István Komáromi

A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives

Abstract The IMOMM, IMOMO, and ONIOM methods have been proven to be powerful tools for the theoretical treatment of large molecular systems where different levels of theory are applied to different parts of a molecule. Within this framework we present a modified handling of the link atoms which are introduced to terminate the dangling bonds of the model system. Using this new scheme the definition of the combined energy gradient, the Hessian matrix, and the integration of higher derivatives of the energy with respect to nuclear coordinates and the electric field vector becomes straightforward. This allows for the first time the consistent combination of vibrational frequencies and the calculation of other molecular properties such as IR intensities, Raman intensities as well as dipole moments, polarizabilities, and hyperpolarizabilities. Test calculations for some typical as well as unusual examples and partitioning schemes are presented to demonstrate the power and limitations of the method and to provide guidelines for its applicability. Users of the method are strongly advised to test, calibrate and confirm for themselves the validity of the method combination and the model subsystem for the properties they want to calculate.

Combining quantum mechanics methods with molecular mechanics methods in ONIOM

The purpose of this paper is 2-fold. First, we present several extensions to the ONIOM(QM:MM) scheme. In its original formulation, the electrostatic interaction between the regions is included at the classical level. Here we present the extension to electronic embedding. We show how the behavior of ONIOM with electronic embedding can be more stable than QM/MM with electronic embedding. We also investigate the link atom correction, which is implicit in ONIOM but not in QM/MM. Second, we demonstrate some of the practical aspects of ONIOM(QM:MM) calculations. Specifically, we show that the potential surface can be discontinuous when there is bond breaking and forming closer than three bonds from the MM region.

Factor XIII: A Coagulation Factor With Multiple Plasmatic and Cellular Functions

Factor XIII (FXIII) is unique among clotting factors for a number of reasons: 1) it is a protransglutaminase, which becomes activated in the last stage of coagulation; 2) it works on an insoluble substrate; 3) its potentially active subunit is also present in the cytoplasm of platelets, monocytes, monocyte-derived macrophages, dendritic cells, chondrocytes, osteoblasts, and osteocytes; and 4) in addition to its contribution to hemostasis, it has multiple extra- and intracellular functions. This review gives a general overview on the structure and activation of FXIII as well as on the biochemical function and downregulation of activated FXIII with emphasis on new developments in the last decade. New aspects of the traditional functions of FXIII, stabilization of fibrin clot, and protection of fibrin against fibrinolysis are summarized. The role of FXIII in maintaining pregnancy, its contribution to the wound healing process, and its proangiogenic function are reviewed in details. Special attention is given to new, less explored, but promising fields of FXIII research that include inhibition of vascular permeability, cardioprotection, and its role in cartilage and bone development. FXIII is also considered as an intracellular enzyme; a separate section is devoted to its intracellular activation, intracellular action, and involvement in platelet, monocyte/macrophage, and dendritic cell functions.

Factor XIII: novel structural and functional aspects.

Summary.  Factor (F)XIII is a protransglutaminase that, in addition to maintaining hemostasis, has multiple plasmatic and intracellular functions. Its plasmatic form (pFXIII) is a tetramer of two potentially active A (FXIII‐A) and two inhibitory/carrier B (FXIII‐B) subunits, whereas its cellular form (cFXIII) is a dimer of FXIII‐A. FXIII‐A belongs to the family of transglutaminases (TGs), which show modest similarity in the primary structure, but a high degree of conservatism in their domain and sub‐domain secondary structure. FXIII‐A consists of an activation peptide, a β‐sandwich, a catalytic and two β‐barrel domains. FXIII‐B is a glycoprotein consisting of 10 repetitive sushi domains each held together by two internal disulfide bonds. The structural elements of FXIII‐A involved in the interaction with FXIII‐B have not been elucidated; in FXIII‐B the first sushi domain seems important for complex formation. In the circulation pFXIII is bound to the fibrinogen γ’‐chain through its B subunit. In the process of pFXIII activation first thrombin cleaves off the activation peptide from FXIII‐A, then in the presence of Ca2+ FXIII‐B dissociates and FXIII‐A becomes transformed into an active transglutaminase (FXIIIa). The activation is highly accelerated by the presence of fibrin(ogen). cFXIII does not require proteolysis for intracellular activation. The three‐dimensional structure of FXIIIa has not been resolved. Based on analogies with transglutaminase‐2, a three‐dimensional structure of FXIIIa was developed by molecular modeling, which shows good agreement with the drastic structural changes demonstrated by biochemical studies. The structural requirements for enzyme‐substrate interaction and for transglutaminase activity are also reviewed.

The mechanism of antibody-dependent cellular cytotoxicity stimulation by somatostatin in rat peritoneal macrophages

Somatostatin (SS) in 10(-9)-10(-7) M concentrations stimulated the lysis and inhibited the incorporation of IgG2a-coated 51Cr-labeled sheep red blood cell (SRBC) by rat peritoneal macrophages (PM). The intracellular killing capacity of PM remained unchanged. The enhancement of Fc receptor (R) activity and generation of active oxygen species were found to be responsible for the antibody-dependent cellular cytotoxicity (ADCC)-stimulating effect of SS. It was demonstrated that the stimulation of ADCC was abolished by the calmodulin inhibitor trifluoperazine (TFP), whereas it proved to be independent of the Ca2+ uptake. In addition, SS in the ADCC-stimulating concentrations diminished the intracellular cAMP generation and progressively increased the cGMP level. In higher (10(-6)-10(-7) M) concentrations, SS had a controversial effect on PM: it inhibited ADCC through the activation of both the adenylate cyclase and Ca2+ influx.

Antithrombin deficiency and its laboratory diagnosis

Abstract Antithrombin (AT) belongs to the serpin family and is a key regulator of the coagulation system. AT inhibits active clotting factors, particularly thrombin and factor Xa; its absence is incompatible with life. This review gives an overview of the protein and gene structure of AT, and attempts to explain how glucosaminoglycans, such as heparin and heparan sulfate accelerate the inhibitory reaction that is accompanied by drastic conformational change. Hypotheses on the regulation of blood coagulation by AT in physiological conditions are discussed. Epidemiology of inherited thrombophilia caused by AT deficiency and its molecular genetic background with genotype-phenotype correlations are summarized. The importance of the classification of AT deficiencies and the phenotypic differences of various subtypes are emphasized. The causes of acquired AT deficiency are also included in the review. Particular attention is devoted to the laboratory diagnosis of AT deficiency. The assay principles of functional first line laboratory tests and tests required for classification are discussed critically, and test results expected in various AT deficiency subtypes are summarized. The reader is provided with a clinically oriented algorithm for the correct diagnosis and classification of AT deficiency, which could be useful in the practice of routine diagnosis of thrombophilia. Clin Chem Lab Med 2010;48:S67–78.

Epigallocatechin‐3‐gallate and penta‐O‐galloyl‐β‐d‐glucose inhibit protein phosphatase‐1

Protein phosphatase‐1 (PP1) and protein phosphatase‐2A (PP2A) are responsible for the dephosphorylation of the majority of phosphoserine/threonine residues in cells. In this study, we show that (–)‐epigallocatechin‐3‐gallate (EGCG) and 1,2,3,4,6‐penta‐O‐galloyl‐β‐d‐glucose (PGG), polyphenolic constituents of green tea and tannins, inhibit the activity of the PP1 recombinant δ‐isoform of the PP1 catalytic subunit and the native PP1 catalytic subunit (PP1c) with IC50 values of 0.47–1.35 μm and 0.26–0.4 μm, respectively. EGCG and PGG inhibit PP2Ac less potently, with IC50 values of 15 and 6.6 μm, respectively. The structure–inhibitory potency relationships of catechin derivatives suggests that the galloyl group may play a major role in phosphatase inhibition. The interaction of EGCG and PGG with PP1c was characterized by NMR and surface plasmon resonance‐based binding techniques. Competitive binding assays and molecular modeling suggest that EGCG docks at the hydrophobic groove close to the catalytic center of PP1c, partially overlapping with the binding surface of microcystin‐LR or okadaic acid. This hydrophobic interaction is further stabilized by hydrogen bonding via hydroxyl/oxo groups of EGCG to PP1c residues. Comparative docking shows that EGCG binds to PP2Ac in a similar manner, but in a distinct pose. Long‐term treatment (24 h) with these compounds and other catechins suppresses the viability of HeLa cells with a relative effectiveness reminiscent of their in vitro PP1c‐inhibitory potencies. The above data imply that the phosphatase‐inhibitory features of these polyphenols may be implicated in the wide spectrum of their physiological influence.

Palmarumycins BG1-BG7 and preussomerin BG1: establishment of their absolute configurations using theoretical calculations of electronic circular dichroism spectra.

Palmarumycins BG1-BG7 (1-7), seven new compounds related to palmarumycins, were isolated from the aerial parts of Bruguiera gymnorrhiza as well as a new preussomerin derivative BG1 (8). The structures of these compounds were determined mainly by the analysis of their NMR and MS data, and their relative configurations were assigned on the basis of their (3)J(H,H) coupling constants. Compounds 4 and 7 have a sulfate group that is unprecedented among members of spirodioxynaphthalene-type natural products. The absolute configurations of 1-8 were determined by TDDFT CD calculations of the solution conformers. Compound 5 displayed inhibitory activity against HL 60 and MCF-7 cell lines.

Diazo Transfer−Click Reaction Route to New, Lipophilic Teicoplanin and Ristocetin Aglycon Derivatives with High Antibacterial and Anti-influenza Virus Activity: An Aggregation and Receptor Binding Study

Semisynthetic, lipophilic ristocetin and teicoplanin derivatives were prepared starting from ristocetin aglycon and teicoplanin psi-aglycon (N-acetyl-D-glucosaminyl aglycoteicoplanin). The terminal amino functions of the aglycons were converted into azido form by triflic azide. Copper catalyzed 1,3-dipolar cycloaddition reaction with lipophilic alkynes resulted in the title compounds. Two of the teicoplanin derivatives showed very good MIC and MBC values against various Gram-positive bacteria, including vanA enterococci. The aggregation and interaction of a n-decyl derivative with bacterial cell wall components was studied. One of the lipophilic ristocetin derivatives displayed favorable anti-influenza virus activity.

Age-Dependent Variations of Intralysosomal Enzyme Release from Human PMN Leukocytes under Various Stimuli

The intralysosomal beta glucuronidase and elastase release from polymorphonuclear leukocytes (PMNL) of young and aged male subjects were determined after 60-min incubation with 10 micrograms/ml Cytochalasin B (CB), 10(-6) M of Ca ionophore A 23187 and various concentrations of human low density lipoprotein (LDL). The beta glucoronidase secretion was triggered by both A 23187 and LDL; however, no significant differences were found between the enzyme release from PMNLs of young and aged subjects. In contrast, a marked elastase release was triggered in the young group only by LDL, whereas in the aged group, all of the applied drugs induced a significant elastase release. LDL caused the most dramatic enzyme release from PMNLs of aged males. It was concluded that the release of PMNL-elastase after LDL incorporation as well as by CB and Ca ionophore stimulation may be an age-related process.