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Backbone Dynamics (backbone + dynamics)
Selected AbstractsBackbone Dynamics of Cyclotide MCoTI-I Free and Complexed with Trypsin,ANGEWANDTE CHEMIE, Issue 39 2010Shadakshara S. Puttamadappa Freies Protein mit kräftigerem Rückgrat: {15N,1H}-NMR-spektroskopischen Studien zufolge sind die meisten NH-Gruppen im Rückgrat des Cyclotids MCoTI-I im freien Zustand fixiert, was für eine kompakte gefaltete Struktur spricht (siehe Bild). Wie der Ordnungsparameter S2 anzeigt, präsentiert sich das Rückgrat in Trypsin-gebundenem MCoTI-I deutlich mobiler. [source] Backbone dynamics of SDF-1, determined by NMR: Interpretation in the presence of monomer,dimer equilibriumPROTEIN SCIENCE, Issue 11 2006Olga K. Baryshnikova Abstract SDF-1, is a member of the chemokine family implicated in various reactions in the immune system. The interaction of SDF-1, with its receptor, CXCR4, is responsible for metastasis of a variety of cancers. SDF-1, is also known to play a role in HIV-1 pathogenesis. The structures of SDF-1, determined by NMR spectroscopy have been shown to be monomeric while X-ray structures are dimeric. Biochemical data and in vivo studies suggest that dimerization is likely to be important for the function of chemokines. We report here the dynamics of SDF-1, determined through measurement of main chain 15N NMR relaxation data. The data were obtained at several concentrations of SDF-1, and used to determine a dimerization constant of ,5 mM for a monomer,dimer equilibrium. The dimerization constant was subsequently used to extrapolate values for the relaxation data corresponding to monomeric SDF-1,. The experimental relaxation data and the extrapolated data for monomeric SDF-1, were analyzed using the model free approach. The model free analysis indicated that SDF-1, is rigid on the nano- to picosecond timescale with flexible termini. Several residues involved in the dimer interface display slow micro- to millisecond timescale motions attributable to chemical exchange such as monomer,dimer equilibrium. NMR relaxation measurements are shown to be applicable for studying oligomerization processes such as the dimerization of SDF-1,. [source] Backbone dynamics of the human MIA protein studied by 15N NMR relaxation: Implications for extended interactions of SH3 domainsPROTEIN SCIENCE, Issue 3 2003Raphael Stoll MIA, melanoma inhibitory activity; NMR, nuclear magnetic resonance Abstract The melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic melanoma stages III and IV. Here, we report the backbone dynamics of human MIA studied by 15N NMR relaxation experiments. The folded core of human MIA is found to be rigid, but several loops connecting ,-sheets, such as the RT-loop for example, display increased mobility on picosecond to nanosecond time scales. One of the most important dynamic features is the pronounced flexibility of the distal loop, comprising residues Asp 68 to Ala 75, where motions on time scales up to milliseconds occur. Further, significant exchange contributions are observed for residues of the canonical binding site of SH3 domains including the RT-loop, the n-Src loop, for the loop comprising residues 13 to 19, which we refer to as the"disulfide loop", in part for the distal loop, and the carboxyl terminus of human MIA. The functional importance of this dynamic behavior is discussed with respect to the biological activity of several point mutations of human MIA. The results of this study suggest that the MIA protein and the recently identified highly homologous fibrocyte-derived protein (FDP)/MIA-like (MIAL) constitute a new family of secreted proteins that adopt an SH3 domain-like fold in solution with expanded ligand interactions. [source] NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognitionPROTEIN SCIENCE, Issue 6 2006Munia Mukherjee Abstract Flaviviruses cause many human diseases, including dengue fever, yellow fever, West Nile viral encephalitis, and hemorrhagic fevers, and are transmitted to their vertebrate hosts by infected mosquitoes and ticks. Domain III of the envelope protein (E-D3) is considered to be the primary viral determinant involved in the virus,host-cell receptor interaction, and thus represents an excellent target for antiviral drug development. Langat (LGT) virus is a naturally attenuated BSL-2 TBE virus and is a model for the pathogenic BSL-3 and BSL-4 viruses in the serogroup. We have determined the solution structure of LGT-E-D3 using heteronuclear NMR spectroscopy. The backbone dynamics of LGT-E-D3 have been investigated using 15N relaxation measurements. A detailed analysis of the solution structure and dynamics of LGT-E-D3 suggests potential residues that could form a surface for molecular recognition, and thereby represent a target site for antiviral therapeutics design. [source] Secondary structure and dynamics of micelle bound ,- and ,-synucleinPROTEIN SCIENCE, Issue 5 2006Yoon-hui Sung Abstract We have used solution state NMR spectroscopy to characterize the secondary structure and backbone dynamics of the proteins ,- and ,-synuclein in their detergent micelle-bound conformations. Comparison of the results with those previously obtained for the Parkinson's disease-linked protein ,-synuclein shows that structural differences between the three homologous synuclein family members are directly related to variations in their primary amino acid sequences. An 11-residue deletion in the lipid-binding domain of ,-synuclein leads to the destabilization of an entire segment of the micelle-bound helical structure containing the deletion site. The acidic C-terminal tail region of ,-synuclein, which displays extensive sequence divergence, is more highly disordered than the corresponding regions in the other two family members. The observed structural differences are likely to mediate functional variations between the three proteins, with differences between ,- and ,-synuclein expected to revolve around their lipid interactions, while differences in ,-synuclein function are expected to result from different protein,protein interactions mediated by its unique C-terminal tail. [source] Effects of denaturants and substitutions of hydrophobic residues on backbone dynamics of denatured staphylococcal nucleasePROTEIN SCIENCE, Issue 7 2003Satoshi Ohnishi NOE, nuclear Overhauser effect; RDC, residual dipolar coupling Abstract Analysis of residual dipolar couplings (RDCs) in the ,131, fragment of staphylococcal nuclease has demonstrated that its ensemble-averaged structure is resistant to perturbations such as high concentrations of urea, low pH, and substitution of hydrophobic residues, suggesting that its residual structure is encoded by local side-chain/backbone interactions. In the present study, the effects of these same perturbations on the backbone dynamics of ,131, were examined through 1H- 15N relaxation methods. Unlike the global structure reported by RDCs, the transverse relaxation rates R2 were quite sensitive to denaturing conditions. At pH 5.2, ,131, exhibits an uneven R2 profile with several characteristic peaks involving hydrophobic chain segments. Protonation of carboxyl side chains by lowering the pH reduces the values of R2 along the entire chain, yet these characteristic peaks remain. In contrast, high concentrations of urea or the substitution of 10 hydrophobic residues eliminates these peaks and reduces the R2 values by a greater amount. The combination of low pH and high urea leads to further decreases in R2. These denaturant-induced increases in backbone mobility are also reflected in decreases in 15N NOEs and in relaxation interference parameters, with the former reporting an increase in fast motions and the latter a decrease in slow motions. Comparison between the changes in chain dynamics and the corresponding changes in Stokes radius and the patterns of RDCs suggests that regional variations in backbone dynamics in denatured nuclease arise primarily from local contacts between hydrophobic side chains and local interactions involving charged carboxyl groups. [source] Backbone dynamics of the human MIA protein studied by 15N NMR relaxation: Implications for extended interactions of SH3 domainsPROTEIN SCIENCE, Issue 3 2003Raphael Stoll MIA, melanoma inhibitory activity; NMR, nuclear magnetic resonance Abstract The melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic melanoma stages III and IV. Here, we report the backbone dynamics of human MIA studied by 15N NMR relaxation experiments. The folded core of human MIA is found to be rigid, but several loops connecting ,-sheets, such as the RT-loop for example, display increased mobility on picosecond to nanosecond time scales. One of the most important dynamic features is the pronounced flexibility of the distal loop, comprising residues Asp 68 to Ala 75, where motions on time scales up to milliseconds occur. Further, significant exchange contributions are observed for residues of the canonical binding site of SH3 domains including the RT-loop, the n-Src loop, for the loop comprising residues 13 to 19, which we refer to as the"disulfide loop", in part for the distal loop, and the carboxyl terminus of human MIA. The functional importance of this dynamic behavior is discussed with respect to the biological activity of several point mutations of human MIA. The results of this study suggest that the MIA protein and the recently identified highly homologous fibrocyte-derived protein (FDP)/MIA-like (MIAL) constitute a new family of secreted proteins that adopt an SH3 domain-like fold in solution with expanded ligand interactions. [source] The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophusPROTEIN SCIENCE, Issue 5 2000Gary S. Thompson Abstract The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35 ± 0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two ,-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. [source] | ||||||||||