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U C Singh

Publications and source records attributed to U C Singh.

26 records · Page 2Linked to original sources
PubMed1986

On loop folding in nucleic acid hairpin-type structures.

In a series of studies, combining NMR, optical melting and T-jump experiments, it was found that DNA hairpins display a maximum stability when the loop part of the molecule comprises four or five nucleotide residues. This is in contrast with the current notion based on RNA hairpin studies, from which it had been established that a maximum hairpin stability is obtained for six or seven residues in the loop. Here we present a structural model to rationalize these observations. This model is based on the notion that to a major extent base stacking interactions determine the stability of nucleic acid conformations. The model predicts that loop folding in RNA is characterized by an extension of the base stacking at the 5'-side of the double helix by five or six bases; the remaining gap can then easily be closed by two nucleotides. Conversely, loop folding in DNA is characterized by extending base stacking at the 3'-side of the double helical stem by two or three residues; again bridging of the remaining gap can then be achieved by one or two nucleotides. As an example of loop folding in RNA the anticodon loop of yeast tRNAPhe is discussed. For the DNA hairpin formed by d(ATCCTAT4TAGGAT) it is shown that the loop structure obtained from molecular mechanics calculations obeys the above worded loop folding principles.

Base Sequence↗
PubMed1986

Modeling complex molecular interactions involving proteins and DNA.

We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.

Base Sequence↗
PubMed1985

A molecular dynamics simulation of double-helical B-DNA including counterions and water.

We present the results of an atomic level molecular dynamical simulation of a 5-base-pair fragment of double-helical DNA with inclusion of water and sodium counterions and a complete description of their electrostatic interactions. The shape of the double helix is preserved throughout the simulation, and the helix repeat is calculated to be 10.0, in reasonable agreement with experimental results. The most flexible conformational angles in the structure are the glycosidic angle and the sugar pucker.

Computers↗
PubMed1985

Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions.

We present the results of molecular dynamics simulations on d(C-G-C-G-A) X d(T-C-G-C-G) with fully charged phosphates with and without inclusion of counterions. The average structures found in the two simulations are similar, but the simulation with counterions does give an average helix repeat, tilt, and twist in better agreement with those found in the x-ray structure of d(C-G-C-G-A-A-T-T-C-G-C-G)2. The average sugar pucker phases and amplitudes are in qualitative agreement with those found in NMR studies of double-helical DNA, and a number of examples of sugar repuckering from C2' endo to C3' endo carbon conformations in the sugar ring are found. The hydrogen bond correlations as well as torsion correlations are analyzed, and some interesting long-range correlations between dihedral angles are found.

Magnetic Resonance Spectroscopy↗
PubMed1981

Systematic variation in bond lengths of peptides.

The lengths of the carbonyl as well as of the adjacent C-N and C-C bonds in peptides are shown to vary systematically with the central C-N bond length. Results of ab initio calculations on N-methylacetamide and its Li+, Na+ and Mg2+ complexes are also discussed.

Acetamides↗
PubMedDate not supplied

Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin.

Site-directed mutagenesis is a very powerful approach to altering the biological functions of proteins, the structural stability of proteins and the interactions of proteins with other molecules. Several experimental studies in recent years have been directed at estimating the changes in catalytic properties, (rates of binding and catalysis) in site-directed mutants of enzymes compared to the native enzymes. Simulation approaches to the study of complex molecules have also become more powerful, in no small measure owing to the increase in computer power. These simulations have often allowed results of experiments to be rationalized and understood mechanistically. A new approach called the free-energy pertubation method, which uses statistical mechanics and molecular dynamics can often be used for quantitative calculation of free energy differences. We have applied such a technique to calculate the differential free energy of binding and free energy of activation for catalysis of a tripeptide substrate by native subtilisin and a subtilisin mutant (Asn 155----Ala 155). Our studies lead to a calculated difference in free energy of binding which is relatively small, but a calculated change in free energy of catalysis which is substantial. These energies are very close to those determined experimentally (J. A. Wells and D. A. Estell, personal communication), which were not known to us until the simulations were completed. This demonstrates the predictive power and utility of theoretical simulation methods in studies of the effects of site-specific mutagenesis on both enzyme binding and catalysis.

Asparagine↗