Sérgio Sousa - Academia.edu (original) (raw)

Papers by Sérgio Sousa

Current Medicinal Chemistry, 2008

Farnesyltransferase (FTase) is a zinc enzyme that has been the subject of particular attention in... more Farnesyltransferase (FTase) is a zinc enzyme that has been the subject of particular attention in anti-cancer research. This enzyme promotes the addition of a farnesyl group from farnesyl diphosphate (FPP) to a cysteine residue of a protein substrate containing a typical -CAAX motif at the carboxyl terminus. Initial interest in FTase inhibition was prompted by the finding that farnesylation was absolutely required for the oncogenic forms of ras proteins to transform cells, as ras proteins have been implicated in around 30% of all human cancers. This discovery led to frenetic search for FTase inhibitors (FTIs), with more than 400 patents registered in less than a decade. However, despite the very promising initial results, the outcome of Phase II and Phase III clinical trials was, is general, rather disappointing, with the most advanced FTIs failing to demonstrate anti-tumor activity in ras dependent cancers, presumably because K-ras, the most frequently mutated form of ras in human cancers, is able to bypass FTI blockade through cross-prenylation by the related enzyme geranylgeranyltransferase I (GGTase I). Surprisingly, several of these compounds were later shown to have anti-tumor activity against non-ras dependent cancers, launching the grounds for a new and exciting era in FTIs research and development, although the precise target for the FTIs activity of these compounds still remains unknown. This review reports the recent progress in the field, presenting a comprehensive summary of the most promising FTIs, in terms of their chemical structure and properties, taking into account the topology of the enzyme's active-site, and the most recent mechanistic results on the catalytic activity of FTase, both at the theoretical and mechanistic level. These features are presented in close linking with the available results on the biological activity of these inhibitors, and with the outcome of the most recent clinical trials.

Biophysical Journal, 2005

Despite the enormous interest that has been devoted to the study of farnesyltransferase, many que... more Despite the enormous interest that has been devoted to the study of farnesyltransferase, many questions concerning its catalytic mechanism remain unanswered. In particular, several doubts exist on the structure of the active-site zinc coordination sphere, more precisely on the nature of the fourth ligand, which is displaced during the catalytic reaction by a peptide thiolate. From available crystallographic structures, and mainly from x-ray absorption fine structure data, two possible alternatives emerge: a tightly zinc-bound water molecule or an almost symmetrical bidentate aspartate residue (Asp-297b). In this study, high-level theoretical calculations, with different-sized active site models, were used to elucidate this aspect. Our results demonstrate that both coordination alternatives lie in a notably close energetic proximity, even though the bidentate hypothesis has a somewhat lower energy. The Gibbs reaction and activation energies for the mono-bidentate conversion, as well as the structure for the corresponding transition state, were also determined. Globally, these results indicate that at room temperature the mono-bidentate conversion is reversible and very fast, and that probably both states exist in equilibrium, which suggests that a carboxylate-shift mechanism may have a key role in the farnesylation process by assisting the coordination/ displacement of ligands to the zinc ion, thereby controlling the enzyme activity. Based on this equilibrium hypothesis, an explanation for the existing contradictions between the crystallographic and x-ray absorption fine structure results is proposed.

Journal of Biological Inorganic Chemistry, 2005

Farnesyltransferase enzyme (FTase) is currently one of the most fascinating targets in cancer res... more Farnesyltransferase enzyme (FTase) is currently one of the most fascinating targets in cancer research. Studies in other areas, namely in the fight against parasites and viruses, have also led to very promising results. However, in spite of the thrilling achievements in the development of farnesyltransferase inhibitors (FTIs) over the past few years, the farnesylation mechanism remains, to some degree, a mystery. This review tries to shed some light on this puzzling enzyme by analyzing seven key mechanistic dilemmas, based on recent studies that have dramatically changed the way this enzyme is currently perceived.

Proteins-structure Function and Bioinformatics, 2007

In spite of the enormous interest that has been devoted to its study, the mechanism of the enzyme... more In spite of the enormous interest that has been devoted to its study, the mechanism of the enzyme farnesyltransferase (FTase) remains the subject of several crucial doubts. In this article, we shed a new light in one of the most fundamental dilemmas that characterize the mechanism of this puzzling enzyme commonly referred to as the “distances paradox”, which arises from the existence of a large 8-Å distance between the two reactive atoms in the reaction catalyzed by this enzyme: a Zn-bound cysteine sulphur atom from a peptidic substrate and the farnesyldiphosphate (FPP) carbon 1. This distance must be overcome for the reaction to occur. In this study, the two possible alternatives were evaluated by combining molecular mechanics (AMBER) and quantum chemical calculations (B3LYP). Basically, our results have shown that an activation of the Zn-bound cysteine thiolate with subsequent displacement from the zinc coordination sphere towards the FPP carbon 1 is not a realistic hypothesis of overcoming the large distance reported in the crystallographic structures of the ternary complexes between the two reactive atoms, but that a rotation involving the FPP molecule can bring the two atoms closer with moderate energetic cost, coherent with previous experimental data. This conclusion opens the door to an understanding of the chemical step in the farnesylation reaction. Proteins 2007. © 2006 Wiley-Liss, Inc.

Proteins-structure Function and Bioinformatics, 2006

Understanding the ruling principles whereby protein receptors recognize, interact, and associate ... more Understanding the ruling principles whereby protein receptors recognize, interact, and associate with molecular substrates and inhibitors is of paramount importance in drug discovery efforts. Protein–ligand docking aims to predict and rank the structure(s) arising from the association between a given ligand and a target protein of known 3D structure. Despite the breathtaking advances in the field over the last decades and the widespread application of docking methods, several downsides still exist. In particular, protein flexibility—a critical aspect for a thorough understanding of the principles that guide ligand binding in proteins—is a major hurdle in current protein–ligand docking efforts that needs to be more efficiently accounted for. In this review the key concepts of protein–ligand docking methods are outlined, with major emphasis being given to the general strengths and weaknesses that presently characterize this methodology. Despite the size of the field, the principal types of search algorithms and scoring functions are reviewed and the most popular docking tools are briefly depicted. Recent advances that aim to address some of the traditional limitations associated with molecular docking are also described. A selection of hand-picked examples is used to illustrate these features. Proteins 2006. © 2006 Wiley-Liss, Inc.

Journal of Physical Chemistry B, 2007

In the present study, we have compared the performance of the density functional theory (DFT) fun... more In the present study, we have compared the performance of the density functional theory (DFT) functionals B1B95, B3LYP, B97-2, BP86, and BPW91 with MP2 for geometry determination in biological mononuclear Zn complexes. A total of 15 different basis sets, of rather diverse complexity, were tested, several which included also three different types of common effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden. In addition, the ability to describe mononuclear Zn biological systems using relatively simple models of the metal coordination sphere, comprising only the metal atom and a simplified representation of the ligands at the first coordination sphere, starting from a set of high-resolution X-ray crystallographic structures, is evaluated for 90 combinations of method/basis set. The results show that the use of such models allows for a relatively accurate description of the Zn-ligand bond lengths, although failing to correctly represent the topology of the metal coordination sphere (namely, the angles involving the metal atom) if constraints at the Calpha atoms are not considered. Globally, B3LYP had the best average performance in the test, closely followed by MP2, whereas B1B95 was the least accurate method. The study also points out B3LYP/CEP-121G and B3LYP/SDD, which use, respectively, the Steven-Basch-Krauss and the Stuttgart-Dresden effective-core potentials, as the best compromise between accuracy and CPU time for the geometrical characterization of metal-ligand bond lengths in Zn biological systems.

Journal of The American Chemical Society, 2007

Zinc is the second most abundant transition element in biology and the only metal known to be rep... more Zinc is the second most abundant transition element in biology and the only metal known to be represented in enzymes from each one of the six classes established by the International Union of Biochemistry. The flexible coordination geometry, the fast ligand exchange, the lack of redox activity, and its role as Lewis acid are just some of the features that make zinc an invaluable element in biological catalysis. In this study, we have analyzed the importance in mononuclear Zn enzymes of an interesting mechanistic phenomenon known as carboxylate shift, which is characterized by a change in the coordination mode of a carboxylate group (mono to bidentate or vice versa) with both ligand entrance or exit from the metal coordination sphere. Using B3LYP calculations, we were able to unveil in detail patterns relating the intrinsic characteristics of a given Zn coordination sphere with the existence or not of a carboxylate-shift mechanism and the additional energy stabilization arising from it. In particular, a specific Zn coordination sphere containing a carboxylate ligand (Asp or Glu), a cysteine, and a histidine has been shown to have the most favorable combination of amino acid residues that ensures a fast ligand exchange.

Journal of Physical Chemistry A, 2007

The density functional theory (DFT) foundations date from the 1920s with the work of Thomas and F... more The density functional theory (DFT) foundations date from the 1920s with the work of Thomas and Fermi, but it was after the work of Hohenberg, Kohn, and Sham in the 1960s, and particularly with the appearance of the B3LYP functional in the early 1990s, that the widespread application of DFT has become a reality. DFT is less computationally demanding than other computational methods with a similar accuracy, being able to include electron correlation in the calculations at a fraction of time of post-Hartree-Fock methodologies. In this review we provide a brief outline of the density functional theory and of the historic development of the field, focusing later on the several types of density functionals currently available, and finishing with a detailed analysis of the performance of DFT across a wide range of chemical properties and system types, reviewed from the most recent benchmarking studies, which encompass several well-established density functionals together with the most recent efforts in the field. Globally, an overall picture of the level of performance of the plethora of currently available density functionals for each chemical property is drawn, with particular attention being dedicated to the relative performance of the popular B3LYP density functional.

Journal of Computational Chemistry, 2007

Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great atte... more Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great attention in anticancer research over the last decade. However, despite the major accomplishments in the field, some very pungent questions on the farnesylation mechanism still persist. In this study, the authors have analyzed a mechanistic paradox that arises from the existence of several contradicting and inconclusive experimental evidence regarding the existence of direct coordination between the active-site zinc cation and the thioether from the farnesylated peptide product, which include UV-vis spectroscopy data on a Co 2þ -substituted FTase, two X-ray crystallographic structures of the FTase-product complex, and extended X-ray absorption fine structure results. Using high-level theoretical calculations on two models of different sizes, and QM/MM calculations on the full enzyme, the authors have shown that the farnesylated product is Zn coordinated, and that a subsequent step where this Zn bond is broken is coherent with the available kinetic results. Furthermore, an explanation for the contradicting experimental evidence is suggested. q

Proteins-structure Function and Bioinformatics, 2007

Zinc is one of the biologically most abundant and important metal elements, present in a plethora... more Zinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X-ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme. Proteins 2007. © 2007 Wiley-Liss, Inc.

Journal of Molecular Structure-theochem, 2005

During the last decade, farnesyltransferase enzyme (FTase) has established itself as a very promi... more During the last decade, farnesyltransferase enzyme (FTase) has established itself as a very promising target in anticancer research, with more than 100 patents describing farnesyltransferase inhibitors (FTIs) published since 2000. However, several crucial doubts in its catalytic mechanism still remain. Understanding the farnesylation mechanism of the natural substrates of FTase would allow the development of more specific and active inhibitors of this enzyme. One of the fundamental dilemmas which characterize the FTase mechanism is the coordination of the peptide substrate. It is known that peptide coordination results in the formation of a zinc thiolate; however, the exact protonation state of the peptide cysteine that reacts with zinc-thiol or thiolate-remains unknown. In this study, the potential energy surfaces for thiol and thiolate peptides entrance into the active-site zinc coordination sphere were determined. The results show that the Gibbs activation barrier for thiolate entrance is of around 20 kcal/mol, whereas for thiol entrance is of only 2.5 kcal/mol. Globally, the results demonstrate that the substrate peptide coordinates zinc as a thiol, subsequently losing a proton to give the thiolate bound minimum, and that a direct thiolate attack is not a kinetically competitive alternative. q

Astronomy & Astrophysics, 2007

Two years ago a new benchmark for the planetary survey was set with the discoveries of three extr... more Two years ago a new benchmark for the planetary survey was set with the discoveries of three extrasolar planets with masses below 20$M_\oplus$. In particular, the serendipitous discovery of the 14$M_\oplus$ planet around mu\mumu Ara found with HARPS with a semi-amplitude of only 4 m s$^{-1}$ put in evidence the tremendous potential of HARPS for the search of this class of very low-mass planets. Aiming to discovering new worlds similar to mu\mumu Ara b, we carried out an intensive campaign with HARPS to observe a selected sample of northern stars covering a range of metallicity from about solar to twice solar. Two stars in our program were found to present radial velocity variations compatible with the presence of a planet-mass companion. The first of these, HD 219218, was found to be orbited by a planet with a minimum mass of 19.8 MoplusM_\oplusMoplus and an orbital period of 3.83 days. It is the 11th Neptune-mass planet found so far orbiting a solar-type star. The radial velocity data clearly show the presence of an additional body to the system, likely of planetary mass. The second planet orbits HD 102195, has a mass of 0.45$M_{Jup}$ and an orbital period of 4.11 days. This planet has been already announced by Ge et al. (2006). Our data confirm and improve the orbital solution found by these authors. We also show that the high residuals of the orbital solution are caused by stellar activity, and use the bisectors of the HARPS cross-correlation function to correct the noise introduced by stellar activity. An improved orbital solution is obtained after this correction. This kind of analysis may be used in the future to correct the radial-velocities for stellar activity induced noise.

We present a uniform study of the chemical abundances of 12 elements (Si, Ca, Sc, Ti, V, Cr, Mn, ... more We present a uniform study of the chemical abundances of 12 elements (Si, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, Na, Mg, and Al) derived from the spectra of 451 stars observed as part of one of the HARPS GTO planet search programs. Sixty eight of these are planet-bearing stars. The main goals of our work are: i) the investigation of possible differences between the abundances of stars with and without planets; ii) the study of the possible differences in the abundances of stars in the thin and the thick disc. We confirm that there is a systematically higher metallicity in planet host stars, when compared to non planet-hosts, common to all studied species. We also found that there is no difference in the galactic chemical evolution trends of the stars with and without planets. Stars that harbour planetary companions simply appear to be in the high metallicity tail of the distribution. We also confirm that Neptunian and super-Earth class planets may be easier to find at lower metallicities. A statistically significative abundance difference between stars of the thin and the thick disc was found for [Fe/H] < 0. However, the populations from the thick and the thin disc cannot be clearly separated.

Nature, 2009

The surface abundance of lithium on the Sun is 140 times less than protosolar 1 , yet the tempera... more The surface abundance of lithium on the Sun is 140 times less than protosolar 1 , yet the temperature at the base of the surface convective zone is not hot enough to burn Li 2,3 . A large range of Li abundances in solar type stars of the same age, mass and metallicity is observed 4,5 , but theoretically difficult to understand 3,6,7 . An earlier suggestion 8,9,10 that Li is more depleted in stars with planets was weakened by the lack of a proper comparison sample of stars without detected planets. Here we report Li abundances for an unbiased sample of solar-analogue stars with and without detected planets. We find that the planet-bearing stars have less than 1 per cent of the primordial Li abundance, while

Astronomy & Astrophysics, 2006

Aims. To date, metallicity is the only parameter of a star that appears to clearly correlate with... more Aims. To date, metallicity is the only parameter of a star that appears to clearly correlate with the presence of planets and their properties. To check for new correlations between stars and the existence of an orbiting planet, we determine accurate stellar parameters for several metal-rich solar-type stars. The purpose is to fill the gap of the comparison sample presented in previous works in the high metal-content regime. Methods. The stellar parameters were determined using an LTE analysis based on equivalent widths (EW) of iron lines and by imposing excitation and ionization equilibrium. We also present a first step in determining these stellar parameters in an automatic manner by using the code DAOSPEC for the EW determination. Results. Accurate stellar parameters and metallicities are obtained for our sample composed of 64 high metal-content stars not known to harbor any planet. This sample will in the future give us the possibility of better exploring the existence of differences in the chemical abundances between planet-host stars and stars without known planets in the metal-rich domain. We also report stellar parameters for some recently discovered planet-host stars. Finally, we present an empirical calibration for DAOSPEC based on the comparison between its EW measurements and the standard "hand made" measurements for the FEROS sample presented in this paper.

Astronomy & Astrophysics, 2007

Aims. We present a new automatic code (ARES) for determining equivalent widths of the absorption ... more Aims. We present a new automatic code (ARES) for determining equivalent widths of the absorption lines present in stellar spectra. We also describe its use for determining fundamental spectroscopic stellar parameters. Methods. The code is written in C++ based on the standard method of determining EWs and is available for the community. The code automates the manual procedure that the users normally carry out when using interactive routines such as the splot routine implemented in IRAF. Results. We test the code using both simulated and real spectra with different levels of resolution and noise and comparing its measurements to the manual ones obtained in the standard way. The results shows a small systematic difference, always below 1.5 mÅ. This can be explained by errors in the manual measurements caused by subjective continuum determination. The code works better and faster than others tested before.

Astronomy & Astrophysics, 2005

We present stellar parameters and metallicities for 29 planet-host stars, as well as for a large ... more We present stellar parameters and metallicities for 29 planet-host stars, as well as for a large volume-limited sample of 53 stars not known to be orbited by any planetary-mass companion. These stars add to the results presented in our previous series of papers, providing two large and uniform samples of 119 planet-hosts and 94 "single" stars with accurate stellar parameters and [Fe/H] estimates. The analysis of the results further confirms that stars with planets are metal-rich when compared with average field dwarfs. Important biases that may compromise future studies are also discussed. Finally, we compare the metallicity distributions for single planet-hosts and planet-hosts in multiple stellar systems. The results show that a small difference cannot be excluded, in the sense that the latter sample is slighly overmetallic. However, more data are needed to confirm this correlation.

Current Medicinal Chemistry, 2008

Farnesyltransferase (FTase) is a zinc enzyme that has been the subject of particular attention in... more Farnesyltransferase (FTase) is a zinc enzyme that has been the subject of particular attention in anti-cancer research. This enzyme promotes the addition of a farnesyl group from farnesyl diphosphate (FPP) to a cysteine residue of a protein substrate containing a typical -CAAX motif at the carboxyl terminus. Initial interest in FTase inhibition was prompted by the finding that farnesylation was absolutely required for the oncogenic forms of ras proteins to transform cells, as ras proteins have been implicated in around 30% of all human cancers. This discovery led to frenetic search for FTase inhibitors (FTIs), with more than 400 patents registered in less than a decade. However, despite the very promising initial results, the outcome of Phase II and Phase III clinical trials was, is general, rather disappointing, with the most advanced FTIs failing to demonstrate anti-tumor activity in ras dependent cancers, presumably because K-ras, the most frequently mutated form of ras in human cancers, is able to bypass FTI blockade through cross-prenylation by the related enzyme geranylgeranyltransferase I (GGTase I). Surprisingly, several of these compounds were later shown to have anti-tumor activity against non-ras dependent cancers, launching the grounds for a new and exciting era in FTIs research and development, although the precise target for the FTIs activity of these compounds still remains unknown. This review reports the recent progress in the field, presenting a comprehensive summary of the most promising FTIs, in terms of their chemical structure and properties, taking into account the topology of the enzyme&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s active-site, and the most recent mechanistic results on the catalytic activity of FTase, both at the theoretical and mechanistic level. These features are presented in close linking with the available results on the biological activity of these inhibitors, and with the outcome of the most recent clinical trials.

Biophysical Journal, 2005

Despite the enormous interest that has been devoted to the study of farnesyltransferase, many que... more Despite the enormous interest that has been devoted to the study of farnesyltransferase, many questions concerning its catalytic mechanism remain unanswered. In particular, several doubts exist on the structure of the active-site zinc coordination sphere, more precisely on the nature of the fourth ligand, which is displaced during the catalytic reaction by a peptide thiolate. From available crystallographic structures, and mainly from x-ray absorption fine structure data, two possible alternatives emerge: a tightly zinc-bound water molecule or an almost symmetrical bidentate aspartate residue (Asp-297b). In this study, high-level theoretical calculations, with different-sized active site models, were used to elucidate this aspect. Our results demonstrate that both coordination alternatives lie in a notably close energetic proximity, even though the bidentate hypothesis has a somewhat lower energy. The Gibbs reaction and activation energies for the mono-bidentate conversion, as well as the structure for the corresponding transition state, were also determined. Globally, these results indicate that at room temperature the mono-bidentate conversion is reversible and very fast, and that probably both states exist in equilibrium, which suggests that a carboxylate-shift mechanism may have a key role in the farnesylation process by assisting the coordination/ displacement of ligands to the zinc ion, thereby controlling the enzyme activity. Based on this equilibrium hypothesis, an explanation for the existing contradictions between the crystallographic and x-ray absorption fine structure results is proposed.

Journal of Biological Inorganic Chemistry, 2005

Farnesyltransferase enzyme (FTase) is currently one of the most fascinating targets in cancer res... more Farnesyltransferase enzyme (FTase) is currently one of the most fascinating targets in cancer research. Studies in other areas, namely in the fight against parasites and viruses, have also led to very promising results. However, in spite of the thrilling achievements in the development of farnesyltransferase inhibitors (FTIs) over the past few years, the farnesylation mechanism remains, to some degree, a mystery. This review tries to shed some light on this puzzling enzyme by analyzing seven key mechanistic dilemmas, based on recent studies that have dramatically changed the way this enzyme is currently perceived.

Proteins-structure Function and Bioinformatics, 2007

In spite of the enormous interest that has been devoted to its study, the mechanism of the enzyme... more In spite of the enormous interest that has been devoted to its study, the mechanism of the enzyme farnesyltransferase (FTase) remains the subject of several crucial doubts. In this article, we shed a new light in one of the most fundamental dilemmas that characterize the mechanism of this puzzling enzyme commonly referred to as the “distances paradox”, which arises from the existence of a large 8-Å distance between the two reactive atoms in the reaction catalyzed by this enzyme: a Zn-bound cysteine sulphur atom from a peptidic substrate and the farnesyldiphosphate (FPP) carbon 1. This distance must be overcome for the reaction to occur. In this study, the two possible alternatives were evaluated by combining molecular mechanics (AMBER) and quantum chemical calculations (B3LYP). Basically, our results have shown that an activation of the Zn-bound cysteine thiolate with subsequent displacement from the zinc coordination sphere towards the FPP carbon 1 is not a realistic hypothesis of overcoming the large distance reported in the crystallographic structures of the ternary complexes between the two reactive atoms, but that a rotation involving the FPP molecule can bring the two atoms closer with moderate energetic cost, coherent with previous experimental data. This conclusion opens the door to an understanding of the chemical step in the farnesylation reaction. Proteins 2007. © 2006 Wiley-Liss, Inc.

Proteins-structure Function and Bioinformatics, 2006

Understanding the ruling principles whereby protein receptors recognize, interact, and associate ... more Understanding the ruling principles whereby protein receptors recognize, interact, and associate with molecular substrates and inhibitors is of paramount importance in drug discovery efforts. Protein–ligand docking aims to predict and rank the structure(s) arising from the association between a given ligand and a target protein of known 3D structure. Despite the breathtaking advances in the field over the last decades and the widespread application of docking methods, several downsides still exist. In particular, protein flexibility—a critical aspect for a thorough understanding of the principles that guide ligand binding in proteins—is a major hurdle in current protein–ligand docking efforts that needs to be more efficiently accounted for. In this review the key concepts of protein–ligand docking methods are outlined, with major emphasis being given to the general strengths and weaknesses that presently characterize this methodology. Despite the size of the field, the principal types of search algorithms and scoring functions are reviewed and the most popular docking tools are briefly depicted. Recent advances that aim to address some of the traditional limitations associated with molecular docking are also described. A selection of hand-picked examples is used to illustrate these features. Proteins 2006. © 2006 Wiley-Liss, Inc.

Journal of Physical Chemistry B, 2007

In the present study, we have compared the performance of the density functional theory (DFT) fun... more In the present study, we have compared the performance of the density functional theory (DFT) functionals B1B95, B3LYP, B97-2, BP86, and BPW91 with MP2 for geometry determination in biological mononuclear Zn complexes. A total of 15 different basis sets, of rather diverse complexity, were tested, several which included also three different types of common effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden. In addition, the ability to describe mononuclear Zn biological systems using relatively simple models of the metal coordination sphere, comprising only the metal atom and a simplified representation of the ligands at the first coordination sphere, starting from a set of high-resolution X-ray crystallographic structures, is evaluated for 90 combinations of method/basis set. The results show that the use of such models allows for a relatively accurate description of the Zn-ligand bond lengths, although failing to correctly represent the topology of the metal coordination sphere (namely, the angles involving the metal atom) if constraints at the Calpha atoms are not considered. Globally, B3LYP had the best average performance in the test, closely followed by MP2, whereas B1B95 was the least accurate method. The study also points out B3LYP/CEP-121G and B3LYP/SDD, which use, respectively, the Steven-Basch-Krauss and the Stuttgart-Dresden effective-core potentials, as the best compromise between accuracy and CPU time for the geometrical characterization of metal-ligand bond lengths in Zn biological systems.

Journal of The American Chemical Society, 2007

Zinc is the second most abundant transition element in biology and the only metal known to be rep... more Zinc is the second most abundant transition element in biology and the only metal known to be represented in enzymes from each one of the six classes established by the International Union of Biochemistry. The flexible coordination geometry, the fast ligand exchange, the lack of redox activity, and its role as Lewis acid are just some of the features that make zinc an invaluable element in biological catalysis. In this study, we have analyzed the importance in mononuclear Zn enzymes of an interesting mechanistic phenomenon known as carboxylate shift, which is characterized by a change in the coordination mode of a carboxylate group (mono to bidentate or vice versa) with both ligand entrance or exit from the metal coordination sphere. Using B3LYP calculations, we were able to unveil in detail patterns relating the intrinsic characteristics of a given Zn coordination sphere with the existence or not of a carboxylate-shift mechanism and the additional energy stabilization arising from it. In particular, a specific Zn coordination sphere containing a carboxylate ligand (Asp or Glu), a cysteine, and a histidine has been shown to have the most favorable combination of amino acid residues that ensures a fast ligand exchange.

Journal of Physical Chemistry A, 2007

The density functional theory (DFT) foundations date from the 1920s with the work of Thomas and F... more The density functional theory (DFT) foundations date from the 1920s with the work of Thomas and Fermi, but it was after the work of Hohenberg, Kohn, and Sham in the 1960s, and particularly with the appearance of the B3LYP functional in the early 1990s, that the widespread application of DFT has become a reality. DFT is less computationally demanding than other computational methods with a similar accuracy, being able to include electron correlation in the calculations at a fraction of time of post-Hartree-Fock methodologies. In this review we provide a brief outline of the density functional theory and of the historic development of the field, focusing later on the several types of density functionals currently available, and finishing with a detailed analysis of the performance of DFT across a wide range of chemical properties and system types, reviewed from the most recent benchmarking studies, which encompass several well-established density functionals together with the most recent efforts in the field. Globally, an overall picture of the level of performance of the plethora of currently available density functionals for each chemical property is drawn, with particular attention being dedicated to the relative performance of the popular B3LYP density functional.

Journal of Computational Chemistry, 2007

Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great atte... more Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great attention in anticancer research over the last decade. However, despite the major accomplishments in the field, some very pungent questions on the farnesylation mechanism still persist. In this study, the authors have analyzed a mechanistic paradox that arises from the existence of several contradicting and inconclusive experimental evidence regarding the existence of direct coordination between the active-site zinc cation and the thioether from the farnesylated peptide product, which include UV-vis spectroscopy data on a Co 2þ -substituted FTase, two X-ray crystallographic structures of the FTase-product complex, and extended X-ray absorption fine structure results. Using high-level theoretical calculations on two models of different sizes, and QM/MM calculations on the full enzyme, the authors have shown that the farnesylated product is Zn coordinated, and that a subsequent step where this Zn bond is broken is coherent with the available kinetic results. Furthermore, an explanation for the contradicting experimental evidence is suggested. q

Proteins-structure Function and Bioinformatics, 2007

Zinc is one of the biologically most abundant and important metal elements, present in a plethora... more Zinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X-ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme. Proteins 2007. © 2007 Wiley-Liss, Inc.

Journal of Molecular Structure-theochem, 2005

During the last decade, farnesyltransferase enzyme (FTase) has established itself as a very promi... more During the last decade, farnesyltransferase enzyme (FTase) has established itself as a very promising target in anticancer research, with more than 100 patents describing farnesyltransferase inhibitors (FTIs) published since 2000. However, several crucial doubts in its catalytic mechanism still remain. Understanding the farnesylation mechanism of the natural substrates of FTase would allow the development of more specific and active inhibitors of this enzyme. One of the fundamental dilemmas which characterize the FTase mechanism is the coordination of the peptide substrate. It is known that peptide coordination results in the formation of a zinc thiolate; however, the exact protonation state of the peptide cysteine that reacts with zinc-thiol or thiolate-remains unknown. In this study, the potential energy surfaces for thiol and thiolate peptides entrance into the active-site zinc coordination sphere were determined. The results show that the Gibbs activation barrier for thiolate entrance is of around 20 kcal/mol, whereas for thiol entrance is of only 2.5 kcal/mol. Globally, the results demonstrate that the substrate peptide coordinates zinc as a thiol, subsequently losing a proton to give the thiolate bound minimum, and that a direct thiolate attack is not a kinetically competitive alternative. q

Astronomy & Astrophysics, 2007

Two years ago a new benchmark for the planetary survey was set with the discoveries of three extr... more Two years ago a new benchmark for the planetary survey was set with the discoveries of three extrasolar planets with masses below 20$M_\oplus$. In particular, the serendipitous discovery of the 14$M_\oplus$ planet around mu\mumu Ara found with HARPS with a semi-amplitude of only 4 m s$^{-1}$ put in evidence the tremendous potential of HARPS for the search of this class of very low-mass planets. Aiming to discovering new worlds similar to mu\mumu Ara b, we carried out an intensive campaign with HARPS to observe a selected sample of northern stars covering a range of metallicity from about solar to twice solar. Two stars in our program were found to present radial velocity variations compatible with the presence of a planet-mass companion. The first of these, HD 219218, was found to be orbited by a planet with a minimum mass of 19.8 MoplusM_\oplusMoplus and an orbital period of 3.83 days. It is the 11th Neptune-mass planet found so far orbiting a solar-type star. The radial velocity data clearly show the presence of an additional body to the system, likely of planetary mass. The second planet orbits HD 102195, has a mass of 0.45$M_{Jup}$ and an orbital period of 4.11 days. This planet has been already announced by Ge et al. (2006). Our data confirm and improve the orbital solution found by these authors. We also show that the high residuals of the orbital solution are caused by stellar activity, and use the bisectors of the HARPS cross-correlation function to correct the noise introduced by stellar activity. An improved orbital solution is obtained after this correction. This kind of analysis may be used in the future to correct the radial-velocities for stellar activity induced noise.

We present a uniform study of the chemical abundances of 12 elements (Si, Ca, Sc, Ti, V, Cr, Mn, ... more We present a uniform study of the chemical abundances of 12 elements (Si, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, Na, Mg, and Al) derived from the spectra of 451 stars observed as part of one of the HARPS GTO planet search programs. Sixty eight of these are planet-bearing stars. The main goals of our work are: i) the investigation of possible differences between the abundances of stars with and without planets; ii) the study of the possible differences in the abundances of stars in the thin and the thick disc. We confirm that there is a systematically higher metallicity in planet host stars, when compared to non planet-hosts, common to all studied species. We also found that there is no difference in the galactic chemical evolution trends of the stars with and without planets. Stars that harbour planetary companions simply appear to be in the high metallicity tail of the distribution. We also confirm that Neptunian and super-Earth class planets may be easier to find at lower metallicities. A statistically significative abundance difference between stars of the thin and the thick disc was found for [Fe/H] < 0. However, the populations from the thick and the thin disc cannot be clearly separated.

Nature, 2009

The surface abundance of lithium on the Sun is 140 times less than protosolar 1 , yet the tempera... more The surface abundance of lithium on the Sun is 140 times less than protosolar 1 , yet the temperature at the base of the surface convective zone is not hot enough to burn Li 2,3 . A large range of Li abundances in solar type stars of the same age, mass and metallicity is observed 4,5 , but theoretically difficult to understand 3,6,7 . An earlier suggestion 8,9,10 that Li is more depleted in stars with planets was weakened by the lack of a proper comparison sample of stars without detected planets. Here we report Li abundances for an unbiased sample of solar-analogue stars with and without detected planets. We find that the planet-bearing stars have less than 1 per cent of the primordial Li abundance, while

Astronomy & Astrophysics, 2006

Aims. To date, metallicity is the only parameter of a star that appears to clearly correlate with... more Aims. To date, metallicity is the only parameter of a star that appears to clearly correlate with the presence of planets and their properties. To check for new correlations between stars and the existence of an orbiting planet, we determine accurate stellar parameters for several metal-rich solar-type stars. The purpose is to fill the gap of the comparison sample presented in previous works in the high metal-content regime. Methods. The stellar parameters were determined using an LTE analysis based on equivalent widths (EW) of iron lines and by imposing excitation and ionization equilibrium. We also present a first step in determining these stellar parameters in an automatic manner by using the code DAOSPEC for the EW determination. Results. Accurate stellar parameters and metallicities are obtained for our sample composed of 64 high metal-content stars not known to harbor any planet. This sample will in the future give us the possibility of better exploring the existence of differences in the chemical abundances between planet-host stars and stars without known planets in the metal-rich domain. We also report stellar parameters for some recently discovered planet-host stars. Finally, we present an empirical calibration for DAOSPEC based on the comparison between its EW measurements and the standard "hand made" measurements for the FEROS sample presented in this paper.

Astronomy & Astrophysics, 2007

Aims. We present a new automatic code (ARES) for determining equivalent widths of the absorption ... more Aims. We present a new automatic code (ARES) for determining equivalent widths of the absorption lines present in stellar spectra. We also describe its use for determining fundamental spectroscopic stellar parameters. Methods. The code is written in C++ based on the standard method of determining EWs and is available for the community. The code automates the manual procedure that the users normally carry out when using interactive routines such as the splot routine implemented in IRAF. Results. We test the code using both simulated and real spectra with different levels of resolution and noise and comparing its measurements to the manual ones obtained in the standard way. The results shows a small systematic difference, always below 1.5 mÅ. This can be explained by errors in the manual measurements caused by subjective continuum determination. The code works better and faster than others tested before.

Astronomy & Astrophysics, 2005

We present stellar parameters and metallicities for 29 planet-host stars, as well as for a large ... more We present stellar parameters and metallicities for 29 planet-host stars, as well as for a large volume-limited sample of 53 stars not known to be orbited by any planetary-mass companion. These stars add to the results presented in our previous series of papers, providing two large and uniform samples of 119 planet-hosts and 94 "single" stars with accurate stellar parameters and [Fe/H] estimates. The analysis of the results further confirms that stars with planets are metal-rich when compared with average field dwarfs. Important biases that may compromise future studies are also discussed. Finally, we compare the metallicity distributions for single planet-hosts and planet-hosts in multiple stellar systems. The results show that a small difference cannot be excluded, in the sense that the latter sample is slighly overmetallic. However, more data are needed to confirm this correlation.