here.
Abstract
We recently introduced the enhanced aromatic sequon as a family of portable structural motifs that are stabilized upon glycosylation in specific reverse turn contexts: a five-residue type I β-turn harboring a G1 β-bulge (using a Phe-Yyy-Asn-Xxx-Thr sequon) and a type II β-turn within a six-residu...
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PMID: 21825145
PDF is available here.
PDF is available here.
Abstract
We have used single-molecule force spectroscopy in combination with molecular dynamics simulations to characterize the mechanics of the myomesin dimer comprising immunoglobulin domains My12-My13. We find that at forces of approximately 30 pN the α-helical linker reversibly elongates allowing the m...
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PMID: 21825161
PDF is available here.
PDF is available here.
Abstract
We use Φ-value and double mutant analyses to probe the folding transition state of the membrane protein bacteriorhodopsin. We focus on the final C-terminal helix, helix G, of this seven transmembrane helical protein. Φ-values could be derived for 12 amino acid residues in helix G, most of which ha...
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PMID: 21831834
PDF is available here.
PDF is available here.
Abstract
These results identify the MinD-dependent conformational changes in MinE that convert it from a latent to an active form and lead to a model of how MinE persists at the MinD-membrane surface. PAPERFLICK:...
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PMID: 21816275
PDF is available here.
PDF is available here.
Abstract
We report three-dimensional structures of individual SipD, SipD in fusion with the needle subunit PrgI, and of SipD:PrgI in complex with the bile salt, deoxycholate. Assembly of the complex involves major conformational changes in both SipD and PrgI. This rearrangement is mediated via a π bulge in...
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PMID: 21829362
PDF is available here.
PDF is available here.
Crystal structure of reovirus attachment protein sigma1 in complex with sialylated oligosaccharides.
Abstract
We determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structu...
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PMID: 21829363
PDF is available here.
PDF is available here.
Abstract
We review here the current knowledge and show that Prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied cata...
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PMID: 20969484
PDF is available here.
PDF is available here.
Abstract
We identify a family in which all known RP/LCA-related genes are unlikely to be associated with their disorder. A combination of homozygosity mapping and exome sequencing identifies a homozygous nonsense mutation, c.496C>T (p.Arg166X), in a gene, KCNJ13, encoding a potassium channel subunit Kir7.1....
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PMID: 21763485
PDF is available here.
PDF is available here.
Abstract
We determined the high-resolution x-ray crystal structure of the GspB binding region (GspB(BR)), both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB(BR) structure revealed that it is comprised of three independently folded subdomains or modules: 1) an Ig...
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PMID: 21765814
PDF is available here.
PDF is available here.
Abstract
Abstract Expansions of sequence databases driven by new sequencing technology continue apace. These result in a continuous supply of protein sequences and domains that cannot be straightforwardly annotated by simple homology methods. For these, structure-based function prediction may...
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PMID: 21348639
PDF is available here.
PDF is available here.
Abstract
Fibrillar aggregates of beta-amyloid peptide (Abeta) are major constituents of the senile plaques found in the brains of patients suffering from Alzheimer's disease (AD). Previous studies have shown that spontaneous isomerization or racemization of aspartyl residues in Abeta peptides...
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PMID: 21812329
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)7 2011
Abstract
We present the solution structure of GIP in membrane-mimicking environments by proton NMR spectroscopy and molecular modelling. GIP adopts an α-helical conformation between residues Phe(6)-Gly(31) and Ala(13)-Gln(29) for micellar and bicellar media, respectively. Previously we examined the effect o...
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PMID: 21539943
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)11 2011
Abstract
[Fe(4)S(4)]- and [Fe(3)S(4)]-clusters are ubiquitous iron-sulfur motifs in biological systems. The [Fe(3)S(4)] composition is, however, of much lower natural abundance than the more typical [Fe(4)S(4)]-clusters. In the present study formation of [Fe(3)S(4)]-clusters has been examined using chemically...
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PMID: 21756871
PDF is available here.
PDF is available here.
Abstract
We have studied the L24A mutant that has been shown previously to form non-native interactions in the folding transition state. A suite of Carr-Purcell-Meiboom-Gill relaxation dispersion NMR experiments have been used to measure backbone chemical shifts and amide bond vector orientations of the invi...
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PMID: 21639149
PDF is available here.
PDF is available here.
Abstract
We also predict that Glu15, Lys43, and Tyr46 may be important in the catalytic efficiency and thermostability of enzyme. The new structural and mechanistic insights obtained from computational study should be valuable for detailed structures and mechanisms of the member of the DJ-1 superfamily....
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PMID: 20711794
PDF is available here.
PDF is available here.
Abstract
A homology model for pig liver esterase was generated on the basis of human carboxyl esterase (hCE) and subjected to extensive molecular dynamics simulations. By virtual mutations the isoenzymes PLE1-6 and APLE were obtained, and the PLE1 trimer was built from the respective model of...
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PMID: 20862595
PDF is available here.
PDF is available here.
Nature Protocols (6)6 2011
Abstract
This protocol provides a detailed procedure for the preparation of stapled α-helical peptides, which have proven their potential as useful molecular probes and as next-generation therapeutics. Two crucial features of this protocol are (i) the construction of peptide substrates conta...
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PMID: 21637196
PDF is available here.
PDF is available here.
Abstract
In the cell, protein folding into stable globular conformations is in competition with aggregation into non-functional and usually toxic structures, since the biophysical properties that promote folding also tend to favor intermolecular contacts, leading to the formation of β-sheet-...
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PMID: 21538897
PDF is available here.
PDF is available here.
Abstract
We could only predict the structure of the main domain, which had central barrel of eight beta-strands surrounded by eight alpha-helices. Superimposition of the 2NPD region of ER domain of Mycobacterium tuberculosis H37Rv on to the corresponding region of 2UVA_G revealed a good structural alignment...
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PMID: 21793307
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)9 2011
Abstract
The twin-arginine translocase (Tat) system is used by many bacteria and plants to move folded proteins across the cytoplasmic or thylakoid membrane. In most bacteria, the TatA protein is believed to form a defined pore in the membrane through homo-oligomerization with other TatA protomers. The predic...
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PMID: 21683683
PDF is available here.
PDF is available here.
Abstract
We find that the transmembrane helix dimer, glycophorin A (GpATM), is actually much less stable in the heterogeneous environment of a natural membrane than it is in model membranes and even common detergents. The primary destabilizing factors are electrostatic interactions between charged lipids and...
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PMID: 21682279
PDF is available here.
PDF is available here.
Abstract
To determine the ability of semiconductors templated by α-helical polypeptides to form higher order structures and the charge carrier properties of the supramolecular assemblies, l-lysine was functionalized with a sexithiophene organic semiconductor unit via iterative Suzuki coupling and the click r...
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PMID: 21568281
PDF is available here.
PDF is available here.
Abstract
We replaced conserved residues at the dimer interface to design a heterodimer with increased stability. One E2R mutant in which histidine was replaced by a glutamate residue showed preferential heterodimer formation in vitro, as well as an increase in plasticity at the interface, as a result of hist...
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PMID: 21482558
PDF is available here.
PDF is available here.
Abstract
Our understanding of the structure of secretins is rapidly progressing, and it is now recognized that features common to all secretins include a cylindrical arrangement of 12-15 subunits, a large periplasmic vestibule with a wide opening at one end and a periplasmic gate at the other. Secretins migh...
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PMID: 21565514
PDF is available here.
PDF is available here.
Physical Chemistry (62) 2011
Abstract
Current interest in amyloid fibrils stems from their involvement in neurodegenerative and other diseases and from their role as an alternative structural state for many peptides and proteins. Solid-state nuclear magnetic resonance (NMR) methods have the unique capability of providing detailed structu...
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PMID: 21219138
PDF is available here.
PDF is available here.
Abstract
Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a sign...
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PMID: 21728568
PDF is available here.
PDF is available here.
Abstract
We were able to obtain direct observations of shifts in the hydrogen-bonding register of an intermolecular β-sheet protein-peptide complex. The β-sheet is formed between the FHA domain of cancer marker protein Ki67 (Ki67FHA) and a peptide fragment of the hNIFK signaling protein. Potential encounte...
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PMID: 21539773
PDF is available here.
PDF is available here.
Abstract
We investigated the role of hydration in collagen recognition by bacterial adhesin CNA by means of first principle molecular-dynamics samplings. Our characterization of the hydration properties of the isolated partners highlights dewetting-prone areas on the surface of CNA that closely match the key...
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PMID: 21539794
PDF is available here.
PDF is available here.
Abstract
We show that the mechanism revealed for activation of the wild-type complex, namely an outward tilt motion of the cytoplasmic part of the receptor helix F and a concomitant rotation of the transmembrane transducer helix TM2, is also valid for the D75N variant. Apparently, the D75N mutation shifts th...
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PMID: 21539797
PDF is available here.
PDF is available here.
Abstract
We examine the extent to which the molecular mechanics force field used in such simulations might influence the observed folding pathways. To that end, we performed equilibrium simulations of a fast-folding variant of the villin headpiece using four different force fields. In each simulation, we obs...
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PMID: 21539772
PDF is available here.
PDF is available here.
Abstract
The spontaneous folding of two Neisseria outer membrane proteins, opacity-associated (Opa)(60) and Opa(50) into lipid vesicles was investigated by systematically varying bulk and membrane properties. Centrifugal fractionation coupled with sodium dodecyl sulfate polyacrylamide gel electrophoresis mobi...
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PMID: 21539780
PDF is available here.
PDF is available here.
Abstract
IDPs in their unbound state can transiently acquire secondary and tertiary structure. Describing such intrinsic structure is important to understand the transition between free and bound state, leading to supramolecular complexes with physiological interactors. IDP structure is highly dynamic and, th...
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PMID: 21539793
PDF is available here.
PDF is available here.
Abstract
We break down the determinants of this behavior and demonstrate that the modulation of contact order effects can be accounted for by the combined contributions of a framework-like mechanism, characterized by intrinsic helix stabilities, together with nonnative helical backbone conformation and nonna...
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PMID: 21539796
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1813)5 2011
Abstract
We determined the structures of human Zn(2+)- and Ca(2+)-loaded S100B at pH 6.5, pH 9, and pH 10 by X-ray crystallography at 1.5, 1.4, and 1.65Å resolution, respectively. Two Zn(2+) ions are coordinated tetrahedrally at the dimer interface by His and Glu residues from both subunits. The crystal str...
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PMID: 20950652
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1813)5 2011
Abstract
We have developed a new strategy for purification of recombinant hSERCA2b and hSPCA1a that is based on overexpression in yeast followed by a two-step affinity chromatography method biasing towards properly folded protein. In a first step, these proteins were purified with the aid of an analogue of t...
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PMID: 21215281
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)5 2011
Abstract
The primary aim of this study is the elucidation of the mechanism of disulfide induced alteration of ligand binding in human tear lipocalin (TL). Disulfide bonds may act as dynamic scaffolds to regulate conformational changes that alter protein function including receptor-ligand interactions. A singl...
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PMID: 21466861
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)5 2011
Abstract
We have carried out a spectroscopical/structural characterization of the recombinant ectodomain in order to obtain information on its dynamic structure in solution and on its ability to form homodimers by itself in the absence of the transmembrane helix and of the potential interactions with the pla...
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PMID: 21352957
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)8 2011
Abstract
In present work the interaction of two TM α-helices of the ErbB3 receptor tyrosine kinase from the ErbB or HER family (residues 639-670) was studied by means of NMR spectroscopy in a membrane-mimicking environment provided by the DPC micelles. The ErbB3 TM segment appeared to form a parallel symmetr...
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PMID: 21575594
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)9 2011
Abstract
We iteratively performed atomistic molecular dynamics simulations and biophysical measurements to probe the interaction of a cyclic antimicrobial peptide and its inactive linear analogue with model membranes. We establish that, relative to the linear peptide, the cyclic one binds stronger to negativ...
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PMID: 21586269
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1813)5 2011
Abstract
We report here the results of studies that test the hypothesis of McNamara et al. (2009) that conformational selection in DAPK's glycine-rich region is key for catalytic activity. The hypothesis was tested by site-directed mutagenesis of glutamine-23 (Q23) in the middle of this loop. The glycine-ric...
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PMID: 21126544
PDF is available here.
PDF is available here.
Abstract
We describe the first experimental data on the isolated and unmodified dimers of human (hIAPP) and nonamyloidogenic rat IAPP (rIAPP). The experiments reveal that the human IAPP dimers are more extended than those formed by rat IAPP and likely descend from extended monomers. Independent all-atom mole...
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PMID: 21517093
PDF is available here.
PDF is available here.
Abstract
We report a new type of unnatural peptidic backbone, containing α-, β-, and γ-amino acid residues in an αγααβα repeat pattern, for this purpose. This unnatural hexad has the same number of backbone atoms as a heptad of α residues. Two-dimensional NMR data clearly establish the formation of...
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PMID: 21520956
PDF is available here.
PDF is available here.
Abstract
Amyloid fibril diseases are characterized by the abnormal production of aggregated proteins and are associated with many types of neuro- and physically degenerative diseases. X-ray diffraction techniques, solid-state magic-angle spinning NMR spectroscopy, circular dichroism (CD) spectroscopy, and tra...
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PMID: 21524071
PDF is available here.
PDF is available here.
Abstract
We have carried out ∼3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fu...
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PMID: 21517079
PDF is available here.
PDF is available here.
Abstract
We focus on Tyr223(5.58) as part of the Y(5.58)X(7)K(R)(5.66) motif. Mutation to Ala, Phe, or Glu results in specific impairments of G(t)-activation measured by intrinsic G(t) fluorescence. UV-vis/FTIR spectroscopy of rhodopsin and its complex with a C-terminal G(t)α peptide allows the assignment o...
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PMID: 21506561
PDF is available here.
PDF is available here.