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Backbone Atoms (backbone + atom)
Selected AbstractsExploring the primary electron acceptor (QA)-site of the bacterial reaction center from Rhodobacter sphaeroidesFEBS JOURNAL, Issue 4 2002Binding mode of vitamin K derivatives The functional replacement of the primary ubiquinone (QA) in the photosynthetic reaction center (RC) from Rhodobacter sphaeroides with synthetic vitamin K derivatives has provided a powerful tool to investigate the electron transfer mechanism. To investigate the binding mode of these quinones to the QA binding site we have determined the binding free energy and charge recombination rate from QA, to D+ (kAD) of 29 different 1,4-naphthoquinone derivatives with systematically altered structures. The most striking result was that none of the eight tested compounds carrying methyl groups in both positions 5 and 8 of the aromatic ring exhibited functional binding. To understand the binding properties of these quinones on a molecular level, the structures of the reaction center-naphthoquinone complexes were predicted with ligand docking calculations. All protein,ligand structures show hydrogen bonds between the carbonyl oxygens of the quinone and AlaM260 and HisM219 as found for the native ubiquinone-10 in the X-ray structure. The center-to-center distance between the naphthoquinones at QA and the native ubiquinone-10 at QB (the secondary electron acceptor) is essentially the same, compared to the native structure. A detailed analysis of the docking calculations reveals that 5,8-disubstitution prohibits binding due to steric clashes of the 5-methyl group with the backbone atoms of AlaM260 and AlaM249. The experimentally determined binding free energies were reproduced with an rmsd of ,,4 kJ·mol,1 in most cases providing a valuable tool for the design of new artificial electron acceptors and inhibitors. [source] NMR solution structure of KP-TerB, a tellurite-resistance protein from Klebsiella pneumoniaePROTEIN SCIENCE, Issue 4 2008Sheng-Kuo Chiang Abstract Klebsiella pneumoniae (KP), a Gram-negative bacterium, is a common cause of hospital-acquired bacterial infections worldwide. Tellurium (Te) compounds, although relatively rare in the environment, have a long history as antimicrobial and therapeutic agents. In bacteria, tellurite (TeO3,2) resistance is conferred by the ter (Ter) operon (terZABCDEF). Here, on the basis of 2593 restraints derived from NMR analysis, we report the NMR structure of TerB protein (151 amino acids) of KP (KP-TerB), which is mainly composed of seven ,-helices and a 310 helix, with helices II to V apparently forming a four-helix bundle. The ensemble of 20 NMR structures was well-defined, with a RMSD of 0.32 ± 0.06 Å for backbone atoms and 1.11 ± 0.07 Å for heavy atoms, respectively. A unique property of the KP-TerB structure is that the positively and negatively charged clusters are formed by the N-terminal positively and C-terminal negatively charged residues, respectively. To the best of our knowledge, the protein sequence and structures of KP-TerB are unique. [source] Solution structure and proposed domain,domain recognition interface of an acyl carrier protein domain from a modular polyketide synthasePROTEIN SCIENCE, Issue 10 2007Viktor Y. Alekseyev Abstract Polyketides are a medicinally important class of natural products. The architecture of modular polyketide synthases (PKSs), composed of multiple covalently linked domains grouped into modules, provides an attractive framework for engineering novel polyketide-producing assemblies. However, impaired domain,domain interactions can compromise the efficiency of engineered polyketide biosynthesis. To facilitate the study of these domain,domain interactions, we have used nuclear magnetic resonance (NMR) spectroscopy to determine the first solution structure of an acyl carrier protein (ACP) domain from a modular PKS, 6-deoxyerythronolide B synthase (DEBS). The tertiary fold of this 10-kD domain is a three-helical bundle; an additional short helix in the second loop also contributes to the core helical packing. Superposition of residues 14,94 of the ensemble on the mean structure yields an average atomic RMSD of 0.64 ± 0.09 Å for the backbone atoms (1.21 ± 0.13 Å for all non-hydrogen atoms). The three major helices superimpose with a backbone RMSD of 0.48 ± 0.10 Å (0.99 ± 0.11 Å for non-hydrogen atoms). Based on this solution structure, homology models were constructed for five other DEBS ACP domains. Comparison of their steric and electrostatic surfaces at the putative interaction interface (centered on helix II) suggests a model for protein,protein recognition of ACP domains, consistent with the previously observed specificity. Site-directed mutagenesis experiments indicate that two of the identified residues influence the specificity of ACP recognition. [source] High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2 -symmetric active siteACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2006Narendra Narayana R67 plasmid-encoded dihydrofolate reductase (R67 DHFR) is an NADPH-dependent homotetrameric enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. The amino-acid sequence and molecular architecture of R67 DHFR and its inhibitory properties toward folate analogues are different from those of chromosomal DHFR. Here, the crystal structure of R67 DHFR refined using 1.1,Å resolution data is presented. Blocked full-matrix least-squares refinement without restraints resulted in a final R factor of 11.4%. The anisotropic atomic displacement parameters analyzed by Rosenfield matrices and translation,libration,screw validation suggested four quasi-rigid domains. A total of ten C,,HO hydrogen bonds were identified between the ,-strands. There is reasonable structural evidence that His62 is not protonated in the tetramer, which is in accord with previous pH-profile studies. The side chain of Gln67 that protrudes into the active site exhibits dual conformation, a feature noticed for the first time owing to the availability of atomic resolution data. The R67 DHFR active site is unique: it has D2 symmetry and is a large active site with a pentagonal network of water molecules and exposure of backbone atoms to solvent; the central pore is favorable for planar ring-stacking interactions. The geometrical shape, overall symmetry, local asymmetry and waters appear to dominate the binding of ligands, catalysis and inhibition. [source] Research Letter: Retroinverso Mimetics of S PeptideCHEMICAL BIOLOGY & DRUG DESIGN, Issue 6 2007Jagdish Rai The S peptide from ribonuclease S was used as a model system to explore the relationship between the native peptide and its retroinverso (RI) analog. As probed by circular dichroism, the conformations of S peptide and retroinverso S peptide (RIS peptide) are each right-handed helical conformation. The helical propensity of retro S peptide is greater than S peptide, in trifluoroethanol (TFE). In 70% TFE, the S peptide possesses greater helicity at pH 4 than at pH 7, whereas RIS peptide possesses greater helicity at pH 7 than at pH 4. The RIS peptide does not mimic the S peptide in binding to S protein. Specifically, the RIS peptide does not mimic the S peptide to effect RNase activity with S protein and it also does not inhibit the RNase activity of S peptide with S protein. The biological mimicry between the S peptide and its RIS analog depends on the conformation and relatedness of both the side chain and backbone substructures. The backbones in the S peptide and its RIS analog are reverted with respect to each other; however, the side chain patterns are predicted to be similar. Importantly, if the molecular interactions of backbone atoms of the S peptide and its binding to S protein, then the RIS analog would be unlikely to mimic this parent peptide. [source] Backbone-Only Protein Solution Structures with a Combination of Classical and Paramagnetism-Based Constraints: A Method that Can Be Scaled to Large MoleculesCHEMPHYSCHEM, Issue 6 2004Renato Barbieri Dr. Abstract Herein, it is shown that a medium-resolution solution structure of a protein can be obtained with the sole assignment of the protein backbone and backbone-related constraints if a derivative with a firmly bound paramagnetic metal is available. The proof-of-concept is provided on calbindin D9k, a calcium binding protein in which one of the two calcium ions can be selectively substituted by a paramagnetic lanthanide ion. The constraints used are HN (and H,) nuclear Overhauser effects (NOEs), hydrogen bonds, dihedral angle constraints from chemical shifts, and the following paramagnetism-based constraints: 1) pseudocontact shifts, acquired by substituting one (or more) lanthanide(s) in the C-terminal calcium binding site; 2) NHN residual dipolar couplings due to self-orientation induced by the paramagnetic lanthanide(s); 3) cross-correlations between the Curie and internuclear dipole,dipole interactions; and 4) paramagnetism-induced relaxation rate enhancements. An upper distance limit for internuclear distances between any two backbone atoms was also given according to the molecular weight of the protein. For this purpose, the paramagnetism-based constraints were collectively implemented in the program CYANA for solution structure determinations, similarly to what was previously done for the program DYANA. The method is intrinsically suitable for large molecular weight proteins. [source] | ||||||||||