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Pai Y, Butchart C, Lunt CJ, Musonda P, Gautham N, Soiza RL, Potter JF, Myint PK. Age, co-morbidity and poor mobility: no evidence of predicting in-patient death and acute hospital length of stay in the oldest old. QJM 2011; 104:671-9. [PMID: 21406460 DOI: 10.1093/qjmed/hcr028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The oldest old (aged over 90 years) are the fastest growing section of the UK population. Limited data exist regarding the effect of age, location, co-morbidity and physical performance status on outcome of acute illness in this age group. METHODS We performed a prospective study in people aged ≥ 90 years using hospital audit data in three hospitals in England and Scotland. We examined the characteristics of those admitted over three consecutive calendar months and calculated risk ratios of death and prolonged length of acute hospital stay (>7 days). RESULTS A total of 419 patients were included in this study (68% female, median age 93 years). There were similarities in presentation and diagnoses, but patients in Scotland (n = 164) were more likely to be admitted from sheltered housing or nursing homes than those in England (n = 255). Patients in England were significantly less likely to be able to mobilize < 10 m (41 vs. 34%, P < 0.001) but had lower prevalence of hypertension (40 vs. 55%, P = 0.02), ischaemic heart disease (30% vs. 45%, P = 0.02) and fewer prescribed medications (median 2 vs. 3, P < 0.001). Mortality was similar for the England and Scotland centres (P = 0.98). Previously recognized risk factors for death following hospital admission and length of stay e.g. older age, higher number of co-morbidities and poor mobility were not predictive in this study. CONCLUSION The 'oldest old' should not be considered as a homogenous group and findings from single-centre studies involving this age group may not be generalizable. We found no conclusive evidence that patient-related factors predict outcome in this age group in acute medical admission settings.
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Venkadesh S, Mandal PK, Gautham N. The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice. Biochem Biophys Res Commun 2011; 407:548-551. [PMID: 21419105 DOI: 10.1016/j.bbrc.2011.03.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 03/14/2011] [Indexed: 05/30/2023]
Abstract
We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind to each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5Å. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.
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Venkadesh S, Mandal PK, Gautham N. The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)₂. Biochem Biophys Res Commun 2011; 407:307-12. [PMID: 21397589 DOI: 10.1016/j.bbrc.2011.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Accepted: 03/02/2011] [Indexed: 11/25/2022]
Abstract
We report the 2.6Å resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4₃. This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours.
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Ramya L, Nehru Viji S, Arun Prasad P, Kanagasabai V, Gautham N. MOLS sampling and its applications in structural biophysics. Biophys Rev 2010; 2:169-179. [PMID: 28510038 DOI: 10.1007/s12551-010-0039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 10/19/2010] [Indexed: 12/01/2022] Open
Abstract
This review describes the MOLS method and its applications. This computational method has been developed in our laboratory primarily to explore the conformational space of small peptides and identify features of interest, particularly the minima, i.e., the low energy conformations. A systematic "brute-force" search through the vast conformational space for such features faces the insurmountable problem of combinatorial explosion, whilst other techniques, e.g., Monte Carlo searches, are somewhat limited in their region of exploration and may be considered inexhaustive. The MOLS method, on the other hand, uses a sampling technique commonly employed in experimental design theory to identify a small sample of the conformational space that nevertheless retains information about the entire space. The information is extracted using a technique that is a variant of the self-consistent mean field technique, which has been used to identify, for example, the optimal set of side-chain conformations in a protein. Applications of the MOLS method to understand peptide structure, predict the structures of loops in proteins, predict three-dimensional structures of small proteins, and arrive at the best conformation, orientation, and positions of a small molecule ligand in a protein receptor site have all yielded satisfactory results.
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Viji SN, Prasad PA, Gautham N. Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK). J Chem Inf Model 2010; 49:2687-94. [PMID: 19968302 DOI: 10.1021/ci900332a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The theoretical prediction of the association of a flexible ligand with a protein receptor requires efficient sampling of the conformational space of the ligand. Several docking methodologies are currently available. We have proposed a docking technique that performs well at low computational cost. The method uses mutually orthogonal Latin squares to efficiently sample the docking space. A variant of the mean field technique is used to analyze this sample to arrive at the optimum. The method has been previously applied to search through both the conformational space of a peptide as well its docking space. Here we extend this method to simultaneously identify both the low energy conformation as well as a high scoring docking mode for the small organic ligand molecules. Application of the method to 45 protein-ligand complexes, in which the number of rotatable torsions varies from 2 to 19, and comparisons with AutoDock 4.0, showed that the method works well.
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Ramya L, Gautham N. Effects of Hydration on the Conformational Energy Landscape of the Pentapeptide Met-Enkephalin. J Chem Theory Comput 2009; 5:2180-90. [DOI: 10.1021/ct9000087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Venkadesh S, Mandal PK, Gautham N. The structure of d(CACACG).d(CGTGTG). Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 65:8-13. [PMID: 19153446 DOI: 10.1107/s1744309108037706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 11/13/2008] [Indexed: 11/10/2022]
Abstract
The crystal structure of d(CACACG).d(CGTGTG) was solved to a resolution of 2.05 A in space group P2(1). The duplex assumes the left-handed Z-DNA structure. The presence of two A.T base pairs in the hexamer does not greatly affect the conformation. The most significant changes compared with the regular structure of Z-DNA are in the values of twist in the central portion of the helix. This variation, as well as others in the values of roll, inclination etc., follow the pattern observed previously in the structure of d(CGCACG).d(CGTGCG).
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Bharanidharan D, Thiyagarajan S, Gautham N. Hexammineruthenium(III) ion interactions with Z-DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:1008-13. [PMID: 18084080 PMCID: PMC2344113 DOI: 10.1107/s1744309107047781] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2007] [Accepted: 09/28/2007] [Indexed: 11/11/2022]
Abstract
The hexamer duplex d(CGCGCA).d(TGCGCG) was crystallized with hexammineruthenium(III) ions in an orthorhombic space group; the crystals diffracted to 1.54 A resolution. Strong ion interactions with the adenine base induce a tautomeric shift from the amino to the imino form. Consequently, the A.T base pairing is disrupted. This structural study may be relevant to metal toxicity.
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Prasad PA, Kanagasabai V, Arunachalam J, Gautham N. Exploring conformational space using a mean field technique with MOLS sampling. J Biosci 2007; 32:909-20. [PMID: 17914233 DOI: 10.1007/s12038-007-0091-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The computational identification of all the low energy structures of a peptide given only its sequence is not an easy task even for small peptides,due to the multiple-minima problem and combinatorial explosion. We have developed an algorithm, called the MOLS technique,that addresses this problem, and have applied it to a number of different aspects of the study of peptide and protein structure. Conformational studies of oligopeptides, including loop sequences in proteins have been carried out using this technique. In general the calculations identified all the folds determined by previous studies,and in addition picked up other energetically favorable structures. The method was also used to map the energy surface of the peptides. In another application, we have combined the MOLS technique, using it to generate a library of low energy structures of an oligopeptide, with a genetic algorithm to predict protein structures. The method has also been applied to explore the conformational space of loops in protein structures.Further, it has been applied to the problem of docking a ligand in its receptor site, with encouraging results.
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Kanagasabai V, Arunachalam J, Prasad PA, Gautham N. Exploring the conformational space of protein loops using a mean field technique with MOLS sampling. Proteins 2007; 67:908-21. [PMID: 17357159 DOI: 10.1002/prot.21333] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have recently developed a computational technique that uses mutually orthogonal Latin square sampling to explore the conformational space of oligopeptides in an exhaustive manner. In this article, we report its use to analyze the conformational spaces of 120 protein loop sequences in proteins, culled from the PDB, having the length ranging from 5 to 10 residues. The force field used did not have any information regarding the sequences or structures that flanked the loop. The results of the analyses show that the native structure of the loop, as found in the PDB falls at one of the low energy points in the conformational landscape of the sequences. Thus, a large portion of the structural determinants of the loop may be considered intrinsic to the sequence, regardless of either adjacent sequences or structures, or the interactions that the atoms of the loop make with other residues in the protein or in neighboring proteins.
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Aravindhan V, Narayanan S, Gautham N, Prasad V, Kannan P, Jacobs WR, Narayanan P. T-h-2 immunity and CD3+CD45RBlow-activated T cells in mice immunized with recombinant bacillus CalmetteâGuérin expressing HIV-1 principal neutralizing determinant epitope. ACTA ACUST UNITED AC 2006; 47:45-55. [PMID: 16706787 DOI: 10.1111/j.1574-695x.2006.00061.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The genetic engineering of Mycobacterium bovis-bacillus Calmette-Guérin to express foreign epitopes is an attractive strategy in the field of epitope vaccines. We constructed an 'epitope-trap vector' with Mycobacterium tuberculosis chaperonin-10 as a carrier antigen and used it to express the HIV-1 principal neutralizing determinant epitope. We also identified a new chaperonin-10 promoter that was hyperexpressive compared with the heat shock protein-65 promoter. Splenocytes from recombinant bacillus Calmette-Guérin-immunized mice showed enhanced lymphocyte proliferation and interleukin-4 (but not interferon-gamma) secretion. The recombinant bacillus Calmette-Guérin-immunized group also exhibited mild delayed-type hypersensitivity reaction and a high frequency of CD3+CD45RBlow-activated T cells, together with high titer of antiprincipal neutralizing determinant immunoglobulin G antibodies. Thus, this epitope delivery system induced strong epitope-specific T-h-2 polarization.
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Thiyagarajan S, Rajan SS, Gautham N. Effect of DNA structural flexibility on promoter strength--molecular dynamics studies of E. coli promoter sequences. Biochem Biophys Res Commun 2006; 341:557-66. [PMID: 16427605 DOI: 10.1016/j.bbrc.2005.12.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2005] [Accepted: 12/30/2005] [Indexed: 05/06/2023]
Abstract
To study possible correlations between promoter activity and the structural flexibility of the DNA helix, we have carried out unrestrained molecular dynamics simulations of the -10 consensus region sequence and five variants forming the -10 region of various Escherichia coli promoter sequences. Analyses of the trajectories obtained from the simulations show that the consensus sequence has a pattern of two structurally flexible nucleotide steps sandwiched between two stiff steps. In the other sequences, this pattern varies in consonance with the change in the sequence. The variations in the patterns show correlation with the promoter strength.
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Arunachalam J, Kanagasabai V, Gautham N. Protein structure prediction using mutually orthogonal Latin squares and a genetic algorithm. Biochem Biophys Res Commun 2006; 342:424-33. [PMID: 16487483 DOI: 10.1016/j.bbrc.2006.01.162] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Accepted: 01/31/2006] [Indexed: 11/29/2022]
Abstract
We combine a new, extremely fast technique to generate a library of low energy structures of an oligopeptide (by using mutually orthogonal Latin squares to sample its conformational space) with a genetic algorithm to predict protein structures. The protein sequence is divided into oligopeptides, and a structure library is generated for each. These libraries are used in a newly defined mutation operator that, together with variation, crossover, and diversity operators, is used in a modified genetic algorithm to make the prediction. Application to five small proteins has yielded near native structures.
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Bharanidharan D, Gautham N. Principal component analysis of DNA oligonucleotide structural data. Biochem Biophys Res Commun 2006; 340:1229-37. [PMID: 16414352 DOI: 10.1016/j.bbrc.2005.12.127] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 12/17/2005] [Indexed: 10/25/2022]
Abstract
The microstructure of a DNA helix is characterized by several base pair and base step parameters such as twist, rise, roll, propeller twist, etc., in addition to conformational parameters such as the backbone and the glycosidic torsion angles. Among these only a few, which are independent of all others and of each other, may be used to precisely characterize the helix. The problem however is to identify these independent parameters. We have used principal component analysis to identify a relatively small set of independent parameters, with which to characterize each DNA helix. We show that these principal components clearly discriminate between A and B DNA helical types. The calculations further suggest that the microstructure of a DNA helix is better characterized using dinucleotides.
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Bharanidharan D, Gautham N. Amino acid variation in cellular processes in 108 bacterial proteomes. Arch Microbiol 2005; 184:168-74. [PMID: 16205912 DOI: 10.1007/s00203-005-0034-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 08/23/2005] [Accepted: 08/29/2005] [Indexed: 11/28/2022]
Abstract
We have analysed 108 bacterial proteomes in the KEGG database to explore the variation of amino acid composition with respect to protein function. The ratio between the observed amino acid composition and that predicted based on mononucleotide composition was calculated for each functional category. This indicated whether the compositional variation arose from mutation or selection pressure. The results showed that charged amino acids (Lys, Arg and Glu), were found more frequently than expected in proteins involved in genetic information processing (i.e. transcription, translation, etc.) Similarly, in the proteins involved in processing environmental information (e.g. signal transduction), the hydrophobic amino acid Leu was found in excess of values expected from the base composition in the genes.
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Thiyagarajan S, Gautham N. Sequence-dependent structural effects in left-handed DNA. CRYSTALLOGR REV 2005. [DOI: 10.1080/08893110500381264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Thiyagarajan S, Rajan SS, Gautham N. Structure of d(TGCGCG).d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2005; 61:1125-31. [PMID: 16041078 DOI: 10.1107/s0907444905016781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Accepted: 05/26/2005] [Indexed: 11/10/2022]
Abstract
The sequence d(TGCGCG).d(CGCGCA) crystallized in two crystal forms, orthorhombic and hexagonal, in the presence of cobalt hexammine chloride, a known inducer of the left-handed Z-form of DNA. The crystal structures have been solved and refined at 1.71 A resolution in space group P2(1)2(1)2(1) and 2.0 A resolution in space group P6(5). The orthorhombic structure contains one Z-DNA hexamer duplex, while the hexagonal structure contains two hexamer duplexes in the structure. Of the latter, one is situated on a crystallographic sixfold screw axis, leading to disorder. This paper reports the effects of sequence and crystal packing on the structure of Z-type DNA. The structures lend additional support to the authors' earlier conclusion that a stretch of four C.G base pairs is sufficient to nucleate and define the regular model of the left-handed helix based on the structure of d(CGCGCG)2.
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Sadasivan C, Karthe P, Gautham N. Space-group degeneracy in the packing of a non-selfcomplementary Z-DNA hexamer. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2005; 50:192-6. [PMID: 15299458 DOI: 10.1107/s0907444993011035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The X-ray diffraction pattern of the crystals of the non-selfcomplementary hexadeoxyribonucleotide d(CGCACG).d(CGTGCG) can be indexed in four different space groups: (i) P6(5) and P2(1), with cell parameters a = 17.75 (1), b = 17.76 (1), c = 42.77 (3) A, alpha = 90, beta = 90, gamma = 120 degrees, and (ii) P2(1)2(1)2(1) and C2, with cell parameters a = 17.75 (1), b = 30.74 (2), c = 42.77 (3) A, alpha = 90, beta = 90, gamma = 90 degrees. While the R(merge) for the equivalent reflections in the different space groups indicates that P2(1) is the correct choice in the present case, it is demonstrated that the near degeneracy of the space groups arises out of the fact that the DNA molecule is nearly cylindrical. A perfect cylinder would show perfect degeneracy.
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Prasad PA, Vengadesan K, Gautham N. MOLS--a program to explore the potential energy surface of a peptide and locate its low energy conformations. In Silico Biol 2005; 5:401-5. [PMID: 16268784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We describe a computer program that uses mutually orthogonal Latin squares (MOLS) to perform an efficient and exhaustive conformational search of the multi-dimensional potential energy hypersurface of an oligopeptide, and locate all its low energy conformations. The software package has been developed with a user-friendly graphical interface using the Fast Light Tool Kit (FLTK)--a cross platform C++ toolkit.
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Thiyagarajan S, Rajan SS, Gautham N. Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms. Nucleic Acids Res 2004; 32:5945-53. [PMID: 15534365 PMCID: PMC528804 DOI: 10.1093/nar/gkh919] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2004] [Revised: 10/14/2004] [Accepted: 10/14/2004] [Indexed: 11/14/2022] Open
Abstract
We report here the crystal structure of the DNA hexamer duplex d(CGCGCA)*d(TGCGCG) at 1.71 A resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson-Crick base pairing to a 'wobble' like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.
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Abstract
Conformational studies of two linear enkephalin molecules, Met-enkephalin and Leu-enkephalin, have been carried using the mutually orthogonal Latin squares (MOLS) technique with the ECEPP/3 force field. This technique was developed recently in our laboratory to perform an unbiased search of the conformational space of peptides and to locate low energy conformations. The present study identified all the folds predicted by other studies, and in addition picked up other energetically favorable structures. The results suggest that the peptide backbone exists as a mixture of folded and unfolded forms (approximately 50% each). The study also provides information on the distribution of the low energy conformations that we have classified on the basis of structural motifs, backbone hydrogen-bonding patterns, and root mean square deviations in atomic positions.
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Vengadesan K, Gautham N. Energy Landscape of Met-Enkephalin and Leu-Enkephalin Drawn Using Mutually Orthogonal Latin Squares Sampling. J Phys Chem B 2004. [DOI: 10.1021/jp049581v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Vengadesan K, Anbupalam T, Gautham N. An application of experimental design using mutually orthogonal Latin squares in conformational studies of peptides. Biochem Biophys Res Commun 2004; 316:731-7. [PMID: 15033460 DOI: 10.1016/j.bbrc.2004.02.114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2004] [Indexed: 10/26/2022]
Abstract
We address the question-can we use experimental design methods to investigate peptide conformation and identify conformational parameters that may contribute more significantly to the potential energy than others? We used mutually orthogonal Latin square design to sample the conformational space of peptides and analysed the samples using analysis of variance. We examined the equality of the effect of the torsion angles on the conformational potential energy. The results showed that different torsion angles contributed differently to the conformational energy. We are able to identify those parameters that may have to be more carefully considered in conformational studies of peptides.
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Bharanidharan D, Bhargavi GR, Uthanumallian K, Gautham N. Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species. Biochem Biophys Res Commun 2004; 315:1097-103. [PMID: 14985126 DOI: 10.1016/j.bbrc.2004.01.129] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2004] [Indexed: 11/21/2022]
Abstract
We studied the correlations between amino acid composition and mononucleotide and dinucleotide frequencies in 115 bacterial genomes of varying G+C content. Observed amino acid frequencies were compared with those expected from the actual mononucleotide and dinucleotide frequencies. Both mononucleotide and dinucleotide frequencies correlate well with the amino acid frequency, with dinucleotide frequencies doing so better. Despite the strong correlations, some of the observed amino acid frequencies, in particular for Arg, Val, Asp, Glu, Ser, and Cys, were consistently different from predicted values in all genomes. We suggest that this variation from predicted values is a consequence of selection pressure at the level of amino acids, while the close correspondence to the predictions in residues such as Thr, Phe, Lys, and Asn arises only from mutation and selection pressure at the level of the nucleic acid sequences.
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