Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA.

Induced fit effects in the complex of a DNA decamer with two even-skipped transcriptional repressor homeodomain molecules were investigated by means of molecular dynamics simulations. Dynamics of these effects are found to be in the time scale from pico- to nanoseconds. First steps are made by the fast-moving DNA backbone phosphates, which upon binding change their B(I)/B(II) substate distribution.

Hydration of hydroxypyrrole influences binding of ImHpPyPy-beta-Dp polyamide to DNA.

Ligands which are able to recognize DNA sequence specifically are of fundamental interest as transcription controlling drugs. Recently a polyamide ligand was developed (ImHpPyPy-beta-Dp) which differentiates in a dimeric arrangement between all four possible base pair steps in the minor groove. This is a landmark for the design of DNA binding drugs because it was believed that such a recognition could only be possible in the major groove of DNA.

Energetic and stereochemical effects of the protein environment on substrate: a theoretical study of methylmalonyl-CoA mutase.

QM/MM methods were used to study the isomerization step from (2R)-methylmalonyl-CoA to succinyl-CoA. A pathway via a "fragmentation-recombination" mechanism is ruled out on energetic grounds. For the other radicalic pathway, involving an addition recombination step, geometries and vibrational contributions have been determined, and a barrier height of 11.

The conformer substates of nonoriented B-type DNA in double helical poly(dG-dC).

A nonoriented hydrated film of poly(dG-dC) with ?20 water molecules per nucleotide (called B* by Loprete and Hartman (Biochem. 32, 4077-4082 (1993)) was studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated sample between 290 and 270 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200 and 220 K. IR spectral changes on isothermal relaxation at 200 and 220 K, caused by interconversion of two conformer substates, are revealed by difference spectra.

Characterization of the vitamin E-binding properties of human plasma afamin.

Human plasma afamin, the fourth member of the albumin gene family, is shown to be a specific binding protein for vitamin E. A radio ligand-binding assay followed by Scatchard and Hill analysis are used to show that afamin has a binding affinity for both alpha-tocopherol and gamma-tocopherol, two of the most important forms of vitamin E, in vitro. The binding-dissociation constant was determined to be 18 microM, indicating that afamin plays a role as vitamin E carrier in body fluids such as human plasma and follicular fluid under physiological conditions.

PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA.

We investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened.

Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2.

The exact understanding of the interaction of minor groove binding drugs with DNA is of interest due to their importance as transcription controlling drugs. In this study we performed four molecular dynamics simulations, one of the uncomplexed d(CGCGAATTCGCG)(2) dodecamer and three simulations of the DNA complexed with the minor groove binder netropsin. The charged guanidinium and amidinium ends of the small ligand were in one simulation formally uncharged, in the second one normally charged, and in the third simulation we doubled the charges of the two ends.

Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions.

Although the trp-repressor-operator complex is one of the best studied transcriptional controlling systems, some questions regarding the specific recognition of the operator by the repressor remain. We performed a 2.35 ns long molecular dynamics simulation to clarify the influence of the two B-DNA backbone conformational substates B(I) and B(II) on complexation.

Towards the experimental decomposition rate of carbonic acid (H2CO3) in aqueous solution.

Dry carbonic acid has recently been shown to be kinetically stable even at room temperature. Addition of water molecules reduces this stability significantly, and the decomposition (H2CO3 + nH2O --> (n+1)H2O + CO2) is extremely accelerated for n = 1, 2, 3. By including two water molecules, a reaction rate that is a factor of 3000 below the experimental one (10 s(-1)) at room temperature was found.

Exocyclic groups in the minor groove influence the backbone conformation of DNA.

Exocyclic groups in the minor groove of DNA modulate the affinity and positioning of nucleic acids to the histone protein. The addition of exocyclic groups decreases the formation of this protein-DNA complex, while their removal increases nucleosome formation. On the other hand, recent theoretical results show a strong correlation between the B(I)/B(II) phosphate backbone conformation and the hydration of the grooves of the DNA.

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study.

This paper presents geometries of copper(II) chelates with L-alanine, L-leucine, and L-N,N-dimethylvaline optimized by the hybrid density functional method B3LYP. According to the molecular quantum mechanics results, a square-planar copper(II) coordination geometry is electronically favored in vacuo. Deviations from the planar configuration observed in the crystal state should be attributed to sterical intramolecular and/or intermolecular effects.

Significance of ligand tails for interaction with the minor groove of B-DNA.

Minor groove binding ligands are of great interest due to their extraordinary importance as transcription controlling drugs. We performed three molecular dynamics simulations of the unbound d(CGCGAATTCGCG)(2) dodecamer and its complexes with Hoechst33258 and Netropsin. The structural behavior of the piperazine tail of Hoechst33258, which has already been shown to be a contributor in sequence-specific recognition, was analyzed.

Complex of B-DNA with polyamides freezes DNA backbone flexibility.

The development of sequence-specific minor groove binding ligands is a modern and rapidly growing field of research because of their extraordinary importance as transcription-controlling drugs. We performed three molecular dynamics simulations in order to clarify the influence of minor groove binding of two ImHpPyPy-beta-Dp polyamides to the d(CCAGTACTGG)(2) decamer in the B-form. This decamer contains the recognition sequence for the trp repressor (5'-GTACT-3'), and it was investigated recently by X-ray crystallography.

The reaction rate constant of chlorine nitrate hydrolysis.

The first-order rate constant for the decomposition of chlorine nitrate (ClONO2) by water in a cyclic 1:3 complex at stratospheric temperatures is shown to be close to the values for the hydrolysis rate coefficient of chlorine nitrate on an ice surface determined in the laboratory. On the other hand the rate constants calculated for the cyclic 1:1 and 1:2 complexes are much lower than the experimental results. From the mechanistic point of view the reaction is found to be similar to a SN2 mechanism and coupled with water-mediated proton transfer in accordance with the intriguing findings of Bianco and Hynes [R.

Prediction of the structure of human Janus kinase 2 (JAK2) comprising the two carboxy-terminal domains reveals a mechanism for autoregulation.

The structure of human Janus kinase 2 (JAK2) comprising the two C-terminal domains (JH1 and JH2) was predicted by application of homology modelling techniques. JH1 and JH2 represent the tyrosine kinase and tyrosine kinase-like domains, respectively, and are crucial for function and regulation of the protein. A comparison between the structures of the two domains is made and structural differences are highlighted.

Toward elimination of discrepancies between theory and experiment: the rate constant of the atmospheric conversion of SO3 to H2SO4.

The hydration rate constant of sulfur trioxide to sulfuric acid is shown to depend sensitively on water vapor pressure. In the 1:1 SO3-H2O complex, the rate is predicted to be slower by about 25 orders of magnitude compared with laboratory results [Lovejoy, E. R.

Elbow flexibility and ligand-induced domain rearrangements in antibody Fab NC6.8: large effects of a small hapten.

Four 700-ps molecular dynamics simulations were carried out to analyze the structural dynamics of the antigen-binding antibody fragment NC6.8, which is known to exhibit large structural changes upon complexation. The first simulation was started from the x-ray structure of the uncomplexed Fab and produced trajectory averages that closely match the crystallographic results.

Automated docking of ligands to antibodies: methods and applications.

Many approaches to studying protein-ligand interactions by computational docking are currently available. Given the structures of a protein and a ligand, the ultimate goal of all docking methods is to predict the structure of the resulting complex. This requires a suitable representation of molecular structures and properties, search algorithms to efficiently scan the configuration space for favorable interaction geometries, and accurate scoring functions to evaluate and rank the generated orientations.

Application of multivariate data analysis methods to comparative molecular field analysis (CoMFA) data: proton affinities and pKa prediction for nucleic acids components.

Multivariate data analysis methods (Principal Component Analysis (PCA) and Partial Least Squares (PLS)) are applied to the analysis of the CoMFA (Comparative Molecular Field Analysis) data for several nucleic acids components. The data set includes nitrogenated bases, nucleosides, linear nucleotides, 3', 5'-cyclic nucleotides and oligonucleotides. PCA is applied to study the structure of the CoMFA data and to detect possible outliers in the data set.

Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion.

Investigations of spontaneous, i.e. not forced, B-DNA's B(I)<==>B(II) substate transitions are carried out on the d(CGCGAATTCGCG)2 EcoRI dodecamer sequence using Molecular Dynamics Simulations.

Unexpected BII conformer substate population in unoriented hydrated films of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes.

Conformational substates of B-DNA had been observed so far in synthetic oligonucleotides but not in naturally occurring highly polymeric B-DNA. Our low-temperature experiments show that native B-DNA from salmon testes and the d(CGCGAATTCGCG)2 dodecamer have the same BI and BII substates. Nonequilibrium distribution of conformer population was generated by quenching hydrated unoriented films to 200 K, and isothermal structural relaxation toward equilibrium by interconversion of substates was followed by Fourier transform infrared spectroscopy.

Ligand binding by antibody IgE Lb4: assessment of binding site preferences using microcalorimetry, docking, and free energy simulations.

Antibody IgE Lb4 interacts favorably with a large number of different compounds. To improve the current understanding of the structural basis of this vast cross-reactivity, the binding of three dinitrophenyl (DNP) amino acids (DNP-alanine, DNP-glycine, and DNP-serine) is investigated in detail by means of docking and molecular dynamics free energy simulations. Experimental binding energies obtained by isothermal titration microcalorimetry are used to judge the results of the computational studies.

Comparative molecular field analysis of artemisinin derivatives: ab initio versus semiempirical optimized structures.

Based on the belief that structural optimization methods, producing structures more closely to the experimental ones, should give better, i.e. more relevant, steric fields and hence more predictive CoMFA models, comparative molecular field analyses of artemisinin derivatives were performed based on semiempirical AM1 and HF/3-21G optimized geometries.

Ligand-induced domain movement in an antibody Fab: molecular dynamics studies confirm the unique domain movement observed experimentally for Fab NC6.8 upon complexation and reveal its segmental flexibility.

Two molecular dynamics simulations were carried out for the antibody Fab NC6.8, both with and without the guanidinium sweetener ligand NC174, in order to assess the segmental flexibility as well as the conformational changes upon ligand binding. Trajectory analyses of the simulation of the uncomplexed Fab suggest low-amplitude motions of the Ig domains with respect to each other, most clearly reflected by a periodic alteration of the elbow angle within a range of 11 degrees.