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BioMod
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BioMod |
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MOLECULAR MODELING OF BIOLOGICAL SYSTEMS (BioMod)
 Paolo Carloni Francois Beaurain Juraj Kona Alessandra Magistrato Paolo Ruggerone Anna TramontanoMain research lines:
Biomolecular modeling (BM) plays a cornerstone role in modern biological sciences, supporting and complementing experimental analysis. BM is based on a a hierarchy of methods, which span from sophisticated high-level quantum-chemical approaches to molecular dynamics simulations, coarse-grain, score function-based, applications[1]) and the modern structral bioinformatics techniques. BM represents today an indispensable tool to understand function/structure relationships of biological systems such as enzymes, receptors, sugars and nucleic acids. It is fundamental for rational drug-design and for biophysical investigations, the BM work on the potassium channel published in an issue of Nature of this month being a representative example. Unfortunately, this rapidly evolving field is not well represented in Italy as it is in other European countries, both in terms of training and research. The activity of the center will help fill up this gap. 1 AB INITIO APPROACH TO PHARMACOLOGICAL RESEARCH Force-field based molecular simulations have a long and successful record in the simulation of biological systems and in drug discovery [2]. Still, in spite of the very many successes, there are several areas where the use of effective potentials might not be fully appropriate. This is due to the fact that there is a large class of phenomena that depend on the electronic structure in such an intricate way that they are difficult to be modeled via effective potentials. Examples include the treatment of polarization and many-body effects and of bond-forming/bond-breaking processes. Hybrid QM/MM approaches, such as Car-Parrinello (CP, [3])/molecular dynamics approaches [4] characterize the intermolecular interactions at the receptor active site from electronic structure calculations as the simulation proceeds [3]. Steric and electrostatic effects of the protein scaffold on the quantum region are included using a classical MD approach for the rest of the system. In these schemes, dispersive interactions such as van der Waals, which are difficult to include in an ab-initio way, can be added empirically whenever they are expected to play a significant role. We would like now to exploit the power of CP/MD methods by investigating few paradigmatic examples that might present the usefulness of the first-principles approach to researchers of the field and eventually help design novel inhibitors. i) Bond breaking/Bond Forming processes . NMR measurements suggest that, in several enzymes, transitions states and their analogs may be stabilized by the formation of proton hopping phenomena (or low-barrier hydrogen bonds, LHBH's) with the protein matrix [5]. We will address this issue by performing CP/MD calculation on the adducts between a phosphinate transition state analog bound to the anti AIDS target HIV-1 protease [6] and eventually model new inhibitors structure having these interactions. ii) Metal-based targets . In metalloproteins, subtle chemical phenomena (such as the partial covalency of the metal-donor atom bond) cannot easily be modeled. Unfortunately, several targets are metal-based enzymes. We plan to investigate drug binding to an important class of bacterial enzymes (b-lactamases), which contain one or two Zn(II) ions at the active site [7]. iii) Ion Permeation in ion channels . These channels constitute a fundamental target for designing new anesthetics agents. Drug design is unfortunately limited by the little knowledge of structure/function relationships, which is a prerequisite for efficient design of new brokers. We plan to investigate aspects of ion permeation in the KcsA K+ channel, which has been so far investigated only by effective potentials [8]. State-of-the-art force fields for alkali ions are non-polarizable and they are parameterized for ion/water interactions. Thus, they may encounter difficulties in estimating the energetics associated to translocation process, which is essentially a ligand-exchange chemical reaction in the presence of a large electric field. iv) Drug Screening . First-principles calculations appear an attractive alternative to parameter-based approaches. In fact, they do not involve the painstaking procedure of developing each set of new parameters for each novel ligand. We will attempt at using as scoring function different sets of electronic properties calculated with the CP/MD approach, as, for instance, the rearrangement of the electronic density and of Wannier centers [9]. We will test this approach on the serine proteases class of enzymes, for which a large wealth of structural and energetics data is available [10]. 2 ENZYMATIC REACTIONS IN PROTEINS AND RNA Enzymatic reactions are involved in most biological processes. Thus, there is a major practical and fundamental interest in finding out what makes enzymes so efficient. Many crucial pieces of this puzzle were provided by biochemical and tructural studies. Yet, as will be shown below, the actual reason for the catalytic power of enzymes is not widely understood. We will use CP/MD approach also to investigate energetics, electronic and structural aspects of paradigmatic enzymatic reactions in rather different contexts. We will focus both in proteins (such as phosphatases and dehyrogenases) and in RNA-based systems such as the ribosome, for which the X-ray structure has been recently available [11]. 3 BIOLOGY INSPIRED MATERIAL SCIENCE The guiding principle of this activity is that biological systems can provide useful paradigms for developing artificial nanoscale devices and, in a feedback process, biology-inspired molecules that carry out many of the functions of the natural process. Indeed, in biomimetics the complicated natural processes are reduced to their basic elements. This can lead to a better understanding of the biological process. Furthermore, rational design of these molecules can lead to an improvement of the function. A remarkable example within this framework is represented by a process of paramount importance in biology, the photosynthesis, for which biomimetics have been chemically synthesized [12]. The heart of these molecules is represented by the reaction center, which use photons to initiate an electron-transfer process which culminates in a long-lived, energetic charge-separated state. A microscopically refined picture of these electron transfers from donor to the final acceptor inside the reaction center is still lacking, although improvements in experiment [12] and theory [13] have provided some insights. We plan to investigate these systems using first-principles approaches. CP/MD techniques will be extended in order to acquire an appropriate description of the energy landscape probed by electrons in the excited states. Theoretical tools appropriate for this investigation will be implemented exploiting the expertise acquired inside the Center. Methods based on the sophisticated time-dependent DFT (TDDFT) as well ab initio MD simulations according to the scheme proposed in Ref. [14] can be used to map the potential energy surfaces of the excited states. Thus, we expect to understand accurately the transfer mechanisms from the antenna molecules to the reaction centers and also their dual, i.e., the quenching process of the excitations. This is an equally important feature since it represents the basis for the photoprotective mechanism through which organisms avoid light-induced damages. Our investigation will provide a better understanding of the transfer mechanism, especially the primary electron transfer, with the related relaxation and polarization effects. It is a crucial steps for optimizing the choice of electron pumps, electron donors and linkages between them. Furthermore, a wide amount of applications can be potentially inspired by these studies, ranging from molecular photovoltaic devices to synthetic optoelectronic switches and medical purposes in handling tumor tissues. INTERACTIONS WITH OTHER RESEARCH GROUPS The activity will use methodologies and codes mostly similar to those of the other groups in the CRS (particularly, the activity on TDDFT in SurfInt for line #3). Furthermore, the activity will greatly benefit by a strong interactions with experimentalists. In particular, the ion channel work (line #1) will be performed in collaboration with the ion channel group in Glaxo-Wellcome-Stevenenge, headed by Dr. Simon Tate, whereas for HIV-1 and Beta lactamases, the synthesis and biological testing of the inhibitors developed in the present research will be performed by Prof. D. Rich (Pharmacy Department, University of Madison, Wisconsin, USA) and Prof. A. Vila (University of Rosario, Argentina) for the protease and the lactamases, respectively. REFERENCES [1] A.R. Leach, Molecular modeling. Principles and applications.(Addison Wesley, Singapore, 1996) [2] W. Wang et al., 'Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions', Ann. Rev. Biophys. Biom. Struct. 30, 211 (2001). [3] R. Car, M. Parrinello, ' Unified approach for molecular dynamics and density-functional theory' Phys. Rev. Lett. 55, 2471 (1985). [4] A. Laio, J. VandeVondele, U. Roethlisberger, 'A Hamiltoniana Electrostatic Coupling Scheme for Hybird Car-Parrinello Molecular Dynamics Simulations', submitted [5] S.S. Abdel-Meguid et al., 'Inhibition of human immunodeficiency virus-1 protease by a C2-symmetric phosphinate. Synthesis and crystallographic analysis', Biochemistry 32, 7972 (1993). [6] Molecular modeling and dynamics of bioinorganic compounds, Eds. L.Banci and P. Comba (Kluwer Academic Publishers, Dorderecht, 1997). [7] J.A. Cricco, A.J. Vila, 'Class B beta-lactamases: the importance of being metallic', Curr. Pharm. Des. 5, 915 (1999). [8] S. Berneche, B. Roux, 'Energetics of ion conduction through the K+ channel', Nature 414, 73 (2001). [9] P.L. Silvestrelli, M. Parrinello, 'Water Molecule Dipole in the Gas and in the Liquid Phase', Phys. Rev. Lett. 82, 3308 (1999). [10] A. Fersht, Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (Freeman and Co, New York, 1999). [11] N. Ban et al., 'The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution', Science 289, 905 (2000). [12] D. Gust et al., 'Mimicking photosynthetic solar energy transduction', Acc. Chem. Res. 34, 40 (2001), and references therein. [13] T. Ritz et al., 'Kinetics of excitation migration and trapping in the photosynthetic unit of purple bacteria', J. Phys. Chem. B 105, 8259 (2001). [14] I. Frank et al., 'Molecular dynamics in low-spin excited states', J. Chem. Phys. 108, 4060 (1998). |
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