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PubMed2005

Theoretical prediction of the enantiomeric excess in asymmetric catalysis. An alignment-independent molecular interaction field based approach.

[reaction: see text] The enantiomeric excess of three different asymmetric catalyses has been predicted in excellent agreement with the experiments using a 3D-QSPR approach. In particular, GRid INdependent Descriptors generated from molecular interaction fields together with a simple partial least-squares method were found to be adequate to describe the enantioselectivity induced by these metal-ligand complexes.

Catalysis↗

PubMed2000

Blue copper proteins: a comparative analysis of their molecular interaction properties.

Blue copper proteins are type-I copper-containing redox proteins whose role is to shuttle electrons from an electron donor to an electron acceptor in bacteria and plants. A large amount of experimental data is available on blue copper proteins; however, their functional characterization is hindered by the complexity of redox processes in biological systems. We describe here the application of a semiquantitative method based on a comparative analysis of molecular interaction fields to gain insights into the recognition properties of blue copper proteins. Molecular electrostatic and hydrophobic potentials were computed and compared for a set of 33 experimentally-determined structures of proteins from seven blue copper subfamilies, and the results were quantified by means of similarity indices. The analysis provides a classification of the blue copper proteins and shows that (I) comparison of the molecular electrostatic potentials provides useful information complementary to that highlighted by sequence analysis; (2) similarities in recognition properties can be detected for proteins belonging to different subfamilies, such as amicyanins and pseudoazurins, that may be isofunctional proteins; (3) dissimilarities in interaction properties, consistent with experimentally different binding specificities, may be observed between proteins belonging to the same subfamily, such as cyanobacterial and eukaryotic plastocyanins; (4) proteins with low sequence identity, such as azurins and pseudoazurins, can have sufficient similarity to bind to similar electron donors and acceptors while having different binding specificity profiles.

Amino Acid Sequence↗

PubMed1991

C1: molecular interactions with activating systems.

The molecular events controlling complement activation have been gradually unravelled over the past three decades, stimulated by improved isolation procedures and a better understanding of the roles of individual proteins. In this review, Bob Sim and Ken Reid examine the interactions between C1q and its numerous ligands in the initiation of the classical pathway cascade.

Animals↗

PubMed2001

Localization of epitopes for monoclonal antibodies to urokinase-type plasminogen activator: relationship between epitope localization and effects of antibodies on molecular interactions of the enzyme.

We localized the epitopes for several murine mAbs to human urokinase-type plasminogen activator (uPA) by Ala scanning mutagenesis and related the localization to the effects of the mAbs on the molecular interactions of uPA. Several antibodies against the serine proteinase domain (SPD) were found to have overlapping epitopes composed of variable combinations of Arg178, Arg179, His180, Arg181, Tyr209, Lys211, and Asp214 in the so-called 37-loop and 60-loop, located near the active site and taking part in the binding of uPA to plasminogen activator inhibitor-1 (PAI-1). Besides inhibiting uPA-catalysed plasminogen activation, all antibodies to SPD strongly delayed the binding of uPA to PAI-1, decreasing the second-order rate constant 15- to 6500-fold. There was no correlation between the relative effects of the 37-loop and 60-loop substitutions on the second-order rate constant and on the binding of the antibodies, indicating that the antibodies did not delay complex formation by blocking residues of specific importance for the uPA-PAI-1 reaction, but rather by steric hindrance of the access of PAI-1 to the active site. The affinity of the SPD antibodies for the uPA-PAI-1 complex was only slightly lower than that for free uPA, indicating that the 37-loop and 60-loop are exposed in the complex. The epitopes for two antibodies to the kringle included Arg108, Arg109, and Arg110. The ability of these antibodies to block the binding of uPA to polyanions correlated with a reduced uPA-polyanion affinity after substitution of the three Arg residues.

Animals↗

PubMed2005

Temperature dependence of the organization and molecular interactions within phospholipid/diacetylene Langmuir films.

Surface pressure-area isotherms and Brewster angle microscopy images of mixed binary films of dimyristoylphosphatidylcholine (DMPC) and the diacetylene 10,12-tricosadiynoic acid (TRCDA) were recorded at different temperatures and mole ratios to investigate the molecular interactions and cooperative properties of the films. The experiments revealed that segregation, on the one hand, and significant intermolecular interactions, on the other hand, both contribute to the thermodynamic properties of the phospholipids and the diacetylene assemblies. In particular, the data demonstrate that higher temperatures and greater percentage of DMPC promote repulsion between the liquid-condensed phospholipid monolayer and the TRCDA domains. In contrast, at high TRCDA mole ratios, film contraction occurred (lower molecular areas) due to TRCDA multilayer formation (at high temperature) or intermolecular affinities (at low temperature).

Acetylene↗

PubMed1987

A new paramagnetic analogue of cholesterol as a tool for studying molecular interactions of genuine cholesterol.

The synthesis of a new paramagnetic (nitroxide) analogue of cholesterol is described. This compound (called CNO) contains a doxyl group in the lateral chain at position 25. Our results show that CNO retains three molecular interactions which characterize authentic cholesterol: It assumes an orientation perpendicular to the phospholipid bilayer with the doxyl group buried in the membrane core, as seen by ESR spectroscopy. It widens the transition temperature of dimyristoylphosphatidylcholine, to the same extent as cholesterol, as measured by Raman and ESR spectroscopies. It interacts with polyene antibiotics, such as amphotericin B and filipin, in the same manner as its model. This was proved on the one hand by the change in fluorescence of self quenched vesicle-entrapped calcein, after dilution in the external medium, provoked by filipin, and on the other hand by fluorescence quenching provoked by cobalt ions entering the vesicles under the influence of amphotericin B. We concluded that CNO, although it has a side chain different from genuine cholesterol, can help to solve many physiologically meaningful questions related to the distribution and movement rate of cholesterol itself.

Amphotericin B↗

PubMed2004

Molecular interactions of Polo-like-kinase 1 with the mitotic kinesin-like protein CHO1/MKLP-1.

Polo-like kinases and kinesin-like motor proteins are among the many proteins implicated in the execution of cytokinesis. Polo-like-kinase 1 (Plk1) interacts with the mitotic kinesin-like motor protein CHO1/MKLP-1 during anaphase and telophase, and CHO1/MKLP-1 is a Plk1 substrate in vitro. Here, we explore the molecular interactions of these two key contributors to mitosis and cytokinesis. Using the transient transfection approach, we show that the C-terminus of Plk1 binds CHO1/MKLP-1 in a Polo-box-dependent manner and that the stalk domain of CHO1/MKLP-1 is responsible for its binding to Plk1. The stalk domain was found to localize with Plk1 to the mid-body, and Plk1 appears to be mislocalized in CHO1/MKLP-1-depleted cells during late mitosis. We showed that Ser904 and Ser905 are two major Plk1 phosphorylation sites. Using the vector-based RNA interference approach, we showed that depletion of CHO1/MKLP-1 causes the formation of multinucleate cells with more centrosomes, probably because of a defect in the early phase of cytokinesis. Overexpression of a non-Plk1-phosphorylatable CHO1 mutant caused cytokinesis defects, presumably because of dominant negative effect of the construct. Finally, CHO1-depletion-induced multinucleation could be partially rescued by co-transfection of a non-degradable hamster wild-type CHO1 construct, but not an unphosphorylatable mutant. These data provide more detailed information about the interaction between Plk1 and CHO1/MKLP-1, and the significance of this is discussed.

Animals↗

PubMed1984

Laminin, proteoglycan, nidogen and collagen IV: structural models and molecular interactions.

Major components of basement membranes, including collagen IV, laminin, heparan sulphate proteoglycan and nidogen, were isolated from the matrix of the EHS sarcoma. The purified components were analysed for their domain structure and for the participation of distinct domains in molecular interactions and cell binding. Collagen IV consists of four domains which have triple helical or non-collagenous structures. Self-assembly of the protein into a network-like organization occurs by specific interactions between N-terminal triple helical segments and between the C-terminal globules. Cell binding requires a central triple helical segment. Laminin has the shape of an asymmetrical cross; different globular domains within this structure mediate binding to proteoglycan and to cells. The proteoglycan consists of four heparan sulphate chains attached to a small protein core. These chains have the potential to bind laminin, fibronectin and collagen IV. Nidogen was isolated in several molecular forms which showed either self-aggregation or binding to laminin.

Animals↗

PubMed1988

Molecular interactions of steroid hormone receptor with its enhancer element: evidence for receptor dimer formation.

A steroid hormone responsive element (GRE/PRE), sufficient to confer glucocorticoid and progesterone inducibility when linked to a reporter gene, was used in band-shift assays to examine its molecular interactions with steroid hormone receptors. Both progesterone and glucocorticoid receptors bound directly and specifically to the GRE/PRE. The purine contact sites for both form A and form B chicken progesterone receptor, as well as those for rat glucocorticoid receptor, are identical. A peptide fragment produced in bacteria that primarily contain the DNA binding domain of the glucocorticoid receptor binds first to the TGTTCT half-site of the GRE/PRE, and a second molecule binds subsequently to the TGTACA (half-site) of the GRE/PRE in a cooperative manner. Utilizing the peptide fragment and the protein A-linked fragment, we demonstrated that the receptor interacts with its cognate enhancer as a dimer.

Animals↗

PubMed2004

Molecular interactions of surface protein peptides of Streptococcus gordonii with human salivary components.

Oral streptococci play a large role in dental biofilm formation, and several types interact as early colonizers with the enamel salivary pellicle to form the primary biofilm, as well as to incorporate other bacteria on tooth surfaces. Interactions of surface molecules of individual streptococci with the salivary pellicle on the tooth surface have an influence on the etiological properties of an oral biofilm. To elucidate the molecular interactions of streptococci with salivary components, binding between surface protein (SspB and PAg) peptides of Streptococcus gordonii and Streptococcus sobrinus were investigated by utilizing BIAcore biosensor technology. The analogous peptide [change of T at position 400 to K in SspB(390-402), resulting in the SspB(390-T400K-402) peptide] from S. gordonii showed the greatest response for binding to salivary components and inhibited the binding of Streptococcus sanguis by more than 50% in a competitive inhibition assay in a comparison with other SspB and PAg peptides. This peptide also bound to the high-molecular-weight protein complex of salivary components and the agglutinin (gp340/DMBT1) peptide (scavenger receptor cysteine-rich domain peptide 2 [SRCRP 2]). In addition, the SspB(390-T400K-402) peptide was visualized by two surface positive charges in connection with the positively charged residues, in which lysine was a key residue for binding. Therefore, the region containing lysine may have binding activity in S. gordonii and S. sanguis, and the SRCRP 2 region may function as a receptor for the binding. These findings may provide useful information regarding the molecular mechanism of early biofilm formation by streptococci on tooth surfaces.

Adhesins, Bacterial↗

PubMed2003

Molecular interactions between STAT3 and protein inhibitor of activated STAT3, and androgen receptor.

STAT3 mainly acts as a signal transducer of IL-6 family cytokines and transcriptionally activates specific target genes. The recently discovered protein inhibitor of activated STAT3 (PIAS3) binds directly to STAT3 and blocks transcriptional activation. In our previous report, we demonstrated that PIAS3 directly interacted with androgen receptor (AR) and affected AR-mediated gene activation. Furthermore, we also showed that AR associated with STAT3 and enhanced its activity. Here, we examined molecular interactions between STAT3, PIAS3, and AR to underline the mechanism of how they regulate each other. AR activation overcame the inhibitory effect on STAT3-mediated transcription by PIAS3. Co-immunoprecipitation experiments revealed that an active form of AR relieved STAT3 from STAT3-PIAS3 complex formation. These results indicate that AR and PIAS3 regulate the STAT3-mediated transcriptional activity by their physical protein-protein competition on STAT3.

Carrier Proteins↗

PubMed2002

Identification of critical molecular interactions mediating heparin activation of antithrombin: implications for the design of improved heparin anticoagulants.

The serpin, antithrombin, and its polysaccharide activator, heparin, are essential anticoagulant regulators of blood-clotting cascade proteases and thereby critical for maintaining hemostasis. The relative importance of the molecular interactions that mediate heparin binding to and activation of antithrombin, and the dynamics of how they are established, have recently been revealed from the effects of mutagenesis of heparin-binding residues of antithrombin and of modifications of the specific pentasaccharide-binding region in heparin. One residue, Lys 125, is pivotal for antithrombin to recognize and bind the nonreducing-end trisaccharide of the pentasaccharide in an initial low-affinity complex. Two other residues, Lys 114 and Arg 129, then cooperate with Lys 125 to induce the low-affinity complex into an activated, high-affinity complex, in which a network of electrostatic interactions between antithrombin and the entire pentasaccharide is established. The identification of three critical basic residues in antithrombin and a trisaccharide in heparin as principal mediators of heparin activation of antithrombin may stimulate the design of small-molecule anticoagulants that mimic the action of heparin and are orally active.

Anticoagulants↗

PubMed1999

Cryo-bioorganic chemistry: molecular interactions at low temperature.

Freezing of aqueous or organic solutions plays a pivotal role in enhancement of rate and/or yield of biomolecular reactions. The smooth conditions of the frozen state at low temperature can also suppress racemization and side-product formation of the reactions. Molecular interactions in liquid undercooled solutions, on the other hand, offer the possibility to study enzyme activity mechanisms in vitro and a chance for survival of organisms in vivo. This review illustrates the differences between frozen and liquid conditions on several small and large biomolecules, together with the synthetic use of freezing. In relation to the freezing effect on enzyme activity, a peculiar phenomenon is discussed: 'cryo-oscillations' are temporal motions of trypsin activity in frozen solution in the presence of Mn2+ ion. The molecular basis of cold adaptation is also discussed, which points to mechanisms evolved by organisms living at subzero temperatures. The factors involved in the freezing effect are shown; i.e. the role of freeze-concentration and frozen solvent surface is demonstrated and elucidated using several examples.

Acetylation↗

PubMed2001

Homogeneous time resolved fluorescence resonance energy transfer using rare earth cryptates as a tool for probing molecular interactions in biology.

A homogeneous assay technology using time resolved fluorescence and fluorescence resonance energy transfer is described. A new class of fluorescent complexes, the cryptates, have been used as fluorescent donor with cross-linked allophycocyanin as acceptor. This new donor/acceptor shows an exceptionally high Förster distance R0 of 9 nm. This allows to build up a set of strategies to probe the interactions of biomolecules in biology, particularly for high throughput screening applications. In this article, we describe the basics of the technology and review applications developed for studying different key molecular interactions involved in cellular processes.

Cell Membrane↗

PubMed1995

Molecular interactions of 3',5'-cyclic purine analogues with the binding site of retinal rod ion channels.

Photoreceptor outer segments transduce information about incoming light levels through a class of ion channels that respond directly to changes in cytosolic 3',5'-cyclic guanosine monophosphate levels. A series of 3',5'-cyclic purine analogues with alterations at N1, C2, C6, or C8 positions was used to examine molecular interactions between the nucleotide and the channel. The maximal current activated by C2-altered analogues in excised membrane patches was less than the current activated by cGMP, and the K0.5, the concentration which activates 50% of the current in a patch, was increased. Nonpolar C8-substituted cAMP analogues activated more current than the parent cAMP with lower K0.5 values. This was in contrast to 8-amino-cAMP, which exhibited greatly reduced activity. The rank order of activity, based on K0.5 values, for C8-cAMP substituents was as follows: 8-azido- > 8-methylamino- > 8-benzylamino- > cAMP > 8-bromo- > 8-hydroxy- >> 8-amino-cAMP. 1,N6-Etheno-cAMP and N6-monobutyryl-cAMP activated a small fraction of the total possible current with high K0.5 values. Other analogues with alterations at N1 or C6 positions including N1-oxide-cAMP, 2-aminopurine riboside 3',5'-monophosphate, and N6-monosuccinyl-cAMP do not bind to the channel, suggesting that interactions with the channel in this region are essential for binding. In order to help interpret the changes in maximal current and K0.5 values compared to cGMP, molecular models of the active analogues were constructed and then docked into a molecular model of the cyclic nucleotide binding site of the retinal channel. This model, proposed by Kumar and Weber [(1992) Biochemistry 31, 4643-4649], was based on the crystal structure of cAMP bound to catabolite activator protein. Our modeling showed that the analogues were sterically accommodated within the binding site. No hydrogen bonds were predicted between the purine rings of cAMP and the pocket; however, Phe 533 on the beta 5 strand was predicted to form weak electrostatic interactions with C6 substituents on both cAMP and cGMP. The importance of contacts in this region of the binding pocket is further emphasized by the inactive analogues, all of which are altered at N1 or C6.

Ambystoma↗

PubMed2004

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

Database Management Systems↗

PubMed1992

Molecular interactions in myosin assembly. Role of the 28-residue charge repeat in the rod.

We have used internal deletions of multiples of seven residues to change the phase of the 28-residue charge repeat in a light meromyosin cDNA construct expressed in Escherichia coli. The solubility behaviour of these mutants was similar to that of the wild-type material, but the molecular packing in the aggregates formed at low ionic strength was different. Whereas wild-type material formed paracrystals in which molecules were in close contact over most of their length, molecules in the paracrystals formed by the mutants were in close contact for only a short distance, which was just short enough to exclude the deletion from the overlap. These data indicate that, although the 28-residue charge periodicity is important in myosin molecular interactions, it is probably not the major driving force for myosin assembly and instead influences the detailed axial stagger of the interacting molecules.

Base Sequence↗

PubMed1999

Molecular interactions in ribose transport: the binding protein module symmetrically associates with the homodimeric membrane transporter.

The Escherichia coli high-affinity ribose transporter is composed of the periplasmic ribose-binding protein (RBP or RbsB), the membrane component (RbsC) and the ATP-binding protein (RbsA). In order to dissect the molecular interactions initiating the transport process, RbsC suppressors for transport-defective rbsB mutations were isolated. These suppressors are localized in two regions of RbsC, which are allele-specific to N- or C-terminal domain mutations of RBP, suggesting that there are two distinct regions of RbsC, each interacting with one of the two domains of RBP. To demonstrate that these two regions provide a homodimeric binding surface for RBP we constructed a dimeric rbsC in which two genes are joined tandemly from head to tail with the addition of a linker. The dimeric RbsC protein is stable and functional in growth and ribose uptake. By exploiting the allele specificity between the domain-specific mutations and their suppressors, we generated all mutation-suppressor combinations in a single rbsB plus the dimeric rbsC genes. Their phenotypes are consistent with the proposal that the binding protein module interacts symmetrically with homodimeric RbsC. The mode of association proposed here for the ribose transport components could be extended to other ABC transporters with similar structural organizations.

ATP-Binding Cassette Transporters↗