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PubMed1996

Risks and synergies from drug interactions.

AIM: To review what is known from in vitro and in vivo studies about the interactions, both potentially beneficial and potentially harmful, of antiretroviral agents with each other and with other classes of drugs. INTERACTIONS WITH NUCLEOSIDE ANALOGUES: Some interactions between nucleoside HIV reverse transcriptase inhibitors and between nucleoside analogues and HIV protease inhibitors result in greater antiretroviral activity (e.g. zalcitabine with saquinavir). Others may increase the risks of toxicity and there are a number of combinations of nucleoside agents with other drugs that should be used with caution or avoided completely. INTERACTIONS WITH PROTEASE INHIBITORS: These drugs are metabolized by cytochrome P450 CYP3A4 in the liver; because they have the potential to inhibit this enzyme they may interact with many other drugs that are metabolized by this pathway. Ritonavir also inhibits other cytochrome P450 enzymes and so interacts with numerous drugs from a range of classes. Potentially beneficial interactions between protease inhibitors include the increase in saquinavir levels brought about by ritonavir. CONCLUSIONS: Knowledge of additive and synergistic interactions between antiretroviral agents should facilitate development of therapeutic regimens with prolonged antiretroviral activity. Thorough investigation of possibly harmful interactions with co-administered drugs and education of clinicians and patients about the risks of these interactions is required.

Anti-HIV Agents↗
PubMed2000

Evidence for a strong sulfur-aromatic interaction derived from crystallographic data.

We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31-37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X-CH(2)-X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur-aromatic interaction descriptors and their CH(2)-aromatic analogues using the Smirnov-Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276-286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209-217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177-180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS Letters, 1985, Vol. 190, pp. 209-213), as well as studies involving molecular mechanics (G. Nemethy and H. A. Scheraga, Biochemistry and Biophysics Research Communications, 1981, Vol. 98, pp. 482-487) and quantum chemical calculations (B. V. Cheney, M. W. Schulz, and J. Cheney, Biochimica Biophysica Acta, 1989, Vol. 996, pp.116-124; J. Pranata, Bioorganic Chemistry, 1997, Vol. 25, pp. 213-219)-all of which point to the possible importance of the sulfur-aromatic interaction. However, the preferred geometry of the interaction, as determined from our analysis of the small-molecule crystal data, differs significantly from that found by other approaches.

Crystallography, X-Ray↗
PubMed2002

Immunoaffinity capillary electrophoresis: determination of binding constant and stoichiometry for antibody-antigen interaction.

Affinity capillary electrophoresis (ACE) can provide both qualitative and quantitative information on molecular interactions and affords the advantages of very low sample consumption, high mass sensitivity, short analysis time, and the use of automated instrumentation. It has been applied clinically and biochemically to the determination of the binding constant and to the measurement of the binding stoichiometry for interactions between antibodies (Ab's) and antigens (Ag's) in free solution. In many situations, the Ag molecule has two or multiple binding sites, each of which has a similar or different intrinsic affinity for binding independently to the combining site(s) on an Ab molecule. The multivalent binding reactions between Ab and Ag molecules often occur. The objective of this review is to describe the uses of ACE in the determination of binding constants and stoichiometry of Ab-Ag interactions (immunoaffnity capillary electrophoresis), focusing especially on multivalent Ab-Ag interaction modes. Five model binding systems developed recently using ACE techniques are described with principles and examples: (i) divalent mAb-monovalent Ag interaction, (ii) divalent mAb-(homo)polyvalent Ag interaction, (iii) cooperativity of two binding sites of mAb-monovalent Ag interaction, (iv) monovalent Fab-divalent Ag interaction, and (v) polyclonal Ab-monovalent Ag interaction. Finally, the determination of binding stoichiometry of Ab-Ag interactions by ACE is described.

Antigen-Antibody Reactions↗
PubMed1995

Energetics of protein-DNA interactions: an exact calculation for binding of ligands to a lattice of overlapping sites.

Exact equations are developed for analyzing the binding of ligands to a linear lattice of overlapping sites in which occupied-unoccupied as well as occupied-occupied interactions are included for the analysis of the binding isotherms. We demonstrate that positive cooperativity on the binding of ligands to multiple sites may derive from either occupied-unoccupied or occupied-occupied interactions. When the binding of proteins to linear polynucleotides and DNA has exhibited positive cooperativity protein-protein (occupied-occupied), interactions have heretofore been invoked as the sole energetic source in determining the cooperative effect. Models and equations developed previously for the analysis of these binding isotherms have included only the protein-protein interactions (usually characterized with the symbol omega). The exact equations of this paper are capable of analyzing binding data in a manner to evaluate the relative importance of both occupied-unoccupied and occupied-occupied interactions. Relations derived here are employed to analyze some existing data, and the resulting parameter values are compared to those developed with equations employing only the protein-protein (occupied-occupied) interactions. The resulting parameter values are qualitatively different. Values of the binding constants differ by about three orders of magnitude. When only protein-protein interactions are taken into account, the resulting free energy of interaction is negative, indicating attractive forces between bound protein molecules; when both occupied-unoccupied and occupied-occupied interactions are applied, the resulting free energies of interaction are positive, indicating destabilizing forces acting primarily on the polynucleotide lattice.

Binding Sites↗
PubMed2004

Quantitative evaluation of d-pi interaction in copper(I) complexes and control of copper(I)-dioxygen reactivity.

Crystal structures of the copper(I) complexes 1(X), 2, and 3 of a series of tridentate ligands L1(X), L2, and L3, respectively (L1(X): p-substituted derivatives of N,N-bis[2-(2-pyridyl)ethyl]-2-phenylethylamine; X=H, Me, OMe, Cl, NO(2); L2: N,N-bis[2-(2-pyridyl)ethyl]-2-methyl-2-phenylethylamine; L3: N,N-bis[2-(2-pyridyl)ethyl]-2,2-diphenylethylamine) were solved to demonstrate that all the copper(I) complexes involve an eta(2) copper-arene interaction with the phenyl ring of the ligand sidearm. The Cu(I) ion in each complex has a distorted tetrahedral geometry consisting of the three nitrogen atoms (one tertiary amine nitrogen atom and two pyridine nitrogen atoms) and C(1)-C(2) of the phenyl ring of ligand sidearm, whereby the Cu-C distances of the copper-arene interaction significantly depend on the para substituents. The existence of the copper-arene interaction in a nonpolar organic solvent (CH(2)Cl(2)) was demonstrated by the observation of an intense MLCT band around 290 nm, and the magnitude of the interaction was evaluated by detailed analysis of the (1)H and (13)C NMR spectra and the redox potentials E(1/2) of the copper ion, as well as by means of the ligand-exchange reaction between the phenyl ring and CH(3)CN as an external ligand. The thermodynamic parameters DeltaH(o) and DeltaS(o) for the ligand-exchange reaction with CH(3)CN afforded a quantitative measure for the energy difference of the copper-arene interaction in the series of copper(I) complexes. Density functional studies indicated that the copper(I)-arene interaction mainly consists of the interaction between the d(z(2) ) orbital of Cu(I) and a pi orbital of the phenyl ring. The copper(I) complexes 1(X) reacted with O(2) at -80 degrees C in CH(2)Cl(2) to give the corresponding (micro-eta(2):eta(2)-peroxo)dicopper(II) complexes 4, the formation rates k(obs) of which were significantly retarded by stronger d-pi interaction, while complexes 2 and 3, which exhibit the strongest d-pi interaction showed significantly lower reactivity toward O(2) under the same experimental conditions. Thus, the d-pi interaction has been demonstrated for the first time to affect the copper(I)-dioxygen reactivity, and represents a new aspect of ligand effects in copper(I)-dioxygen chemistry.

Journal Article↗
PubMed2005

Molecular aptamers for real-time protein-protein interaction study.

Protein-protein interactions play critical roles in cellular functions, but current techniques for real-time study of these interactions are limited. We report the real-time monitoring of protein-protein interactions without labeling either of the two interacting proteins; this procedure poses minimum effects on the binding properties of the proteins. Our strategy uses a protein/aptamer complex to probe the interactions in a competitive assay where the binding of an aptamer to its target protein is altered by a second protein that interacts with the target protein. Two signal transduction strategies, fluorescence resonance energy transfer (FRET) and fluorescence anisotropy, have been designed to study the interactions of human alpha-thrombin with different proteins by using two aptamers specific for two binding sites on alpha-thrombin. Our method has been shown to be simple and effective, does not require labeling of proteins, makes use of easily obtainable aptamers, provides detailed protein-protein interaction information and has excellent sensitivity for protein detection and protein-protein interaction studies. The FRET and the fluorescent anisotropy approaches complement each other in providing insight into the kinetics, mechanisms, binding sites and binding dynamics of the interacting proteins.

Base Sequence↗
PubMed2006

Interactions between mouse IgG2 antibodies are common and mediated by plasma C1q.

BACKGROUND: The simultaneous use of multiple antibodies for multicolor flow cytometry is increasingly common and presents the opportunity for antibody interactions. METHODS: Antibodies of differing isotypes were evaluated in pair-wise combinations for the presence of antibody interactions, using a standard whole blood lysing method or variations thereof. RESULTS: Artifactual interactions were identified and preferentially involved IgG2a (58%) or IgG2b (33%) antibodies and a single IgG1 antibody (3%). The interactions were present in all 10 random peripheral blood samples evaluated and required only whole blood and the two antibodies. Plasma removal prior to antibody incubation eliminated the interaction, as did switching any single IgG2 antibody to an IgG1 clone. Heat-inactivated plasma eliminated the interactions, and the addition of purified C1q to washed cells was capable of recreating the interaction in its entirety, confirming the mediation by complement C1q. CONCLUSIONS: Complement C1q mediates significant interactions between mouse IgG2 class antibodies; these interactions are very common and may be prevented by either complete serum removal or use of alternate IgG1 clones. Such interactions represent a significant potential source of artifact in the use of whole blood lysis methods for specimen preparation for multicolor flow cytometry.

Animals↗
PubMed2004

Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning.

Accurate and fast evaluation of electrostatic interactions in molecular systems is still one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry, including molecular recognition, protein modeling and drug design. One of the most convenient and accurate approaches is based on a Buckingham-type approximation that uses the multipole moment expansion of molecular/atomic charge distributions. In the mid-1980s it was shown that the pseudoatom model commonly used in experimental X-ray charge density studies can be easily combined with the Buckingham-type approach for calculation of electrostatic interactions, plus atom-atom potentials for evaluation of the total interaction energies in molecular systems. While many such studies have been reported, little attention has been paid to the accuracy of evaluation of the purely electrostatic interactions as errors may be absorbed in the semiempirical atom-atom potentials that have to be used to account for exchange repulsion and dispersion forces. This study is aimed at the evaluation of the accuracy of the calculation of electrostatic interaction energies with the Buckingham approach. To eliminate experimental uncertainties, the atomic moments are based on theoretical single-molecule electron densities calculated at various levels of theory. The electrostatic interaction energies for a total of 11 dimers of alpha-glycine, N-acetylglycine and L-(+)-lactic acid structures calculated according to Buckingham with pseudoatom, stockholder and atoms-in-molecules moments are compared with those evaluated with the Morokuma-Ziegler energy decomposition scheme. For alpha-glycine a comparison with direct "pixel-by-pixel" integration method, recently developed Gavezzotti, is also made. It is found that the theoretical pseudoatom moments combined with the Buckingham model do predict the correct relative electrostatic interactions energies, although the absolute interaction energies are underestimated in some cases. The good agreement between electrostatic interaction energies computed with Morokuma-Ziegler partitioning, Gavezzotti's method, and the Buckingham approach with atoms-in-molecules moments demonstrates that reliable and accurate evaluation of electrostatic interactions in molecular systems of considerable complexity is now feasible.

Algorithms↗
PubMed2003

Molecular mechanisms of S100-target protein interactions.

S100 proteins have no known enzymatic activity and exert their intracellular effects via interaction with and regulation of the activity of other proteins, termed target proteins, in both a Ca(2+)-dependent and Ca(2+)-independent manner. Structural studies have identified the linker region between the two EF-hand Ca(2+) binding domains and the C-terminus as Ca(2+)-dependent target protein binding sites in several S100 family members. In fact, C-terminal aromatic residues are obligatory for interaction of S100A1 with several of its Ca(2+)-dependent target proteins. Pharmacological studies suggest the presence of additional Ca(2+)-dependent binding motifs on some family members. A minimum of seven family members interact with and regulate the activity of aldolase A in a Ca(2+)-independent manner. In the case of S100A1, Ca(2+)-independent target protein interactions utilize a binding motif distinct from the C-terminal Ca(2+)-dependent target protein binding site. Several studies suggest that ionic interactions participate in the interaction of S100 family members with Ca(2+)-independent target proteins. While some target proteins are activated by multiple family members, other target proteins exhibit family member-specific activation, i.e., they are activated by a single family member. As predicted, family member specific interactions appear to be mediated by regions that exhibit the most divergence in amino acid sequence among family members, the linker or "hinge" region and the C terminus. Further specificity in S100-target protein interactions may arise from the different biochemical/biophysical properties of the individual family members, including affinity for metal ions (Ca(2+), Zn(2+), and Cu(2+)), oligomerization properties, heterodimerization, post-translational modifications, and lipid-binding. Delineation of the structural motifs that mediate S100-target protein interactions and determination of the in vivo relevance of these interactions are needed to fully understand the role of S100 proteins in normal and diseased cells.

Amino Acid Sequence↗
PubMed1996

Target recognition by calmodulin: dissecting the kinetics and affinity of interaction using short peptide sequences.

The interaction between calmodulin (CaM) and peptide M13, its target binding sequence from skeletal muscle myosin light chain kinase, involves predominantly two sets of interactions, between the N-terminal target residues and the C-domain of calmodulin, and between the C-terminal target residues and the N-domain of calmodulin (Ikura M et al., 1992, Science 256:632-638). Using short synthetic peptides based on the two halves of the target sequence, the interactions with calmodulin and its separate C-domain have been studied by fluorescence and CD spectroscopy, calcium binding, and kinetic techniques. Peptide WF10 (residues 1-10 of M13) binds to CaM with Kd approximately 1 microM; peptide FW10 (residues 9-18 of M13, with Phe-17-->Trp substitution) binds to CaM with Kd approximately 100 microM. The effect of peptide WF10 on calcium binding to calmodulin produces a biphasic saturation curve, with marked enhancement of affinity for the binding of two calcium ions to the C-domain, forming a stable half-saturated complex, Ca2-CaM-peptide, and confirming the functional importance of the interaction of this sequence with the C-domain. Stopped-flow studies show that the EGTA-induced dissociation of WF10 from Ca4-CaM proceeds by a reversible relaxation mechanism from a kinetic intermediate state, also involving half-saturation of CaM, and the same mechanism is evident for the full target peptide. Interaction of the N-terminal target residues with the C-domain is energetically the most important component, but interaction of calmodulin with the whole target sequence is necessary to induce the full cooperative interaction of the two contiguous elements of the target sequence with both N- and C-domains of calmodulin. Thus, the interaction of calmodulin with the M13 sequence can be dissected on both a structural and kinetic basis into partial reactions involving intermediates comprising distinct regions of the target sequence. We propose a general mechanism for the calcium regulation of calmodulin-dependent enzyme activation, involving an intermediate complex formed by interaction of the calmodulin C-domain and the corresponding part of the target sequence. This intermediate species can function to regulate the overall calcium sensitivity of activation and to determine the affinity of the calmodulin target interaction.

Amino Acid Sequence↗
PubMed1997

Surface Element Integration: A Novel Technique for Evaluation of DLVO Interaction between a Particle and a Flat Plate

A novel method, the surface element integration (SEI), is developed to determine the van der Waals and electrostatic double layer interactions between a particle and an infinite flat plate from the corresponding interactions per unit area between two infinite flat plates. Comparison with the Hamaker expression for nonretarded van der Waals interaction reveals that the new technique gives the exact interaction energy between a spherical particle and a flat plate. Available analytical expressions for the electrostatic double layer interaction energy between two infinite flat plates, based on the linearized Poisson-Boltzmann equation, are used in SEI to obtain the sphere-flat plate interaction energy. These sphere-flat plate interaction energies determined using SEI are compared with the corresponding interaction energies obtained from a detailed numerical solution of the Poisson-Boltzmann equation based on finite element analysis. The comparisons reveal that SEI scales the flat plate interaction to the corresponding sphere-flat plate geometry exactly, while the scaling based on the conventional Derjaguin approximation technique grossly overpredicts the interaction energy for small particles and low electrolyte concentrations. Copyright 1997 Academic Press. Copyright 1997Academic Press

Journal Article↗
PubMed1997

Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction.

One of the most common RNA tertiary interactions involves the docking of GNRA hairpin loops into stem-loop structures on other regions of RNA. Domain 5 of the group II intron interacts with Domain 1 through such an interaction, which has been characterized thermodynamically and kinetically for the ai5g intron. Using this system, it was possible to test the morphological tolerances of the GNRA tetraloop involved in tertiary interactions. The data presented herein show that a GNRA tetraloop can still participate in tertiary interaction after being physically cut at any phosphodiester linkage within the loop. The "nicked tetraloop" can be expanded by many nucleotides in either direction and the covalently continuous loop can also be expanded without loss of interaction energy. In the context of the nicked tetraloop, the second nucleotide of the tetraloop sequence can be completely deleted without loss of function. By examining radical alterations in tetraloop structure, this study helps define the minimal sequence and structural requirements of a GNRA motif involved in long-range tertiary interaction. It shows that "tetraloop"-like structures capable of forming tertiary interactions can be imbedded in unexpected contexts, such as internal loops and apparently open structure within RNA. It demonstrates that pentaloops and hexaloops can form the same type of interaction, with almost equal affinity, as a tetraloop. Taken together, these data suggest a more generic term for the GNRA tetraloop-receptor interaction: It is proposed herein that the term "GNRA tetraloop" be replaced by "GNn/RA", where n represents a variable number of nucleotides and / indicates that the loop can be divided and interrupted by other sequences.

Kinetics↗
PubMed2001

Correlated sequence-signatures as markers of protein-protein interaction.

As protein-protein interaction is intrinsic to most cellular processes, the ability to predict which proteins in the cell interact can aid significantly in identifying the function of newly discovered proteins, and in understanding the molecular networks they participate in. Here we demonstrate that characteristic pairs of sequence-signatures can be learned from a database of experimentally determined interacting proteins, where one protein contains the one sequence-signature and its interacting partner contains the other sequence-signature. The sequence-signatures that recur in concert in various pairs of interacting proteins are termed correlated sequence-signatures, and it is proposed that they can be used for predicting putative pairs of interacting partners in the cell. We demonstrate the potential of this approach on a comprehensive database of experimentally determined pairs of interacting proteins in the yeast Saccharomyces cerevisiae. The proteins in this database have been characterized by their sequence-signatures, as defined by the InterPro classification. A statistical analysis performed on all possible combinations of sequence-signature pairs has identified those pairs that are over-represented in the database of yeast interacting proteins. It is demonstrated how the use of the correlated sequence-signatures as identifiers of interacting proteins can reduce significantly the search space, and enable directed experimental interaction screens.

Computational Biology↗
PubMed1995

A potyvirus polymerase interacts with the viral coat protein and VPg in yeast cells.

The two-hybrid system was used to test for pairwise interactions between the tobacco vein mottling virus (TVMV)-encoded RNA-dependent RNA polymerase (or NIb protein) and two other TVMV-encoded proteins: the NIa protein, which consists of genome-linked protein (VPg) and proteinase domains, and the viral coat protein (CP). Using this approach, we find that the NIb protein interacts with both the NIa protein and the CP in yeast cells. Moreover, we find that a mutation in the conserved GDD domain of the NIb protein diminishes the NIb-CP interaction but not the NIb-NIa interaction. Likewise, mutations in the vicinity of the NIa protein to which the genomic RNA is covalently attached eliminate the NIb-NIa interaction. We conclude that the NIb protein interacts with the VPg domain of the NIa protein and that this interaction requires a functional RNA attachment site. This interaction may be important for the initiation of viral RNA synthesis in infected cells. We also conclude that the CP interacts with the NIb in a manner that is sensitive in changes in the highly conserved GDD motif. The role of this interaction in the functioning of the NIb protein or the CP is unclear, but may involve regulation of viral RNA synthesis in infected cells.

Amino Acid Sequence↗
PubMed2000

Multiple interactions among proteins encoded by the mite-transmitted wheat streak mosaic tritimovirus.

The genome organization of the mite-transmitted wheat streak mosaic virus (WSMV) appears to parallel that of members of the Potyviridae with monopartite genomes, but there are substantial amino acid dissimilarities with other potyviral polyproteins. To initiate studies on the functions of WSMV-encoded proteins, a protein interaction map was generated using a yeast two-hybrid system. Because the pathway of proteolytic maturation of the WSMV polyprotein has not been experimentally determined, random libraries of WSMV cDNA were made both in DNA-binding domain and activation domain plasmid vectors and introduced into yeast. Sequence analysis of multiple interacting pairs revealed that interactions largely occurred between domains within two groups of proteins. The first involved interactions among nuclear inclusion protein a, nuclear inclusion protein b, and coat protein (CP), and the second involved helper component-proteinase (HC-Pro) and cylindrical inclusion protein (CI). Further immunoblot and deletion mapping analyses of the interactions suggest that subdomains of CI, HC-Pro, and P1 interact with one another. The two-hybrid assay was then performed using full-length genes of CI, HC-Pro, P1, P3, and CP, but no heterologous interactions were detected. In vitro binding assay using glutathione-S-transferase fusion proteins and in vitro translation products, however, revealed mutual interactions among CI, HC-Pro, P1, and P3. The failure to detect interactions between full-length proteins by the two-hybrid assay might be due to adverse effects of expression of viral proteins in yeast cells. The capacity to participate in multiple homomeric and heteromeric molecular interactions is consistent with the pleiotropic nature of many potyviral gene mutants and suggests mechanisms for regulation of various viral processes via a network of viral protein complexes.

Animals↗
PubMed2001

Identification and functional analysis of an interaction between domains of the 126/183-kDa replicase-associated proteins of tobacco mosaic virus.

The Tobacco mosaic virus (TMV) 126-kDa and read-through 183-kDa replicase-associated proteins have been shown to interact [Watanabe, T., Honda, A., Iwata, A., Ueda, S., Hibi, T., Ishihama, A. (1999). J. Virol. 73, 2633-2640]. To identify and investigate the sequence required for this interaction, five segments covering different portions of the 126/183-kDa open reading frame, including the methyl-transferase, intervening region (IR), helicase-like (HEL), and polymerase domains, were screened via the yeast two-hybrid system against a library of TMV protein segments. Only one specific interaction between the HEL domain clone and a TMV library clone, IRnHEL, encoding the C-terminal half of the IR and the N-terminal portion of the HEL domain was identified. Sequence and deletion analysis revealed that the interacting clones share a region containing the helicase NTP-binding motif and that this region was essential for the interaction. To determine the functional significance of this interaction, mutants of the HEL domain segment that conferred a temperature-sensitive (ts) defect in the yeast interaction were identified and cloned into a recombinant TMV strain. Of the five selected mutants, three (V823I/S824N/V1042M, A877V, V1087I) produced a ts replication phenotype in protoplasts while the other two (A1073V, T884I) abolished TMV replication at both the permissive and the nonpermissive temperatures. An additional mutation, K839S, designed to disrupt the shared NTP-binding motif, nearly abolished the two-hybrid interaction and prevented virus replication, suggesting that NTP-binding and/or the structure of this motif is a contributing factor in the interaction. Taken together, these results provide support for an interaction between TMV replicase-associated proteins that involves specific structural features of the HEL and IR domains.

Amino Acid Motifs↗
PubMedDate not supplied

Effect of sulfated xylans during the interaction of [125I]-thrombin with antithrombin III or heparin cofactor II of human plasma.

[125I]-Labeled thrombin was incubated with human plasma and its interactions with the two plasma protease inhibitors antithrombin III (AT-III) or heparin cofactor II (HC-II) were investigated in the presence of oat spelts xylan sulfate (OSXS), sodium pentosan polysulfate (SP-54), and the results were compared with heparin and dermatan sulfate. Addition of OSXS or SP-54 enhanced the complexation of thrombin with HC-II or with both AT-III and HC-II depending upon the concentration and the duration of the interactions of the sulfated compounds with plasma. During the 30 s interaction, OSXS and SP-54 enhanced both AT-III-thrombin and HC-II-thrombin interaction while heparin was more selective and enhanced only the AT-III-thrombin interaction. However after a 2 min interaction, heparin showed an increase in the HC-II-thrombin interaction at higher concentrations. The complexations of AT-III-thrombin and HC-II-thrombin were reversed in the presence of 200 micrograms/ml of SP-54 during a 30 s interaction or in presence of 100 micrograms/ml of OSXS during a 2 min interaction. The Western blotting method of detecting thrombin showed that during the 10 s interaction, heparin enhanced the thrombin-AT-III complex formation while OSXS enhanced the thrombin-HC-II complex formation.

Antithrombin III↗
PubMed2003

Interactions between 33 solutes and four cyano-containing stationary phases: gas chromatographic activity coefficients and the solvation parameter model.

Infinite-dilution gas-liquid chromatographic activity coefficients at 393.15 K (with their thermal and athermal components) and derived excess partial molar Gibbs energies, enthalpies, and entropies have been determined for each of 33 solutes of different polarity on four stationary phases with cyano groups, using retention data taken from the literature. The strongest interactions predicted by the solvation model are the dipolarity/polarizability, the acidic solute-basic stationary phase interaction, and nonpolar cavity formation and dispersion. These interactions were compared with those evaluated from the solute activity coefficients; the effect of the solute connectivity index and dipole moment on nonpolar and polar interactions, respectively, is discussed. The dependence of the thermal activity coefficient on nonpolar interactions, and the influence of stationary phase polarity on the four solute-stationary phase interactions, were evaluated. The nonpolar interaction increases with increasing connectivity and with increasing athermal activity coefficient. The dipolarity/polarizability interaction increases with increasing solute dipole moment. Finally, polar interactions increase with increasing stationary phase polarity whereas the nonpolar interaction is independent of stationary phase polarity.

Journal Article↗