microRNA 1307 Is a Potential Target for SARS-CoV-2 Infection: An in Vitro Model

microRNAs (miRs) are proposed as critical molecular targets in SARS-CoV-2 infection. Our recent in silico studies identified seven SARS-CoV-2 specific miR-like sequences, which are highly conserved with humans, including miR-1307-3p, with critical roles in COVID-19. In this current study, Vero cells were infected with SARS-CoV-2, and miR expression profiles were thereafter confirmed by qRT-PCR. miR-1307-3p was the most highly expressed miR in the infected cells; we, therefore, transiently inhibited its expression in both infected and uninfected cells. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) cell proliferation assay assessed cell viability following SARS-CoV-2 infection, identifying that miR-1307 expression is inversely correlated with cell viability. Lastly, changes in miR-1307-dependent pathways were analyzed through a detailed miRNOME and associated in silico analysis. In addition to our previously identified miRs, including miR-1307-3p, the upregulation of miR-193a-5p, miR-5100, and miR-23a-5p and downregulation of miR-130b-5p, miR34a-5p, miR-505-3p, miR181a-2-3p, miR-1271-5p, miR-598-3p, miR-34c-3p, and miR-129-5p were also established in Vero cells related to general lung disease-related genes following SARS-CoV-2 infection. Targeted anti-miR-1307-3p treatment rescued cell viability in infection when compared to SARS CoV-2 mediated cell cytotoxicity only. We furthermore identified by in silico analysis that miR-1307-3p is conserved in all SARS-CoV-2 sequences/strains, except in the BA.2 variant, possibly contributing to the lower disease severity of this variant, which warrants further investigation. Small RNA seq analysis was next used to evaluate alterations in the miRNOME, following miR-1307-3p manipulation, identifying critical pathobiological pathways linked to SARS-CoV-2 infection-mediated upregulation of this miR. On the basis of our findings, miRNAs like miR-1307-3p play a critical role in SARS-CoV-2 infection, including via effects on disease progression and severity.

Inhibition on JNK Mimics Silencing of Wnt-11 Mediated Cellular Response in Androgen-Independent Prostate Cancer Cells

Prostate cancer (PCa) is one of the most common cancers among men, and one of the leading causes of cancer death for men. The c-Jun N-terminal kinase (JNK) pathway is required for several cellular functions, such as survival, proliferation, differentiation, and migration. Wnt-11, a member of the Wnt family, has been identified for its upregulation in PCa; however, downstream signalling of Wnt-11 remains to be fully characterized. In this study, we investigated the role of the JNK pathway as a potential downstream factor for Wnt-11 signalling. For this purpose, LNCaP, DU145, and PC-3 PCa cells and normal epithelial PNT1A cells were treated with a specific JNK kinase inhibitor: JNKVIII. Our results showed that JNK inhibition decreased mitochondrial membrane potential and promoted cell death in a cell type-dependent manner. We found that JNK inhibition led to an increase in autophagy and prevented epithelial–mesenchymal transition (EMT) in independently growing androgen cells. JNK inhibition and the silencing of Wnt-11 showed similar responses in DU145 and PC-3 cells and decreased metastasis-related biomarkers, cell migration, and invasion. Overall, our results suggest that JNK signalling plays a significant role in the pathophysiology of PCa by mediating Wnt-11 induced signals. Our data highlights that both the JNK pathway and Wnt-11 could be a useful therapeutic target for the combinatory application of current PCa.

The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the betacoronavirus family, which causes COVID-19 disease. SARS-CoV-2 pathogenicity in humans leads to increased mortality rates due to alterations of significant pathways, including some resulting in exacerbated inflammatory responses linked to the “cytokine storm” and extensive lung pathology, as well as being linked to a number of comorbidities. Our current study compared five SARS-CoV-2 sequences from different geographical regions to those from SARS, MERS and two cold viruses, OC43 and 229E, to identify the presence of miR-like sequences. We identified seven key miRs, which highlight considerable differences between the SARS-CoV-2 sequences, compared with the other viruses. The level of conservation between the five SARS-CoV-2 sequences was identical but poor compared with the other sequences, with SARS showing the highest degree of conservation. This decrease in similarity could result in reduced levels of transcriptional control, as well as a change in the physiological effect of the virus and associated host-pathogen responses. MERS and the milder symptom viruses showed greater differences and even significant sequence gaps. This divergence away from the SARS-CoV-2 sequences broadly mirrors the phylogenetic relationships obtained from the whole-genome alignments. Therefore, patterns of mutation, occurring during sequence divergence from the longer established human viruses to the more recent ones, may have led to the emergence of sequence motifs that can be related directly to the pathogenicity of SARS-CoV-2. Importantly, we identified 7 key-microRNAs (miRs 8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) with significant links to KEGG pathways linked to viral pathogenicity and host responses. According to Bioproject data (PRJNA615032), SARS-CoV-2 mediated transcriptomic alterations were similar to the target pathways of the selected 7 miRs identified in our study. This mechanism could have considerable significance in determining the symptom spectrum of future potential pandemics. KEGG pathway analysis revealed a number of critical pathways linked to the seven identified miRs that may provide insight into the interplay between the virus and comorbidities. Based on our reported findings, miRNAs may constitute potential and effective therapeutic approaches in COVID-19 and its pathological consequences.

Modelling, inference and big data in biophysics

In recognition of the increasing importance of big data in biophysics, a new session called 'Modelling, inference, big data' is incorporated into the IUPAB/EBSA Congress on 18 July 2017 at Edinburgh, UK.

Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine

Aromatic groups are now acknowledged to play an important role in many systems of interest. However, existing molecular mechanics methods provide a poor representation of these groups. In a previous paper, we have shown that the molecular mechanics treatment of benzene can be improved by the incorporation of an explicit representation of the aromatic π electrons. Here, we develop this concept further, developing charge-separation models for toluene, phenol, and pyridine. Monte Carlo simulations are used to parametrize the models, via the reproduction of experimental thermodynamic data, and our models are shown to outperform an existing atom-centered model. The models are then used to make predictions about the structures of the liquids at the molecular level and are tested further through their application to the modeling of gas-phase dimers and cation-π interactions.

The Structure of Liquid Benzene

The interactions of aromatic groups have been identified as playing a crucial role in many systems of interest. Unfortunately, conventional atom-centered force fields provide only an approximate representation of these molecules owing to their failure to consider the quadrupole moment arising from the π electrons. In this paper the structure of liquid benzene, the prototypical aromatic system, is investigated using a novel approach to Monte Carlo simulation, parametrized against experimental thermodynamic data, which incorporates an explicit representation of the aromatic π electrons. In contrast to previous simulations of liquid benzene it is found that a perpendicular arrangement of benzene molecules is preferred to a parallel arrangement. This result is in good agreement with experimental data.

Binding modes of diketo-acid inhibitors of HIV-1 integrase: a comparative molecular dynamics simulation study

HIV-1 integrase (IN) has become an attractive target since drug resistance against HIV-1 reverse transcriptase (RT) and protease (PR) has appeared. Diketo acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN: however the action mechanism is not well understood. Here, to study the inhibition mechanism of DKAs we performed 10 ns comparative molecular dynamics simulations on HIV-1 IN bound with three most representative DKA inhibitors: Shionogi inhibitor, S-1360 and two Merck inhibitors L-731,988 and L-708,906. Our simulations show that the acidic part of S-1360 formed salt bridge and cation-π interactions with Lys159. In addition, the catalytic Glu152 in S-1360 was pushed away from the active site to form an ion-pair interaction with Arg199. The Merck inhibitors can maintain either one or both of these ion-pair interaction features. The difference in potencies of the DKA inhibitors is thus attributed to the different binding modes at the catalytic site. Such structural information at atomic level, not only demonstrates the action modes of DKA inhibitors but also provides a novel starting point for structural-based design of HIV-1 IN inhibitors.

The distinct conformational dynamics of K-Ras and H-Ras A59G

Ras proteins regulate signaling cascades crucial for cell proliferation and differentiation by switching between GTP- and GDP-bound conformations. Distinct Ras isoforms have unique physiological functions with individual isoforms associated with different cancers and developmental diseases. Given the small structural differences among isoforms and mutants, it is currently unclear how these functional differences and aberrant properties arise. Here we investigate whether the subtle differences among isoforms and mutants are associated with detectable dynamical differences. Extensive molecular dynamics simulations reveal that wild-type K-Ras and mutant H-Ras A59G are intrinsically more dynamic than wild-type H-Ras. The crucial switch 1 and switch 2 regions along with loop 3, helix 3, and loop 7 contribute to this enhanced flexibility. Removing the gamma-phosphate of the bound GTP from the structure of A59G led to a spontaneous GTP-to-GDP conformational transition in a 20-ns unbiased simulation. The switch 1 and 2 regions exhibit enhanced flexibility and correlated motion when compared to non-transitioning wild-type H-Ras over a similar timeframe. Correlated motions between loop 3 and helix 5 of wild-type H-Ras are absent in the mutant A59G reflecting the enhanced dynamics of the loop 3 region. Taken together with earlier findings, these results suggest the existence of a lower energetic barrier between GTP and GDP states of the mutant. Molecular dynamics simulations combined with principal component analysis of available Ras crystallographic structures can be used to discriminate ligand- and sequence-based dynamic perturbations with potential functional implications. Furthermore, the identification of specific conformations associated with distinct Ras isoforms and mutants provides useful information for efforts that attempt to selectively interfere with the aberrant functions of these species.

Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation

The Polo-Like Kinase 1 (PLK1) acts as a central regulator of mitosis and is over-expressed in a wide range of human tumours where high levels of expression correlate with a poor prognosis. PLK1 comprises two structural elements, a kinase domain and a polo-box domain (PBD). The PBD binds phosphorylated substrates to control substrate phosphorylation by the kinase domain. Although the PBD preferentially binds to phosphopeptides, it has a relatively broad sequence specificity in comparison with other phosphopeptide binding domains. We analysed the molecular determinants of recognition by performing molecular dynamics simulations of the PBD with one of its natural substrates, CDC25c. Predicted binding free energies were calculated using a molecular mechanics, Poisson-Boltzmann surface area approach. We calculated the per-residue contributions to the binding free energy change, showing that the phosphothreonine residue and the mainchain account for the vast majority of the interaction energy. This explains the very broad sequence specificity with respect to other sidechain residues. Finally, we considered the key role of bridging water molecules at the binding interface. We employed inhomogeneous fluid solvation theory to consider the free energy of water molecules on the protein surface with respect to bulk water molecules. Such an analysis highlights binding hotspots created by elimination of water molecules from hydrophobic surfaces. It also predicts that a number of water molecules are stabilized by the presence of the charged phosphate group, and that this will have a significant effect on the binding affinity. Our findings suggest a molecular rationale for the promiscuous binding of the PBD and highlight a role for bridging water molecules at the interface. We expect that this method of analysis will be very useful for probing other protein surfaces to identify binding hotspots for natural binding partners and small molecule inhibitors.

Structure, electronic circular dichroism and Raman optical activity in the gas phase and in solution: a computational and experimental investigation

A computational (ab initio and molecular dynamics) and experimental exploration of the relative importance of molecular conformation and explicit solvent effects on the electronic circular dichroism (ECD) of chiral molecules, is presented. The exploration includes an assessment of the validity of angular correlation (sector) rules linking ECD to molecular conformation. It is based upon studies of 1-(R) phenylethanol (including its Raman optical activity spectrum), the corresponding 'benchmark' base, 1-(R)-phenylethylamine and its protonated cation; their hydrated clusters in the gas phase; and their non-polar and aqueous solutions. Emphasis is placed on the influence of specific, hydrogen bonded interactions with the aqueous solvent. The theoretical validity of the (otherwise empirical) sector rule in the neutral molecules and in their specifically hydrated clusters has been established--but with a reversal of the 'historical' sign convention. Protonation of the amine leads to a breakdown of the conventional sector rule but the change in its ECD intensity can still be related to the side chain dihedral angular dependence of its rotatory strength, computed ab initio for its explicitly hydrated clusters. Comparisons between ECD spectra measured in aqueous and in hydrocarbon solutions and the results of molecular dynamics calculations for aqueous solutions at 300 K, identify solvent induced structural change as the principal determinant of their relative ECD spectral intensities. Further links connecting the structures and conformations of chiral molecules and their explicitly solvated clusters in the gas phase, to their structures and conformational populations in solution can be expected through measurement, ab initio computation and analysis of their vibrational, ROA spectra.

Dynamics of conserved waters in human Hsp90: implications for drug design

The flexibility of a promising protein target, human heat shock protein 90 (Hsp90), is investigated by molecular dynamics simulations. These simulations focus on: (i) the interactions between the protein and conserved water molecules; and (ii) the interactions of the ligand PU3, the conserved water molecules and the protein. This is followed by a virtual screening docking study of the PU3 family of compounds and Hsp90 incorporating several conserved water molecules.

Classification of proteins based on similarity of two-dimensional protein maps

Data reduction techniques are now a vital part of numerical analysis and principal component analysis is often used to identify important molecular features from a set of descriptors. We now take a different approach and apply data reduction techniques directly to protein structure. With this we can reduce the three-dimensional structural data into two-dimensions while preserving the correct relationships. With two-dimensional representations, structural comparisons between proteins are accelerated significantly. This means that protein-protein similarity comparisons are now feasible on a large scale. We show how the approach can help to predict the function of kinase structures according to the Hanks' classification based on their structural similarity to different kinase classes.

Distance measurements in the borderline region of applicability of CW EPR and DEER: a model study on a homologous series of spin-labelled peptides

Inter-spin distances between 1 nm and 4.5 nm are measured by continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) methods for a series of nitroxide-spin-labelled peptides. The upper distance limit for measuring dipolar coupling by the broadening of the CW spectrum and the lower distance limit for the present optimally-adjusted double electron electron resonance (DEER) set-up are determined and found to be both around 1.6-1.9 nm. The methods for determining distances and corresponding distributions from CW spectral line broadening are reviewed and further developed. Also, the work shows that a correction factor is required for the analysis of inter-spin distances below approximately 2 nm for DEER measurements and this is calculated using the density matrix formalism.

The effect of solvation on biomolecular conformation: 2-amino-1-phenylethanol

Small molecule neurotransmitters form one the most important classes of pharmaceutical molecules. While the behavior of these molecules in their neutral forms in the gas phase is well understood, their behavior in more biologically relevant scenarios (protonated and in aqueous solution) has received comparatively little attention. Here we address this problem by using molecular mechanics simulations to build up a detailed picture of the conformational behavior of 2-amino-1-phenylethanol, a noradrenaline analogue, in aqueous solution in both its neutral and protonated forms. For the sake of comparison, equivalent simulations are also performed on the gas-phase molecules and gas-phase hydrated clusters. These calculations reveal the important role that water has to play in determining the conformational preferences and dynamic behavior of the molecules. Water molecules are found to bridge between the various functional groups within the molecule, significantly affecting their relative stabilities in comparison to the gas-phase values. The reorganization of these solvation structures also provides a mechanism for conformational interconversion. The role of the solvent in mediating interactions between the various functional groups within the molecule suggests that in noradrenaline the catechol groups will be able to interact, albeit indirectly, with the other functional groups, thereby influencing the behavior of the molecule.

Role of aromatic amino acids in protein-nucleic acid recognition

Statistical analysis of structures from the PBD has been used to examine the role that the aromatic amino acids play in protein-nucleic acid recognition. In protein-DNA complexes, the residues Phe and His are found to bind selectively to the DNA chain--Phe to A and T, and His to T and G. The preferred binding modes are identified, and the interactions involving Phe are shown to be important in the transcription process. In protein-RNA complexes, Phe is found to occur far less often and is instead replaced by Trp, which binds selectively to C and G, offering a possible mechanism for differentiation between the two nucleic acids. SASA analysis of the two sets of complexes suggests that all of the aromatic amino acids are more heavily involved in binding than would be expected on the balance of probability. Phe and Tyr occur approximately equal in both sets of data, whereas the proportions of His and Trp vary considerably, supporting the idea that these residues may be involved in differentiating between the two nucleic acids.

Diketoacid HIV-1 integrase inhibitors: An ab initio study

The stable tautomeric forms of two representative arene-substituted diketoacid HIV-1 integrase inhibitors, 5-ClTEP and L-731,988, were investigated by B3LYP with 6-31G*, 6-31G(d,p), and 6-31+G(d,p) basis sets. Optimization with MP2/6-31G* was also performed for 5-ClTEP. The solvation effect was considered using a conductor-like screening model. With the density functional theory method, the trans diketo conformations are more stable than the cis conformers. The difference is 14 kJ mol(-1) for 5-ClTEP and 33 kJ mol(-1) for L-731,988. Two trans diketo structures were obtained. The difference between these two trans diketo structures is less than 4 kJ mol(-1) calculated at the B3LYP/6-311+G(3df,2p) level. Two enol forms prevail over the diketo tautomers and are calculated to have the same free energy. Because there is no barrier observed between these two enol forms, they can interchange easily such that a delocalized transition state is suggested to be the observed form. Contradictory to the results of the MP2 method that predicts a preference for the trans diketo forms, the B3LYP method predicts a preference for the enol tautomers, which is in agreement with the experimental results.

Characterization and tissue-specific expression of two lepidopteran farnesyl diphosphate synthase homologs: Implications for the biosynthesis of ethyl-substituted juvenile hormones

The sesquiterpenoid juvenile hormone (JH) regulates insect development and reproduction. Most insects produce only one chemical form of JH, but the Lepidoptera produce four derivatives featuring ethyl branches. The biogenesis of these JHs requires the synthesis of ethyl-substituted farnesyl diphosphate (FPP) by FPP synthase (FPPS). To determine if there exist more than one lepidopteran FPPS, and whether one FPPS homolog is better adapted for binding the bulkier ethyl-branched substrates/products, we cloned three lepidopteran FPPS cDNAs, two from Choristoneura fumiferana and one from Pseudaletia unipuncta. Amino acid sequence comparisons among these and other eukaryotic FPPSs led to the recognition of two lepidopteran FPPS types. Type-I FPPSs display unique active site substitutions, including several in and near the first aspartate-rich motif, whereas type-II proteins have a more "conventional" catalytic cavity. In a yeast assay, a Drosophila FPPS clone provided full complementation of an FPPS mutation, but lepidopteran FPPS clones of either type yielded only partial complementation, suggesting unusual catalytic features and/or requirements of these enzymes. Although a structural analysis of lepidopteran FPPS active sites suggested that type-I enzymes are better suited than type-II for generating ethyl-substituted products, a quantitative real-time PCR assessment of their relative abundance in insect tissues indicated that type-I expression is ubiquitous whereas that of type-II is essentially confined to the JH-producing glands, where its transcripts are approximately 20 times more abundant than those of type-I. These results suggest that type-II FPPS plays a leading role in lepidopteran JH biosynthesis in spite of its apparently more conventional catalytic cavity.

A solvent induced mechanism for conformational change

Molecular dynamics simulations have been used to investigate the dynamic behaviour of two small molecule neurotransmitter analogues in aqueous solution, leading to the elucidation of a mechanism for conformational change which is driven by the presence of the solvent molecules.

Kanamycin reveals the role played by glutamate receptors in shaping plant resource allocation

Ionotropic glutamate receptors (iGluRs) play important roles in neurotransmission in animals. There is growing evidence that iGluRs also play important roles in plants. Using a chemical genetics approach, which combined a pH-homeostasis mutant of Arabidopsis thaliana (de-etiolated3), several different iGluR agonists, molecular modelling, and reporter gene expression in transgenic plants, we provide evidence that iGluR agonism can induce dramatic changes in plant development and metabolism. Systematic hypothesis testing revealed a signalling circuit that integrates amino acid and sugar signals to affect elongation growth and the deposition of carbon into starch and lignins. The data show that aminoglycoside antibiotics, such as kanamycin, and polyamines impinge upon this circuit. These findings provide a mechanism for the conversion of amino acid and sugar signals into an appropriate response at the gene expression level, and underline the similarities in iGluR agonism between animals and plants.

The function of the amino terminal domain in NMDA receptor modulation

N-methyl-D-aspartate (NMDA) receptors are ligand-gated channels important in neurotransmission which are activated by the combined presence of glutamate and glycine. They are comprised of four subunits that form a dimer of dimers. The activity of NMDA receptors is modulated by a variety of endogenous ligands such as zinc ions, phenylethanolamines, polyamines and protons. Findings show that the binding sites for these modulators are found in the amino terminal domain of such receptors, but different modulators appear to affect different subunits. However, despite the enormous efforts expended in mutagenesis and patch clamp experiments on NMDA receptors, the exact assembly of these subunits and the effects of the modulatory species are not well understood. We have modelled dimers of the amino terminal domains of these receptors based on their homology with the extracellular dimer of a metabotropic glutamate receptor. Conserved cysteine residues, which have been highlighted as important in previous work, are shown to form a disulphide bridge, stabilizing a four-helix bundle between subunits. This establishes a hinge in the receptor. The model also highlights a zinc binding site in the binding crevice of the NR2a subunit of the receptor that stabilizes the open state of the amino terminal domain. The similar effect of ifenprodil is thus explained by its stabilization of the open state of the amino terminal domain (ATD). The presence of three histidine residues in the zinc site is used to explain the pH dependence of zinc inhibition. Previous work has also implicated certain residues in spermine stimulation of such receptors. The homology model shows that this site is found at the inter-subunit boundary of the dimer. This predicts a binding site between subunits, a result not calculable by the homology modelling of single subunits done previously. Finally, these results are drawn together to yield a consistent picture of NMDA receptor activation and desensitization. An understanding of how these receptors work and how they can be modulated is an important step toward rational drug design.

Helix-Forming Carbohydrate Amino Acids

[reaction: see text] The solution-phase conformational properties of tetrameric and octameric chains of C-glycosyl alpha-d-lyxofuranose configured tetrahydrofuran amino acids (where the C-2 and C-5 substituents on the tetrahydrofuran ring are trans to each other) were examined using NMR and IR and CD in organic solvents. Studies by NMR and IR demonstrated that in chloroform solution, the tetramer 7 does not adopt a hydrogen-bonded conformation whereas the octamer 10 populates a well-defined helical secondary structure stabilized by 16-membered (i, i - 3) interresidue hydrogen bonds, similar to a pi-helix. Circular dichroism studies in trifluoroethanol are consistent with this conformation for the octamer 10, and also indicate that the tetramer 7 adopts a rigid conformation not stabilized by hydrogen bonds.

Combating bioterrorism with personal computers

Using personal computers in a grid is permitting the in silico screening of millions of molecules to seek out potential inhibitors of agents that pose bioterror threats. Current projects are targeting anthrax and smallpox, but the approach has many attractions for investigating any known protein target and its inhibition.

Evaluation of structural similarity based on reduced dimensionality representations of protein structure

Protein similarity estimations can be achieved using reduced dimensional representations and we describe a new application for the generation of two-dimensional maps from the three-dimensional structure. The code for the dimensionality reduction is based on the concept of pseudo-random generation of two-dimensional coordinates and Monte Carlo-like acceptance criteria for the generated coordinates. A new method for calculating protein similarity is developed by introducing a distance-dependent similarity field. Similarity of two proteins is derived from similarity field indices between amino acids based on various criteria such as hydrophobicity, residue replacement factors and conformational similarity, each showing a one factor Gaussian dependence. Results on comparisons of misfolded protein models with data sets of correctly folded structures show that discrimination between correctly folded and misfolded structures is possible. Tests were carried out on five different proteins, comparing a misfolded protein structure with members of the same topology, architecture, family and domain according to the CATH classification.

The C-4 stereochemistry of leucocyanidin substrates for anthocyanidin synthase affects product selectivity

Anthocyanidin synthase (ANS), an iron(II) and 2-oxoglutarate (2OG) dependent oxygenase, catalyses the penultimate step in anthocyanin biosynthesis by oxidation of the 2R,3S,4S-cis-leucoanthocyanidins. It has been believed that in vivo the products of ANS are the anthocyanidins. However, in vitro studies on ANS using optically active cis- and trans-leucocyanidin substrates identified cyanidin as only a minor product; instead both quercetin and dihydroquercetin are products with the distribution being dependent on the C-4 stereochemistry of the leucocyanidin substrates.

A role for glycine in the gating of plant NMDA-like receptors

The amino acid glycine has a well-established role in signalling in the mammalian central nervous system. For example, glycine acts synergistically with the major excitatory neurotransmitter, glutamate, to regulate the influx of ions such as calcium, through N-methyl-d-aspartate (NMDA) receptors. Plants possess NMDA-like receptors, generically referred to as glutamate receptors (GLRs), named on the basis of their presumed ligand, glutamate. Previously, glycine has not been implicated in plant GLR activity or any other aspect of plant signalling. Using transgenic Arabidopsis seedlings expressing aequorin to monitor ligand-mediated changes in the cytosolic concentration of Ca2+ ([Ca2+]cyt), the data presented herein show that glutamate and glycine act synergistically to control ligand-mediated gating of calcium in plants. Glutamate and glycine synergism also regulates hypocotyl elongation. Transient increases in [Ca2+]cyt mediated by glutamate and glycine, as well as hypocotyl elongation, were inhibited by 6,7-dinitroquinoxaline-2,3 dione (DNQX), a competitive inhibitor of animal GLRs. Using a multiscale docking algorithm in combination with a molecular model of the ligand-binding domain of plant GLRs, evidence is provided indicating that glycine, and not glutamate, is likely to be the natural ligand for most plant GLR subunits. These findings uncover a hitherto unconsidered role for glycine signalling in plants, and suggest that the synergistic action of glutamate and glycine at NMDA-like receptors predates the divergence of plants and animals.

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 11.70 kcal/mol was found. The effect of adjacent hydrogen-donating groups was found to reduce the energy barrier by 1-2 kcal/mol each and thus to provide a significant catalytic effect for this reaction. By means of molecular dynamics studies, the stereochemistry of the methylmalonyl-CoA mutase catalyzed reaction was examined. It is shown that TYR89 is essential for maintaining stereoselectivity of the abstraction of a hydrogen in the backreaction. The subsequent selective formation of one isomer of methylmalonyl-CoA is probably due to the presence of a bulky side chain.

Catalytic enantioselective [3 + 2]-cycloadditions of diazoketone-derived aryl-substituted carbonyl ylides

An evaluation of alpha-aryl-alpha-diazodiones in tandem carbonyl ylide formation-enantioselective [3 + 2]-cycloaddition reactions is described. Such substrates were designed to allow investigation of the electronic characteristics of the dipole upon asymmetric induction. Intramolecular cycloadditions (with a tethered alkene dipolarophile) were found to occur in good to quantitative yields, with a difference in ee exhibited by the two electronically different diazodiones 8 and 9. Intermolecular cycloadditions using diazodiones 12 and 13 with DMAD and arylacetylenes 16-18 again demonstrated that electronics play a key role in determining the outcome of the cycloaddition reactions. Enantioselectivities of up to 76% were observed.

Calculation of protein domain structural similarity using two-dimensional representations

By reducing protein structures to two-dimensional representations, it is possible to speed up the alignment of the structures and hence calculate similarity indices faster that using three-dimensional representations. Using amino acid based representations gives much better discrimination between proteins and faster calculations. Taking into account the relative similarity of the amino acids involved allowed improved accuracy at very little time cost.

Docking of flexible molecules using multiscale ligand representations

Structural genomics will yield an immense number of protein three-dimensional structures in the near future. Automated theoretical methodologies are needed to exploit this information and are likely to play a pivotal role in drug discovery. Here, we present a fully automated, efficient docking methodology that does not require any a priori knowledge about the location of the binding site or function of the protein. The method relies on a multiscale concept where we deal with a hierarchy of models generated for the potential ligand. The models are created using the k-means clustering algorithm. The method was tested on seven protein-ligand complexes. In the largest complex, human immunodeficiency virus reverse transcriptase/nevirapin, the root mean square deviation value when comparing our results to the crystal structure was 0.29 A. We demonstrate on an additional 25 protein-ligand complexes that the methodology may be applicable to high throughput docking. This work reveals three striking results. First, a ligand can be docked using a very small number of feature points. Second, when using a multiscale concept, the number of conformers that require to be generated can be significantly reduced. Third, fully flexible ligands can be treated as a small set of rigid k-means clusters.

Theoretical descriptors for the quantitative rationalisation of plastocyanin mutant functional propertiess

A quantitative rationalisation of the effect of specific amino acids on the recognition process and redox characteristics of plastocyanin towards cytochrome f, as determined by point mutation experiments, has been attempted in this study. To achieve this goal we derived theoretical descriptors directly from the three-dimensional structure of the plastocyanin mutants, in the same manner as it is usually done for small drug-like molecules. The protein descriptors computed can be related to: (a) the electrostatic and dipole-dipole interactions, effective at long distance; (b) polar interactions whose features are encoded by charged partial surface area descriptors; (c) the propensity of the surface residues to form hydrogen bonding interactions; and (d) dispersion and repulsive interactions. Moreover, an estimation of mutation-dependent variation of redox potential observed has been obtained by electrostatic free energy calculations. The quantitative structure-activity relationship (QSAR) models offer structural interpretation of the point mutation experiment responses and can be of help in the design of new protein engineering experiments.

Identification of ligand binding sites on proteins using a multi-scale approach

Identification of a ligand binding site on a protein is pivotal to drug discovery. To date, no reliable and computationally feasible general approach to this problem has been published. Here we present an automated efficient method for determining binding sites on proteins for potential ligands without any a priori knowledge. Our method is based upon the multiscale concept where we deal with a hierarchy of models generated using a k-means clustering algorithm for the potential ligand. This is done in a simple approach whereby a potential ligand is represented by a growing number of feature points. At each increasing level of detail, a pruning of potential binding site is performed. A nonbonding energy function is used to score the interactions between molecules at each step. The technique was successfully employed to seven protein-ligand complexes. In the current paper we show that the algorithm considerably reduces the computational effort required to solve this problem. This approach offers real opportunities for exploiting the large number of structures that will evolve from structural genomics.

Similarity calculations using two-dimensional molecular representations

Molecular similarity calculations are important for rational drug design. Time constraints prevent these techniques being used on large data sets or on large molecules. By reducing the molecular representation to a two-dimensional form, the alignment of the molecules can be greatly speeded up. The accuracy of the resulting similarity values can be improved by using a neural network.

Computer modelling of the receptor-binding domains of VEGF and PIGF

Models of the platelet-derived growth factor (PDGF)-like domains of vascular endothelial growth factor (VEGF) and placenta growth factor (PIGF) were built based on their homology to PDGF. These domains contain most of the determinants for receptor binding. The sequences of these proteins exhibit limited but significant homology to that of platelet-derived growth factor (PDGF), a member of the cystine knot growth factor family. The eight cysteine residues that are involved in intra- and interchain disulphide bonds are conserved. Two high affinity receptors for VEGF have been identified, only one of which binds PIGF. The models presented here are consistent with results that show that VEGF receptor binding is mediated by charged residues in the loops. A comparison of the models suggests that the difference in receptor-binding specificity between VEGF and PIGF may be due to differences in the distribution of positively charged residues and the exposure of hydrophobic residues in the loops.

Structural basis of p21H-ras molecular switch inhibition by a neutralizing antibody

The ras oncogene product p21 functions as a molecular switch in the early section of the signal transduction pathway that is involved in cell growth and differentiation. When the protein is in its GTP-complexed form it is active in signal transduction, whereas it is inactive in its GDP-complexed form. The transforming activity of p21ras is neutralized by the mouse monoclonal antibody Y13-259, possibly by preventing GDP-GTP exchange. A molecular model of the variable fragment of Y13-259 has been derived using a knowledge-based prediction approach and computer-assisted modeling techniques. An analysis of this model while complexed with p21ras/(GDP) indicated that the two molecular switch regions are constrained by complex formation. Antibody binding inhibits GDP-GTP exchange through a mechanism of steric hindrance. Having identified necessary bound sites for inhibition, and explored their electrostatic properties, it should be possible to proceed with the design of antibody mimics as therapeutic agents in cancer control.

Modeling cytochrome P450 14 alpha demethylase (Candida albicans) from P450cam

The tertiary structure of cytochrome P450 14 alpha demethylase--Candida albicans (P450 CA) is modeled on the basis of sequence alignment with two closely related proteins and the crystallographic structure of Pseudomonas putida P450cam. The secondary structure prediction system used combines the information from several algorithms and trains the data to offer an optimized prediction of the known P450cam. The trained algorithm was then used to predict the secondary structure of the other P450 sequences. The prediction of the surface coil regions was aided by an alignment between P450 CA and the homologous sequences P450 14 alpha demethylase--Saccharomyces cerevisiae (66 SD) and P450 14 alpha demethylase--Candida tropicalis (72 SD). The prediction and alignment information was combined to establish an alignment between P450 CA and P450cam, and to assign full secondary structure to the target protein. This secondary structure was folded from the template of P450cam and the predicted structure was relaxed by molecular dynamics. Model checking highlighted minor adjustments in the alignment, correctly orienting hydrophobic and hydrophilic side chains. The model offers explanations for several known experimental results and suggests further investigations that may prove fruitful in understanding the structure and mechanisms of the P450 family (Porter, T.D. and Coon, M.J. Minireview cytochrome P450. J. Biol. Chem. 1991, 266, 13469-13472. Waterman, M.R. Cytochrome P450 cellular distribution and structural considerations. Current Opinion in Structural Biology 1992, 2, 384-387. Aoyama, Y., Yoshida, Y., Sonohdo, Y. and Sato, Y. Structural analysis of the interaction between the side-chain of substrates and the active site of lanosterol 14 alpha demethylase (P450 14DM) of yeast. Biochim. Biophys. Acta 1992, 1122, 251-255.).

A computer model of the interleukin-4/receptor complex

Interleukin-4 is a member of the cytokine family, a group of related messenger proteins which collectively help to moderate and control the immune response. It is believed that the folding topology of the beta-sheets of the interleukin-4 receptor (IL4R) is the same as that seen in the crystal structure of CD4. Although the sequence identity is low, homology modeling techniques have been used to model the IL4R structure from CD4. Refinement by molecular dynamics leads to a suggested structure which has been docked to interleukin-4 (IL4). Several residues of apparent importance for binding are identified.

Charge calculations in molecular mechanics. IX. A general parameterisation of the scheme for saturated halogen, oxygen and nitrogen compounds

The CHARGE2 program for the calculation of partial atomic charges has been amended to include bond parameters for a number of organic functional groups, including halogens, nitrogen and oxygen. These minor amendments to the original scheme produce dipole moments for the fluoro and chloro compounds which are in complete agreement with the observed values. The less complete data sets for the bromo and iodo compounds are also well reproduced, and the dipole moments of a variety of mixed halo compounds are now in better agreement with experiment than previously. The calculated dipole moments of the saturated nitrogen and oxygen compounds are now in much better agreement than in the original scheme, thus the revised parameterisation may be employed with confidence to predict the electrostatic energies of these compounds. Furthermore, the revised scheme now gives a precise proportionality between the charge on the proton in a CH group and the 1H chemical shift of the corresponding proton, allowing the general prediction, in principle, of 1H chemical shifts. In addition, attempts to include variable electronegativity in the alpha effect are described for fluoro compounds.