Analytically defined surfaces to analyze molecular interaction properties

Molecular surfaces are widely used for characterizing molecules and displaying and quantifying their interaction properties. Here we consider molecular surfaces defined as isocontours of a function (a sum of exponential functions centered on each atom) that approximately represents electron density. The smoothness is advantageous for surface mapping of molecular properties (e.g., electrostatic potential). By varying parameters, these surfaces can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy. We describe numerical algorithms to operate on the analytically defined surfaces. Two applications are considered: (1) We define and locate extremal points of molecular properties on the surfaces. The extremal points provide a compact representation of a property on a surface, obviating the necessity to compute values of the property on an array of surface points as is usually done; (2) a molecular surface patch or interface is projected onto a flat surface (by introducing curvilinear coordinates) with approximate conservation of area for analysis purposes. Applications to studies of protein-protein interactions are described.     

Understanding the overdispersed molecular clock

Rates of molecular evolution at some protein-encoding loci are more irregular than expected under a simple neutral model of molecular evolution. This pattern of excessive irregularity in protein substitutions is often called the "overdispersed molecular clock" and is characterized by an index of dispersion, R(T) > 1. Assuming infinite sites, no recombination model of the gene R(T) is given for a general stationary model of molecular evolution. R(T) is shown to be affected by only three things: fluctuations that occur on a very slow time scale, advantageous or deleterious mutations, and interactions between mutations. In the absence of interactions, advantageous mutations are shown to lower R(T); deleterious mutations are shown to raise it. Previously described models for the overdispersed molecular clock are analyzed in terms of this work as are a few very simple new models. A model of deleterious mutations is shown to be sufficient to explain the observed values of R(T). Our current best estimates of R(T) suggest that either most mutations are deleterious or some key population parameter changes on a very slow time scale. No other interpretations seem plausible. Finally, a comment is made on how R(T) might be used to distinguish selective sweeps from background selection.     

Native (Na-+ + K-+)-dependent adenosine triphosphatase has two trypsin-sensitive sites.

Sodium and potassium adenosine triphosphatase ((Na + K)-ATPase) consists of two polypeptides, a large molecular weight polypeptide (MW 84,000 to 102,000) and a sialoglycoprotein (MW 35,000 to 57,000). Trypsin treatment of this complex selectively cleaves the large polypeptide into two fragments with molecular weights of 62,000 and 43,000. Simultaneously with the appearance of these fragments, (Na + K)-APTase activity is destroyed. Trypsin treatment of phosphorylated enzyme shows that he 43,000 molecular weight fragment is phosphorylated. If (Na + K)-ATPase is digested with trypsin in the presence of ATP, a 90,000 molecular weight fragment is produced. Disappearance of the large polypeptide, and loss of ATPase activity parallel the production of this fragment. Addition of strophanthidin to this mixture significantly lowers the amount of the 90,000 molecular weight fragment produced. Experiments on (Na + K)-ATPase of the red cell membrane suggest that trypsin is cleaving (Na + K)-ATPase at the interior surface of the plasma membrane.     

Quantitative 13C and 2H NMR relaxation studies of the 723-residue enzyme malate synthase G reveal a dynamic binding interface

A detailed understanding of molecular recognition is predicated not only on high-resolution static structures of the free and bound states but also on information about how these structures change with time, that is, molecular dynamics. Here we present a deuterium ((2)H) and carbon ((13)C) NMR relaxation study of methyl side chain dynamics in the 82 kDa enzyme malate synthase G (MSG) that is a promising target for the development of new antibiotic agents. It is shown that excellent agreement between (2)H- and (13)C-derived measures of dynamics is obtained, with correlation coefficients exceeding 0.95. The binding interface formed by MSG and its substrates is found to be highly dynamic in the ligand-free state of the enzyme with rigidification upon binding substrate. This study establishes that detailed, quantitative information about methyl side chain dynamics can be obtained by NMR on proteins with molecular masses on the order of 100 kDa and opens up the possibilities for studies of motion in a large number of important systems.     

Modeling of Supramolecular Properties of Molecular Tweezers, Clips, and Bowls

The electrostatic potential surface (EPS) is calculated for molecular tweezers, clips, and bowls at different levels of theory (semiempirical AM1, ab initio HF/6-31G*, and density functional theory pBP/DN**). According to these calculations, the molecular electrostatic potential (MEP) on the concave side of the molecular tweezers and clips is suprisingly negative for hydrocarbons. This finding seems to be a general phenomenon in nonconjugated ?-electron systems with concave-convex topology and it explains the receptor properties of the molecular tweezers and clips. Analogous calculations performed for the conjugated aromatic molecular bowls show different results. The DFT calculations predict that in these systems the more negative MEP lies on the concave side similar to the findings for the nonconjugated molecular tweezer- and clip-systems, whereas the AM1 calculation leads to the opposite result that the MEP is more negative on convex side of the bowl-systems.     

Towards molecularly imprinted polymers selective to peptides and proteins. The epitope approach

In this paper, we describe the epitope approach to molecular imprinting. The applicability of molecular imprinting, a method that allows the preparation of biomimetic compounds (artificial receptors and antibodies), is extended by this approach. Our approach makes it possible to obtain imprinted polymers selective to peptides and proteins whereas, to date, molecular imprinting has been used primarily for the preparation of polymers that selectively bind to relatively low molecular weight substances. The epitope approach is based on using (as a template) a short peptide that represents only part of a larger peptide or protein (as an epitope represents an antigen), which in turn can be recognized by the synthesized polymer. It is demonstrated that although other parts of peptides can influence the process of molecular recognition, the polymers imprinted with a short peptide efficiently recognize both the template and larger peptides (for example, oxytocin) that possess the same C-terminal part of the structure.     

Identification of a gastrin binding protein in porcine gastric mucosal membranes by covalent cross-linking with iodinated gastrin

A gastrin binding protein (GBP) has been identified in detergent extracts of porcine gastric mucosal membranes by covalent cross-linking to 125I-[Nle15]gastrin with disuccinimidyl suberate. The apparent molecular weight of the cross-linked complex (80,000) is uneffected by reduction suggesting that the GBP is not composed of disulfide-bonded subunits. Subtraction of the molecular weight of 125I-gastrin indicates that the molecular weight of the GBP is 78,000. A similar molecular weight has been observed previously for the gastrin receptor (74,000) on intact canine parietal cells and plasma membranes therefrom, and for the receptor for the related hormone cholecystokinin (76,000-85,000) on pancreatic acinar membranes under reducing conditions. The similarity in molecular weight between the gastrin receptor and the solubilized GBP suggests that the latter protein is probably the gastrin receptor. However, the concentration (2 microM) of [Nle15]gastrin required for 50% inhibition of cross-linking of gastrin to the GBP solubilized in 0.1% Triton X-100 is 200-fold greater than the value (10 nM) observed for the gastrin receptor on isolated canine gastric parietal cells. A lower concentration (0.3 microM) of [Nle15]gastrin was required to inhibit cross-linking in a milder detergent (0.4% digitonin, 0.08% cholate). Thus, the reduced affinity for gastrin of the putative solubilized form of the gastrin receptor appears to be a result of detergent extraction.     

Congruence of Morphological and Molecular Phylogenies

When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori.     

The different mechanisms of sporophytic self-incompatibility

Flowering plants have evolved a multitude of mechanisms to avoid self-fertilization and promote outbreeding. Self-incompatibility (SI) is by far the most common of these, and is found in ca. 60% of flowering plants. SI is a genetically controlled pollen-pistil recognition system that provides a barrier to fertilization by self and self-related pollen in hermaphrodite (usually co-sexual) flowering plants. Two genetically distinct forms of SI can be recognized: gametophytic SI (GSI) and sporophytic SI (SSI), distinguished by how the incompatibility phenotype of the pollen is determined. GSI appears to be the most common mode of SI and can operate through at least three different mechanisms, two of which have been characterized extensively at a molecular level in the Solanaceae and Papaveraceae. Because molecular studies of SSI have been largely confined to species from the Brassicaceae, predominantly Brassica species, it is not yet known whether SSI, like GSI, can operate through different molecular mechanisms. Molecular studies of SSI are now being carried out on Ipomoea trifida (Convolvulaceae) and Senecio squalidus (Asteraceae) and are providing important preliminary data suggesting that SSI in these two families does not share the same molecular mechanism as that of the Brassicaceae. Here, what is currently known about the molecular regulation of SSI in the Brassicaceae is briefly reviewed, and the emerging data on SSI in I. trifida, and more especially in S. squalidus, are discussed.     

Nanoindentation response of nickel surface using molecular dynamics simulation

The mechanisms of dislocation nucleation on a nickel (Ni) (001) surface under nanoindentation behaviours are investigated using molecular dynamics simulation. The characteristic mechanisms include the molecular models of a thermal layer (TL) and thermal with a free layer (TFL), multi-step load/unload cycles, tilt angles and shapes of the indenter, and slip vectors. The model of a TL has higher reaction force than a TFL. The maximum forces of nanoindentation decrease with increasing time of the multi-step load/unload cycle. The indenter with the tilt angle has larger force to act on the molecular model than the indenter along the normal direction. The effect of the indentation shape is presented such that the conical tip has larger load force to act on the molecular model. The defects along Shockley partials on the (111) plane are produced during nanoindentation involving nucleation, glide and slip.     

Characterization of phosphatidylinositol-specific phospholipase C from cultured vascular smooth muscle cells.

Phosphoinositide-specific phospholipase C (PLC) activities have been partially purified from cultured vascular smooth muscle cells and analyzed for substrate specificity, calcium and pH requirements, and molecular weight. The purification procedure involved DEAE-cellulose and heparin-Sepharose chromatographies followed by Mono Q and size exclusion high performance liquid chromatography. This technique resolves multiple peaks of activity using phosphatidylinositol (PI) and PI 4,5-bisphosphate (PIP2) as substrates. The major peak was purified to near homogeneity as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PLC activity in vascular smooth muscle cells can be divided into two types based on their calcium and pH requirements, substrate preferences, and molecular weights. The low molecular weight PLC hydrolyzes both PI and PIP2, has a molecular mass of 58 kDa, requires the most calcium for full activation, and has a PI-pH profile that shifts slightly with calcium concentration. Screening a cDNA library with oligonucleotides directed against several of the known PLCs identified a highly expressed PLC cDNA that is 99% homologous to PLC-alpha, suggesting that this low molecular weight peak in fact corresponds to PLC-alpha. The high molecular mass peak (157 kDa) shows much greater activity against PI than PIP2, is active at lower calcium concentrations, and has a PI-pH optimum of 5.0 regardless of calcium concentration. Each of the PIP2 PLC activities is strongly dependent on the relative levels of calcium and pH in the assay buffer. These observations suggest that vascular smooth muscle contains both a high and low molecular weight PLC whose activities are affected markedly by the changes in calcium and pH accompanying hormonal stimulation of the cell.     

The channel-forming component of the Theridiidae spider venom neurotoxins

It is known that Steatoda (Lityphantes) paykulliana and Latrodectus mactans tredecimguttatus spider venoms are toxic to mammals and insects. These venoms act presynaptically eliciting massive release of transmitters. They also form channels in bilayer lipid membranes (BLM) that are selective for cations. Venoms of both spider species were fractionated by gel filtration on a Sephadex G-100 column. The fraction obtained were tested on neuromuscular preparations of frog and locust and on BLM. A fraction of low molecular weight components (about 5000 daltons and less) was disclosed. This fraction showed presynaptic and channel-forming effects similar to those of crude venoms and of high molecular weight toxin fractions, obtained simultaneously from these venoms. It was shown that channels formed in BLM by crude venoms and its different fractions are identical. Also, it was found that the low molecular weight channel-forming component is a construction element of high molecular weight toxins. On the basis of data obtained a toxin structure model of the Theridiidae family spider venoms was proposed.     

The three-dimensional structure of trichocyte (hard alpha-) keratin intermediate filaments: features of the molecular packing deduced from the sites of induced crosslinks

The spatial distribution of the crosslinks that can be induced between lysine residues in trichocyte (alpha-) keratin intermediate filaments (IF) using disulfosuccinimidyl tartrate has been analyzed in detail and the results used to provide information about the three-dimensional (3-D) structure. The pattern of inter-molecular interactions derived from earlier studies is essentially two-dimensional in that it involves projection on to a cylinder followed by unwrapping to give a sheet. Crosslinks are observed between molecular strands four apart and it is shown that this can only occur if the paths of the molecular strands through the IF are systematically distorted. These crosslinks are clustered axially at intervals of around 15 nm, a value closely related to the pitch length of the constituent coiled-coil molecules in the rod domains. The number of crosslinks between adjacent molecular strands shows a striking difference depending on lateral direction and provides support for the concept of a head-to-tail stacking of tetramers defined by the A(CN) mode of packing to form protofilament substructures in the fully formed IF. Each protofilament would consist of a pair of oppositely directed molecular strands stabilized by A(11) and A(22) interactions identified in earlier work. A detailed model for the IF in the reduced state comprising a ring of eight protofilaments is suggested. When combined with earlier studies of crosslink formation in the oxidized state, the present findings lead to the conclusion that there is a major reorganization of the molecular packing within the protofilaments during keratinization in vivo. Taken in conjunction with existing X-ray data on the fully keratinized structures, the new evidence for a protofilament substructure also enables a detailed 3-D model for the mature IF to be suggested.     

Analysis of polymer molecular weight distributions in aqueous two-phase systems.

The partitioning of proteins and other biomaterials between two aqueous phases containing polyethyleneglycol and dextran is a strong function of the molecular weight of the two polymers. Although both polymers are polydispersed (especially Dx) most theoretical treatments refer only to the average molecular weight (number or mass) and assume that the molecular weight distribution of each polymer is the same in both phases. In this work the molecular weight distribution of each polymer is the same in both phases. In this work the molecular weight distributions of four stock solutions of PEG (4000, 6000, 10,000 and 20,000) and four stock solutions of Dx (10,000, 40,000, 110,000 and 500,000) were measured using High Performance Gel Chromatography. The measurements were repeated on the phases formed by the polymer solutions after they were mixed and allowed to equilibrate. The molecular weight distribution of the Dx differed in the top and bottom phase; both differed from that of the stock solution. Although we believe that the molecular weight distribution for PEG also differs in the top and bottom phases, we were unable to determine this within the resolution of our instruments.     

Subunit structure and multiple phosphorylation sites of phospholamban

The phosphorylation-induced mobility shift of the high molecular weight form of phospholamban (24,500 daltons) in the cardiac sarcoplasmic reticulum produced on 3',5'-cyclic AMP (cAMP)-dependent phosphorylation with 5 mM ATP was resolved into five clear steps on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and on Ca2+-calmodulin-dependent phosphorylation into ten steps. The mobility shift of the low molecular weight form of phospholamban (less than 14,400 daltons) in these reactions occurred in one step and two steps, respectively. With the two protein kinase activities, the electrophoretic pattern of the mobility shifts of the high and low molecular weight forms of phospholamban was similar to that obtained with Ca2+-calmodulin-dependent protein kinase alone. The results of pulse-chase experiments involving the centrifuge column method suggested that the site(s) of phosphorylation by cAMP- and Ca2+-calmodulin-dependent protein kinase activities are on the same phospholamban molecule. Two-dimensional tryptic peptide maps of phosphorylated phospholamban indicated that cAMP-dependent protein kinase phosphorylates at a single site, A, and Ca2+-calmodulin-dependent protein kinase phosphorylates at sites C1 and C2 in the low molecular weight form, where A is different from C1 but may be the same as C2. The high molecular weight form of phospholamban is suggested to be a pentamer of identical monomers (low molecular weight form) having one phosphorylation site for cAMP-dependent protein kinase and two for Ca2+-calmodulin-dependent protein kinase.     

A method for fast safety screening of explosives in terms of crystal packing and molecular stability

Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.     

Molecular aspects of magnetic resonance imaging and spectroscopy

Magnetic resonance imaging (MRI) is a well known diagnostic tool in radiology that produces unsurpassed images of the human body, in particular of soft tissue. However, the medical community is often not aware that MRI is an important yet limited segment of magnetic resonance (MR) or nuclear magnetic resonance (NMR) as this method is called in basic science. The tremendous morphological information of MR images sometimes conceal the fact that MR signals in general contain much more information, especially on processes on the molecular level. NMR is successfully used in physics, chemistry, and biology to explore and characterize chemical reactions, molecular conformations, biochemical pathways, solid state material, and many other applications that elucidate invisible characteristics of matter and tissue. In medical applications, knowledge of the molecular background of MRI and in particular MR spectroscopy (MRS) is an inevitable basis to understand molecular phenomenon leading to macroscopic effects visible in diagnostic images or spectra. This review shall provide the necessary background to comprehend molecular aspects of magnetic resonance applications in medicine. An introduction into the physical basics aims at an understanding of some of the molecular mechanisms without extended mathematical treatment. The MR typical terminology is explained such that reading of original MR publications could be facilitated for non-MR experts. Applications in MRI and MRS are intended to illustrate the consequences of molecular effects on images and spectra.