A putative bioactive conformation for the altered peptide ligand of myelin basic protein and inhibitor of experimental autoimmune encephalomyelitis [Arg91, Ala96] MBP87-99

[Arg(91), Ala(96)] MBP(87-99) is an altered peptide ligand (APL) of myelin basic protein (MBP), shown to actively inhibit experimental autoimmune encephalomyelitis (EAE), which is studied as a model of multiple sclerosis (MS). The APL has been rationally designed by substituting two of the critical residues for recognition by the T-cell receptor. A conformational analysis of the APL has been sought using a combination of 2D NOESY nuclear magnetic resonance (NMR) experiments and detailed molecular dynamics (MD) calculations, in order to comprehend the stereoelectronic requirements for antagonistic activity, and to propose a putative bioactive conformation based on spatial proximities of the native peptide in the crystal structure. The proposed structure presents backbone similarity with the native peptide especially at the N-terminus, which is important for major histocompatibility complex (MHC) binding. Primary (Val(87), Phe(90)) and secondary (Asn(92), Ile(93), Thr(95)) MHC anchors occupy the same region in space, whereas T-cell receptor (TCR) contacts (His(88), Phe(89)) have different orientation between the two structures. A possible explanation, thus, of the antagonistic activity of the APL is that it binds to MHC, preventing the binding of myelin epitopes, but it fails to activate the TCR and hence to trigger the immunologic response. NMR experiments coupled with theoretical calculations are found to be in agreement with X-ray crystallography data and open an avenue for the design and synthesis of novel peptide restricted analogues as well as peptide mimetics that rises as an ultimate goal.     

Iron(II) triggered conformational changes in Escherichia coli fur upon DNA binding: a study using molecular modeling

In order to identify the Fur dimerization domain, a three-dimensional structure of the ferric uptake regulation protein from Escherichia coli (Fur EC) was determined using homology modeling and energy minimization. The Fur monomer consists of turn- helix -turn motif on the N-terminal domain, followed by another helix-turn-helix-turn motif, and two beta-strands separated by a turn which forms the wing. The C-terminal domain, separated by a long coil from the N-terminal, and consisting of two anti parallel beta strands, and a turn-helix-turn-helix-turn motif. Residues in central domain were found to aid the dimer formation, residues 45-70 as evident in the calculated distances; this region is rich in hydrophobic residues. Most interactions occur between residues Val55, Leu53, Gln52, Glu49 and Tyr56 with closest contacts occurring at residues 49-56. These residues are part of an alpha-helix (alpha(4)) near the N-terminal. Upon raising the Fe(2+) concentration the binding of Fur dimer to DNA was enhanced, this was evident when, the Fur EC dimer was docked onto DNA "iron box" (it was found to bind the AT-rich region) and upon addition of Fe(2+) the helices near the N-terminal bound to the major groove of the DNA. Addition of high Fe(2+) concentration triggered further conformational changes in the Fur dimer as was measured by distances between the two subunits, Fe(2+) mediated the Fur binding to DNA by attaching itself to the DNA. At the same time DNA changed conformation as was evident in the distortion in the backbone and the shrinking of major groove distance from 11.4 to 9.3A. Two major Fe(2+) sites were observed on the C-terminal domain: site 1, the traditional Zn site, the cavity contains the residues Cys92, Cys95, Asp137, Asp141, Arg139, Glu 140, His 145 and His 143 at distances range from 1.3 to 2.2A. Site 2 enclave consists of His71, Ile50, Asn72, Gly97, Asp105 and Ala109 at very close proximity to Fe(2+). The closest contacts between Fur dimer and DNA at the AT-rich region were at residues Ala11, Gly12, Leu13, Pro18 and Arg19 mostly hydrophobic residues near the N-terminal domain. Close contacts repeated at His87, His88 and Arg112, and a third region near the C-terminal at Asn137, Arg 139, Glu140, Asn141, His143, Asn141 and His145. Fur dimer has three major contact regions with DNA, the first on the N-terminal domain, a second smaller region at His87, His88 and Arg112 mediated by Fe(2+) ions, and a third region on the C-terminal domain consisting mainly of hydrophobic contacts and mediated by Fe(2+) ions at high concentration.     

Structure analysis of the protein transduction domain of human Period1 and its mutant analogs

Human Period1 (hPer1) has been proved to be able to translocate into cells in a protein transduction manner. The segment of amino acids 830-845 of hPer1 is its protein transduction domain (PTD). In order to explore the membrane penetrating mechanism of hPer1-PTD and the physico-chemical properties necessary in the process, Ala scanning mutation method was used to investigate the variation in the peptide internalization. To further investigate the related physico-chemical requirements, the three dimensional structures of hPer1-PTD and its mutant analogs were simulated by Rosetta method. The electrostatic potentials and energies of these structures were calculated using the Delphi algorithm to solve Poisson-Boltzman equation. The hydrophobicity was assessed by the percentage of the nonpolar area in SAS (solvent accessible surface (SAS)). It has been proved that the Arg836 was the key residue for peptide internalization. When this Arg mutated into Ala, the peptide could not cross the membrane. The large enough area with positive charge was the decisive factor for hPer1-PTD. The alpha-helical structure seemed to play an assistant role so as to enable the positive charge connected in spatial arrangement.     

Modeling and molecular dynamics of glutamine transaminase K/cysteine conjugate beta-lyase

The homodimeric, pyridoxal 5'-phosphate (PLP)-dependent enzyme glutamine transaminase K/cysteine conjugate beta-lyase (GTK/beta-lyase) has been implicated in the bioactivation of chemopreventive compounds. This paper describes the first homology model of rat renal GTK/beta-lyase and its active site residues, deduced from molecular dynamics (MD) simulations of the binding mode of 13 structurally diverse cysteine S-conjugates and amino acids after Amber-parametrization of PLP. Comparison with Thermus thermophilus aspartate aminotransferase (tAAT) and Trypanosoma cruzi tyrosine aminotransferase (tTAT), used as templates for modeling GTK/beta-lyase, showed that the PLP-binding site of GTK/beta-lyase is highly conserved. Binding of the ligand alpha-carboxylate-group occurred via the conserved residues Arg(432) and Asn(219), and Asn(50) and Gly(70). Two pockets accommodated the various ligand side chains. A small pocket, located directly above PLP, was of a highly hydrophobic and aromatic character. A larger pocket, formed partly by the substrate access channel, was more hydrophilic and notably involved the salt bridge partners Glu(54) and Arg(99*) (* denotes the other subunit). Ligand-binding residues included Leu(51), Phe(71), Tyr(135), Phe(373) and Phe(312*), and pi-stacking interactions were often observed. Tyr(135) and Asn(50) were prominent in hydrogen bonding with the sulfur-atom of cysteine S-conjugates.The observed binding mode of the ligands corresponded well with their experimentally determined inhibitory potency toward GTK/beta-lyase. The current homology model thus provides a starting point for further validation of the role of active site residues in ligand-binding by means of mutagenesis studies. Ultimately, insight in the binding of ligands to GTK/beta-lyase may result in the rational design of new ligands and selective inhibitors.     

Tauberian theorems for statistically convergent double sequences

In [F. Moricz, Tauberian theorems for Cesàro summable double sequences, Studia Math. 110 (1994) 83-96], Moricz has proved some Tauberian theorems for Cesàro summable double sequences and deduced the Tauberian theorems of Landau [E. Landau, Über die Bedeutung einiger neuerer Grenzwertsätze der Herren Hardy and Axer, Prac. Mat.-Fiz. 21 (1910) 97-177] and Hardy [G.H. Hardy, Divergent Series, Univ. Press, Oxford 1956] type. In [J.A. Fridy, M.K. Khan, Statistical extension of some classical Tauberian theorems, Proc. Amer. Math. Soc. 128 (2000) 2347-2355], Fridy and Khan have given statistical extensions of some classical Tauberian theorems. The concept of statistical convergence for double sequences has recently been introduced by Mursaleen and Edely [M. Mursaleen, Osama H. H. Edely, Statistical convergence of double sequences, J. Math. Anal. Appl. 288 (2003) 223-231] and by Moricz [F. Moricz, Statistical convergence of multiple sequences, Arch. Math. 81 (2003) 82-89] independently. In this paper we give some Tauberian theorems for statistically convergent double sequences. We have also provided some examples including an example to Problem 1 of Moricz [F. Moricz, Tauberian theorems for Cesàro summable double sequences, Studia Math. 110 (1994) 83-96].     

Optimal randomized parallel algorithms for computational geometry

We present parallel algorithms for some fundamental problems in computational geometry which have a running time ofO(logn) usingn processors, with very high probability (approaching 1 asn ). These include planar-point location, triangulation, and trapezoidal decomposition. We also present optimal algorithms for three-dimensional maxima and two-set dominance counting by an application of integer sorting. Most of these algorithms run on a CREW PRAM model and have optimal processor-time product which improve on the previously best-known algorithms of Atallah and Goodrich [5] for these problems. The crux of these algorithms is a useful data structure which emulates the plane-sweeping paradigm used for sequential algorithms. We extend some of the techniques used by Reischuk [26] and Reif and Valiant [25] for flashsort algorithm to perform divide and conquer in a plane very efficiently leading to the improved performance by our approach.This is a substantially revised version of the paper that appeared as Optimal Randomized Parallel Algorithms for Computational Geometry in theProceedings of the 16th International Conference on Parallel Processing, St. Charles, Illinois, August 1987.This research was supported by DARPA/ARO Contract DAAL03-88-K-0195, Air Force Contract AFOSR-87-0386, DARPA/ISTO Contracts N00014-88-K-0458 and N00014-91-J-1985, and by NASA Subcontract 550-63 of Primecontract NAS5-30428.     

Ordinal optimization of DEDS

In this paper we argue thatordinal rather thancardinal optimization, i.e., concentrating on finding good, better, or best designs rather than on estimating accurately the performance value of these designs, offers a new, efficient, and complementary approach to the performance optimization of systems. Some experimental and analytical evidence is offered to substantiate this claim. The main purpose of the paper is to call attention to a novel and promising approach to system optimization.This work is supported by NSF grants CDR-88-03012, DDM-89-14277, ONR contracts N00014-90-J-1093, N00014-89-J-1023, and army contracts DAAL-03-83-K-0171, DAAL-91-G-0194.     

Molecular docking and dynamic simulation evaluation of Rohinitib — Cantharidin based novel HSF1 inhibitors for cancer therapy

Recent developments in the target based cancer therapies have identified HSF1 as a novel non oncogenic drug target. The present study delineates the design and molecular docking evaluation of Rohinitib (RHT) — Cantharidin (CLA) based novel HSF1 inhibitors for target-based cancer therapy. Here, we exploited the pharmacophoric features of both the parent ligands for the design of novel hybrid HSF1 inhibitors. The RHT-CLA ligands were designed and characterized for ADME/Tox features, interaction with HSF1 DNA binding domain and their pharmacophoric features essential for interaction. From the results, amino acid residues Ala17, Phe61, His63, Asn65, Ser68, Arg71 and Gln72 were found crucial for HSF1 interaction with the Heat shock elements (HSE). The hybrid ligands had better affinity towards the HSF1 DNA binding domain, in comparison to RHT or CLA and interacted with most of the active site residues. Additionally, the HSF1-ligand complex had a reduced affinity towards HSE in comparison to native HSF1. Based on the results, ligand RC15 and RC17 were non carcinogenic, non mutagenic, completely biodegradable under aerobic conditions, had better affinity for HSF1 (1.132 and 1.129 folds increase respectively) and diminished the interaction of HSF1 with HSE (1.203 and 1.239 folds decrease respectively). The simulation analysis also suggested that the ligands formed a stable complex with HSF1, restraining the movement of active site residues. In conclusion, RHT-CLA hybrid ligands can be used as a potential inhibitor of HSF1 for non-oncogene target based cancer therapy.     

A Multi-formalism Approach for the Validation of UML Models

Our approach is based on UML models. They are edited with the rational Rose^™ tool [Rat96] and complemented with annotations that state several constraints. The class diagram is the starting point of a translation process that produces formal specifications in Z [Spi92] and Lustre [CHP87]. The RoZ tool is used to translate the class diagram into Z automatically. The Z and Lustre specifications are used to validate the UML models by means of a prover and a testing environment. Received February 2000 / Accepted in revised form December 2000     

Molecular determinants of LXRalpha agonism

Liver X receptors (LXRs) are nuclear receptors that participate in the regulation of cholesterol, bile acid, and glucose metabolism. Despite the identification of the natural oxysterol and nonsteroidal ligands for LXRalpha, little is known about the structure of the LXRalpha ligand-binding domain (LBD). We constructed a three-dimensional (3D) homology model of the LBD of LXRalpha based on the crystal structure of the retinoic acid receptor gamma (RARgamma) and all-trans retinoic acid complex. We combined molecular modeling and classical structure-function techniques to define the interactions between the LBD and three structurally diverse ligands, 22(R)-hydroxycholesterol (22RHC), N-(2,2,2-trifluoro-ethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide (T0901317) and (3-[3-[(2-chloro-3-trifluoromethyl-benzyl)-(2,2-diphenyl-ethyl)-amino]-propoxy]-phenyl)-acetic acid (GW3965). Sixteen individual amino acid point mutations were made in the predicted ligand-binding cavity of the LBD, and each of these mutant receptors was assessed for their ability to be activated by these three ligands. The majority of individual mutations resulted in lack of activation by all three ligands. Two residues were identified that resulted in a significant increase in basal activity while retaining responsiveness to the ligands. Interestingly, a number of residues were identified that appear to be selective in their response to a particular ligand, indicating that these three ligands recognize distinct structural components within the ligand-binding cavity. These data, together with our docking study, enable us to identify the amino acids that coordinate the interaction of both steroidal and non-steroidal ligands in the ligand-binding pocket of LXRalpha.     

A logic for reasoning with inconsistency

Most known computational approaches to reasoning have problems when facing inconsistency, so they assume that a given logical system is consistent. Unfortunately, the latter is difficult to verify and very often is not true. It may happen that addition of data to a large system makes it inconsistent, and hence destroys the vast amount of meaningful information. We present a logic, called APC (annotated predicate calculus; cf. annotated logic programs of [4, 5]), that treats any set of clauses, either consistent or not, in a uniform way. In this logic, consequences of a contradiction are not nearly as damaging as in the standard predicate calculus, and meaningful information can still be extracted from an inconsistent set of formulae. APC has a resolution-based sound and complete proof procedure. We also introduce a novel notion of epistemic entailment and show its importance for investigating inconsistency in predicate calculus as well as its application to nonmonotonic reasoning. Most importantly, our claim that a logical theory is an adequate model of human perception of inconsistency, is actually backed by rigorous arguments.A preliminary report on this research appeared in LICS'89.Work of M. Kifer was supported in part by the NSF grants DCR-8603676, IRI-8903507.Work of E. L. Lozinskii was supported in part by Israel National Council for Research and Development under the grants 2454-3-87, 2545-2-87, 2545-3-89 and by Israel Academy of Science, grant 224-88.     

Towards a practitioners' approach to Abadi and Lamport's method

Our own basic intuitions are presented when introducing the method developed by Abadi and Lamport in [AbL88a] for proving refinement between specifications of nondeterministic programs correct to people unacquainted with it. The example we use to illustrate this method is a nontrivial communication protocol that provides a mechanism analogous to message passing between migrating processes within a fixed finite network of nodes due to Kleinman, Moscowitz, Pnueli and Shapiro [KMP91]. Especially the cruel last step of a three step refinement proof of that protocol gives rise to a deeper understanding of, and some small enhancements to, Abadi and Lamport's 1988 method.Supported by ESPRIT BRA project REACT (no. 6021)     

Ligand-receptor interaction at the neural nicotinic acetylcholine binding site: a theoretical model

Recent mutagenesis experiments have identified some of the functional amino acids that are essential in the interaction of nicotinic agents with the binding site of the neural nicotinic acetylcholine receptor (nAChR). Although this receptor is one of the best studied and characterized the lack of detailed experimental information regarding its quaternary structure has turned it into a challenge for computational chemistry. We have previously reported [J. Comput. Aided Mol. Design 13 (1999) 57-68] a computational protocol based on molecular mechanics and molecular dynamics (MD) where SER82, ASP83, TRP86, ASP89, TYR93, TYR190, TYR198 and ARG209 were placed around selected agonists and antagonists aided by stereoelectronic criteria. Explicit water molecules were used with the double goal of simulating aqueous environment and keeping the system from falling apart. The protocol was stable enough to allow the ligands to evolve to their thermodynamically most probable structure while maintaining the key interactions. In this communication we use the average model for the agonists (one average structure for each agonist) to calculate quantum mechanically the interactions of the binding site with one neurotransmitter acetylcholine (ACh, 1), as well as with two of the most potent agonists described so far [nicotine (2) and epibatidine (3)] and the modeled binding site. A wide variety of methods as well as basis sets were used in order to rationalise the best way to treat the problem. In this limited set of compounds, a good correlation between total interaction energies and biological affinity is observed.     

Automated Analysis of Fault-Tolerance in Distributed Systems

A method for automated analysis of fault-tolerance of distributed systems is presented. It is based on a stream (or data-flow) model of distributed computation. Temporal (ordering) relationships between messages received by a component on different channels are not captured by this model. This makes the analysis more efficient and forces the use of conservative approximations in analysis of systems whose behavior depends on such inter-channel orderings. To further support efficient analysis, our framework includes abstractions for the contents, number, and ordering of messages sent on each channel. Analysis of a reliable broadcast protocol illustrates the method.Supported in part by NSF under Grant CCR-9876058 and ONR under Grants N00014-99-1-0358, N00014-01-1-0109, and N00014-02-1-0363.Supported in part by ARPA/RADC grant F30602-96-1-0317, AFOSR grant F49620-00-1-0198, Defense Advanced Research Projects Agency (DARPA) and Air Force Research Laboratory Air Force Material Command USAF under agreement number F30602-99-1-0533, National Science Foundation Grant 9703470, and a grant from Intel Corporation. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of these organizations or the U.S. Government.Some of the material contained herein previously appeared in [32]     

PessimalPrint: a reverse Turing test

Abstract. We exploit the gap in ability between human and machine vision systems to craft a family of automatic challenges that tell human and machine users apart via graphical interfaces including Internet browsers. Turing proposed [Tur50] a method whereby human judges might validate “artificial intelligence” by failing to distinguish between human and machine interlocutors. Stimulated by the “chat room problem” posed by Udi Manber of Yahoo!, and influenced by the CAPTCHA project [BAL00] of Manuel Blum et al. of Carnegie-Mellon Univ., we propose a variant of the Turing test using pessimal print: that is, low-quality images of machine-printed text synthesized pseudo-randomly over certain ranges of words, typefaces, and image degradations. We show experimentally that judicious choice of these ranges can ensure that the images are legible to human readers but illegible to several of the best present-day optical character recognition (OCR) machines. Our approach is motivated by a decade of research on performance evaluation of OCR machines [RJN96,RNN99] and on quantitative stochastic models of document image quality [Bai92,Kan96]. The slow pace of evolution of OCR and other species of machine vision over many decades [NS96,Pav00] suggests that pessimal print will defy automated attack for many years. Applications include `bot' barriers and database rationing. Received: February 14, 2002 / Accepted: March 28, 2002 An expanded version of: A.L. Coates, H.S. Baird, R.J. Fateman (2001) Pessimal Print: a reverse Turing Test. In: {\it Proc. 6th Int. Conf. on Document Analysis and Recognition}, Seattle, Wash., USA, September 10–13, pp. 1154–1158 Correspondence to: H. S. Baird     

User support: revealing structure instead of surface

The development of different help systems and the application of numerous approaches to user support have shown (a) that end-users may encounter insuperably complex use situations, and (b) that it is possible to assist users significantly by implementing computerized help systems. There are many approaches to the realization of user support, varying from the use of natural language to user modelling. However, the current help systems seem to focus on relatively technical data processing issues, ignoring the organizational context in which the use takes place. It is asserted in this paper that it is relevant for users to perceive the organizational context and that it is possible to reflect the context in a support system. Representing the context in a support system is made possible by introducing a context database. A context database is parallel to the actual database and contains information about task flows, task-connected information objects and the like. Therefore the analysis of work and information systems has to be based on related areas. The areas of inquiry are (a) tasks, (b) job design, (c) organization of work, (d) computer applications and (e) information media. The following kinds of mappings can be incorporated within the context database: [organizational unit Ol]-T_person PI in job]-[job task Tl]-[task-connected information Il]-[task-connected information 12]-[job task T2]-[person in job P2]-[organizational unit O2], This type of chain (or parts of it) can then be visualized as context support.