Structure, 21, DiMaio, F. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature methods 10, Edayathumangalam, R. Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT. Proceedings of the National Academy of Sciences,, In Advancing Methods for Biomolecular Crystallography, pp. Uervirojnangkoorn, M. Improving experimental phases for strong reflections prior to density modification. Model morphing and sequence assignment after molecular replacement. Hung, L. Crystal structure of AcrB complexed with linezolid at 3.
Genomics 14, Finding non-crystallographic symmetry in density maps of macromolecular structures. Adams P. Annual Reviews of Biophysics, Buchko, G. Chemical shift assignments for Rv, a putative glyoxylase associated with virulence from Mycobacterium tuberculosis.
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Biomolecular NMR Assignments 6. Grosse-Kunstleve R. Source Code Biol Med. Adams, Paul D. The Phenix software for automated determination of macromolecular structures.
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Methods 55, Genomics 13, Improved crystallographic models through iterated local density-guided model deformation and reciprocal space refinement. D68, Grosse-Kunstleve, R. Urhumtsev, A. Towards automated crystallographic structure refinement with phenix. Brunger, A. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing:the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.
Pedelacq, J. Experimental mapping of soluble protein domains using a hierarchical approach. Nucleic Acids Res. Lockard, M. A high-throughput immobilized bead screen for stable proteins and multi-protein complexes. Protein Engineering, Design, and Selection 24, Chim, N. Baker Improving molecular replacement by density and energy guided protein structure optimization Nature , Habel, J.
Structure of Rv UreA , the Mycobacterium tuberculosis urease gamma subunit.
F66, Tuberculosis, 90, Rapid chain-tracing of polypeptide backbones in electron density maps. D66, H Chim N. An extracellular disulfide bond forming protein DsbF from Mycobacterium tuberculosis: Structural, biochemical and gene expression analysis. Lessons from Structural Genomics. Annual Reviews of Biophysics Kim, C. M, Moon, J. Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases.
Genomics 10, Recent developments in phasing and structure refinement for macromolecular crystallography. Current Opinion in Structural Biology 19, — Acta Cryst D65, Listwan, P. Automated, high-throughput platform for protein solubility screening using and split-GFP system. Roberts, J. In Systems Chemistry, Martin G. Kim, K. From no expression to high-level soluble expression in Escherichia coli by screening a library of the target proteins with randomized N-termini. Methods in Molecular Biology, Vol. Kobe, M. Guss and T. Huber, Eds. Zwart, P. D Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias.
Acta Cryst D, 64, Protein production and purification. Nature Methods.
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Murillo, A. High throughput crystallography of TB drug targets. Infectious Disorders - Drug Targets; 7, Kim, S. D, Strong, M.
Functional linkages can reveal protein complexes for structure determination. Structure 15, Bursey E. Friedland, N. Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation. Biochemistry 46, Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. D63, Ligand identification using electron-density map correlations Acta Cryst..
Goulding, C. Mol Biol. Automated ligand fitting by core-fragment fitting and extension into density. D62, Rho, B. Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis. Prabu, J. Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination. Acta Cryst F62, Furnham, N. Is one solution good enough? Engineering and characterization of a superfolder green fluorescent protein.
Nature Biotechnology, 24, Genomics 6, C, Terwilliger, T. Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum. Protein Science 14, Kantardjieff, K. Structure of pyrR Rv from Mycobacterium tuberculosis: a persistence gene and protein drug target. Acta Cryst D 61, Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein. Nature Biotechnology 23, Harvesting should be a complete and repeatable record of experimen t.
As can be seen from Additional file 1 : Table S7, the highest calculated bond order is for the bond C3—C4 1. The bond order between C1—C2 is 1. The bond order C6—N5 is 1.
The experimental Infrared and Raman spectra in solid phase were shown in Figs. The expected three C—H symmetric stretching vibrations correspond to mode nos. In the case of 2A3MP three modes are associated mainly with the C—H in-plane-bending vibrations: mode nos. The C—H out-of-plane bending vibrations correspond mainly to the mode nos. There are six internal modes of vibrations in the NH 2 group.
These are the symmetric stretching, the anti-symmetric stretching, the scissoring, the rocking, the wagging and torsional mode. The NH 2 group has two N—H stretching vibrations, one being asymmetric and another symmetric. The computed —NH 2 scissoring vibration mode no. Nine modes of vibration Sundaraganesan and Doinic are assigned to each CH 3 group; the symmetrical and asymmetrical stretching, in plane stretching modes, deformation modes symmetrical and asymmetrical , in-plane and out-of-plane rocking, and twisting modes.
It is found that there is a good agreement between this experimental value and the calculated value mode no. The C—CH 3 in-plane bending vibration mode no. These assignments are in good agreement with the literature Hameka and Jensen The identification of C—N vibrations is very difficult because of the interference of many bands in the area where the vibration of this bond happens. These values are consistent with the theoretically calculated values mode No. The most stable tautomer is the canonical structure, 2A4MP1.
Activation energy of the hydrogen proton transfer and pyramidal inversion at amino N is calculated as Bond order and natural atomic charges were also calculated. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution and using Gauss View software. The difference between the observed and scaled wave number values of the most of the fundamentals is very small. The instrument is equipped with Nd:YAG laser source operating at 1.
All electronic structure calculations were performed using the Gaussian03 suite of programs Pittsburgh For each stationary point, we carried out vibrational frequency calculation at the same level to characterize their nature as minima or transition states and to correct energies for zero-point energy and thermal contribution. The transition states for tautomerization have been located using the eigenvalue-following EF optimization procedure as implemented in the Gaussian programs. The nature of the transition states was confirmed by the presence of one negative eigenvalue in the Hessian matrix.
In this study two different scaling factors Sundaraganesan et al. Partial charge distributions were calculated using the natural population analysis NPA method. Akai N, Ohno K, Aida M Photochemistry of p-toluidine in a low-temperature argon matrix: infrared spectrum and geometrical structure of 4-methylaniino radical. Chem Phys Lett — Alkorta I, Elguero J Influence of intermolecular hydrogen bonds on the tautomerism of pyridine derivatives. J Org Chem 67 5 — J Mol Struct Theochem — J Mol Struct — Arivazhagan M, Krishnakumar V Vibrational and normal coordinate analysis of thymine hydrochloride.
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Indian J Pure Appl Phys — Cluster approach to corrosion inhibition problems: interaction studies. Mater Chem Phys — Appl Surf Sci — J Chem Phys Davoodnia A, Attar P, Morsali A, Eshghi H, Hoseini NT, Khadem S Experimental and theoretical studies on the tautomerism in 2-aminopyridines and 2 1H -pyridinones: synthesis of 2-aminoarylcyano 3,4-dimethoxyphenyl pyridines and 4-Arylcyano 3,4-dimethoxyphenyl -2 1H -pyridinones.
Bull Korean Chem Soc 32 6 — Diem M Introduction to modern vibrational spectroscopy. Wiley, New York. J Raman Spectrosc Draeger JA Methylpyridines: vibrational assignments and an approximate force field. Ford RG The microwave spectra and dipole moments of the cyanopyridines. J Mol Spectrosc — Gaussian Inc. Acta Crystallogr B — Inorg Chem — J Mol Struct Theochem 3 — J Phys Chem A 29 — Polyhedron — Synthesis and antihistaminic activity of N- 4-piperidinyl -3H-imidazo[4,5-b]pyridinamines. J Med Chem — Jose SP, Mohan S Vibrational spectra and normal co-ordinate analysis of 2-aminopyridine and 2-amino picoline.
Res J Chem Sci 3 10 — Krishnakumar V, Prabavathi N Simulation of IR and Raman spectral based on scaled DFT force fields: a case study of 2-amino 4-hydroxy 6-trifluoromethylpyrimidine, with emphasis on band assignment. Lashkari M, Arshadi MR DFT studies of pyridine corrosion inhibitors in electrical double layer: solvent, substrate, and electric field effects. Chem Phys — Academic Press, Boston. Advances in Chemical Physics. Stuart A. Gregoire Nicolis. Computational Chemistry. Errol G. Colloidal Foundations of Nanoscience.
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