Stereochemical model for proflavin intercalation in A-DNA.

Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming trans, with all sugars retaining the characteristics C3'-endo pucker. This extended conformation results in virtually no helical unwinding, suggesting it may be an appropriate model for an intercalative intermediary in mutagenesis by virtue of its similarity to standard helical DNA.     

Ribonuclease S-peptide. A model for molecular recognition.

The relationship of structure to function in the recognition of ribonuclease S-peptide by S-protein was studied by several methods. Liquid phase peptide synthesis was employed to generate analogs of S-peptide in which from 1 to 8 residues were deleted from the NH2-terminal end of the S-peptide. Additional derivatives were made by substitutions in the NH2-terminal three amino acids or by modifying the S-peptide analogs by trifluoroacetylation. The analogs were generated in the following way. S-Peptide was cleaved with chymotrypsin. The fragment obtained, RNase(9-20), was purified and lengthened step by step using liquid phase peptide synthesis. A second set of analogs were prepared by cleavage of CF3CO-S-peptide with elastase and the resulting CF3CO-RNase(7-20), similarly lengthened. The various analogs of S-peptide were tested in their capacity to combine with S-protein and regenerate biological activity as measured by Vmax and Kb. This work shows a positive contribution of every one of the first 8 NH2-terminal residues of S-peptide to the molecular recognition of S-protein in the presence of RNA substrate. Substitution of the first 3 residues by alanine or blocking of the free amino groups decreases recognition, indicating that the original primary structure is the most favorable one.     

A molecular model for persister in E. coli

Like many other bacteria, Escherichia coli remain as tiny viable individuals named persisters after being exposed to an antibiotic. These persisters are believed to be phenotypic heterogeneous one rather than mutants, because their progenies are as susceptible to antibiotics as their ancestors. Recently, two persister-related genes (hipB/hipA) were confirmed to belong to a toxin-antitoxin (TA) module. Their control circuit was believed to be responsible for generation of the persister subpopulation. For the well-studied TA module, we build a simple genetic regulation model to explain the phenotypic heterogeneity. We find that a sole double-negative feedback loop is not enough to explain the phenotypic heterogeneity; the cooperation mechanisms in HipB and HipA are indispensable. Moreover, our model illustrates an important persister-related experimental phenomenon: the emergence of the persister depends on the growth rate in continuous culture.     

A molecular model for vesicle formation

A molecular model is proposed to explain vesicle formation. The model is based on a balance between elastic and ‘hydrophobic’ forces for various micelle and bilayer geometries in dilute aqueous solutions. It predicts bilayered disc-like transition structures and is in agreement with experimental data.     

RNA polymerase-rifamycin. A molecular model of inhibition

By fluorimetric titration of Rifs (E. coli B) and Rifr (E. coli rpoB255) RNA polymerases with rifamycin, the mutant polymerase was demonstrated to bind rifamycin. A comparison of spatial structures of rifamycin and dinucleotide fragment of RNA in the hybrid with DNA revealed their similarity. Taking into account this structural similarity and also the fact that two phosphodiester bonds can be formed by RNA polymerase in the presence of rifamycin, a model for the inhibition mode was proposed. According to this model, rifamycin occupies the place of two terminal nucleotides of synthesized, but not translocated pentanucleotide in the transcribing complex. Asp-516 of the wild type beta-subunit was assumed to form a hydrogen bond with the rifamycin C(23) hydroxyl group. On the base of this model, reduced "cycling" synthesis of tetra-, penta-... up to decanucleotides by the Rifr RNA polymerase, in comparison with Rifs, was predicted.     

A stochastic evolutionary model of molecular sequences.

A stochastic evolutionary model of molecular sequences is proposed. The basic forces in evolution are supposed to be mutation and selection. The concept is somewhat similar to Kauffman-Levin's concept of adaptive walks and corresponding analytical expressions have been developed. The selective force is divided into two parts: a slowly-varying part and a rapidly-changing fluctuation. The latter influences the distribution of sequences and results in an equation of motion along the flow line. The former plays a more important role in the emergence of evolutionary order. It is demonstrated that the asymmetry of selective forces would lead to a definite order of the system.     

A detailed molecular model for human aromatase

Using a variety of techniques, including sequence alignment, secondary struucture prediction, molecular mechanics and molecular dynamics, we have constructed a model for the three-dimensional structure of P-450_AROM (human aromatase) based on that of P-450_cam, the only cytochrome P-450 enzyme for which crystal structure is known. The predicted structure is found to be in good agreement with current experimental data; both direct, from site-directed mutagenesis studies, and indirect, from the consideration of the structures and activities of known substrates and inhibitors.     

A molecular model for sporadic human aneuploidy

Aneuploidy is a leading cause of birth defects and a significant contributor to infertility in humans. Maternal age is the only well-established risk factor for gametic aneuploidy in the general population, with the underlying cause(s) yet to be identified. Here we present an extension of the 'two-hit' model for sporadic human aneuploidy. An important implication of this model is that the genetic makeup of an individual will influence the threshold where recombinationally at-risk oocytes (hit-1 events) become sensitive to the effects of advancing age (hit-2 events). Consequently, the age-related risk of gametic aneuploidy in many individuals is likely to differ significantly from the population average, and single nucleotide polymorphisms (SNPs) associated with altered risk should be identifiable.     

Cholesterol in model membranes. A molecular dynamics simulation.

Molecular dynamics simulations of a model membrane with inserted cholesterol molecules have been performed to study the perturbing influence of cholesterol. In the fluid phase of a lipid bilayer at 13 mol% concentration of cholesterol, local ordering of the hydrocarbon chains is induced. This perturbation decays with the distance from the cholesterol, and the effect extends 1.25 nm. It can be monitored in several ways, e.g., by an order parameter corresponding to deuterium nuclear magnetic resonance quadrupolar splittings, by the fraction of gauche bonds, or by the local bilayer thickness. At constant surface density, the local ordering is accompanied by disordering of the bulk phase, and, consequently, the net ordering effect is small. After compressing the system laterally in accordance with experimentally known surface areas, the bulk order parameters agree with those of a pure system, and the average order parameters are in accordance with experimental data. The necessity for this lateral compression is supported by calculated lateral pressures. At lower cholesterol concentration (3%), no direct perturbing effect is observed. A smaller lateral pressure than in a pure system indicates that the system with cholesterol is expected to have a smaller surface area, which would result in an increase of the order parameters, thus accounting for the experimental observations. The lack of spatial variation is, however, puzzling and may indicate a cooperative ordering effect.     

A molecular model for diacylglycerol acyltransferase from Mortierella ramanniana var. angulispora

Acyl CoA diacylglycerol acyltransferase (DGAT, EC 2.3.120) is recognized as a key player of cellular diacylglycerol metabolism. It catalyzes the terminal, yet the committed step in triacylglycerol synthesis using diacylglycerol and fatty acyl CoA as substrates. The protein sequence of diacylglycerol acyltransferse (DGAT) Type 2B in Moretierella ramanniana var. angulispora (Protein_ID = {"type":"entrez-protein","attrs":{"text":"AAK84180.1","term_id":"15099961"}}AAK84180.1) was retrieved from GenBank. However, a structure is not yet available for this sequence. The 3D structure of DGAT Type 2B was modeled using a template structure (PDB ID: 1K30) obtained from Protein databank (PDB) identified by searching with position specific iterative BLAST (PSI-BLAST). The template (PDB ID: 1K30) describes the structure of DGAT from Cucurbita moschata. Modeling was performed using Modeller 9v2 and protein model is hence generated. The DGAT type 2B protein model was subsequently docked with six inhibitors (sphingosine; trifluoroperazine; phosphatidic acid; lysophospatidylserine; KCl; 1, 2-diolein) using AutoDock (a molecular docking program). The binding of inhibitors to the protein model of DGAT type 2B is discussed.     

A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices.

A number of studies have concluded that strand exchange between a RecA-complexed DNA single strand and a homologous DNA duplex occurs via a single-strand invasion of the minor groove of the duplex. Using molecular modeling, we have previously demonstrated the possibility of forming a parallel triple helix in which the single strand interacts with the intact duplex in the minor groove, via novel base interactions (Bertucat et al., J. Biomol. Struct. Dynam. 16:535-546). This triplex is stabilized by the stretching and unwinding imposed by RecA. In the present study, we show that the bases within this triplex are appropriately placed to undergo strand exchange. Strand exchange is found to be exothermic and to result in a triple helix in which the new single strand occupies the major groove. This structure, which can be equated to so-called R-form DNA, can be further stabilized by compression and rewinding. We are consequently able to propose a detailed, atomic-scale model of RecA-promoted strand exchange. This model, which is supported by a variety of experimental data, suggests that the role of RecA is principally to prepare the single strand for its future interactions, to guide a minor groove attack on duplex DNA, and to stabilize the resulting, stretched triplex, which intrinsically favors strand exchange. We also discuss how this mechanism can incorporate homologous recognition.     

A hand-over-hand diffusing model for myosin-VI molecular motors

Single molecules of dimeric myosin-VI have been demonstrated to be able to move processively towards the pointed end of actin filament with a mean step size of approximately 36 nm. Here we present a hand-over-hand diffusing mechanism for this unidirectional movement. Based on this mechanism, its dynamical behaviors such as the step-size distribution, dwell-time distributions and mean dwell time at various ATP and ADP concentrations and under various loads are studied in detail. The calculated results show good agreement with previous experimental results. The processive movement of mutant myosin-V with its neck domains truncated to only one IQ motif can also be explained by using this hand-over-hand diffusing model.     

Optically detected zero field magnetic resonance studies of proflavine-DNA and 3,4-benzpyrene-DNA complexes.

Optical detection of magnetic resonance has been used to observe the photoexcited triplet state zero-field transitions of proflavine in DNA and 3,4-benzpyrene in DNA at 2°K. The results suggest that optically detected magnetic resonance may be utilized for determining the local site distribution of small molecules bound to DNA.     

A basic molecular model for the H2 histamine receptor. Part 1

A 3D model of the canine H2 receptor was built and analysed. This model was constructed using primary sequence comparisons and three-dimensional homology building with bacteriorhodopsin serving as a template. The energy analysis of the interaction between the N3H⁺ form and the N1H⁺ form of histamine with the receptor shows that both have the same binding affinity for the H2 receptor, but only the N3H⁺ form provokes structural changes. The calculated potential energies are consistent with the published binding data and suggest that Asp 98 is the principal residue for ligand recognition. On the basis of sequence alignment studies we postulate that Glu 270 in helix 7 may be important for activation of the H2 receptor. Docking studies of the N3H⁺ folded conformation in our model show that an intramolecular hydrogen bond between N3 and the amino group of the histamine molecule is broken, and the histamine then adopts a conformation similar to the N3H⁺ extended form to interact optimally with the H2 receptor. Mutations were made in the H2 receptor model to mimic published experimental point mutations. The interactions of the mutated receptor models with histamine are consistent with the experimental data.     

A dynamic continuum model for molecular regulation of the humoral immune response.

Based on current concepts of the nature of specific immunocompetent cell surface receptors, hematopoietic stem cell differentiation and membrane dynamics, a simple model is proposed by which the event of immunogen binding by cell surface receptors specifically stimulates a constitutive process. The concept that enhancement of process flows in two directions with time allows for correlation of recent experimental findings into a molecular theory for antibody induction. The Model helps explain antibody specificity, heterogeneity and affinity changes and rationalizes immune memory.