Farnesyltransferase (FTase) is an enzyme composed by a 48 kDa α-subunit and a 46 kDa β-subunit th... more Farnesyltransferase (FTase) is an enzyme composed by a 48 kDa α-subunit and a 46 kDa β-subunit that contains a catalytically relevant zinc ion in its composition 14. This enzyme catalyzes the addition of an isoprenoid farnesyl group from farnesyl diphosphate (FPP), to a ...
Protein farnesyltransferase (FTase) is a particularly interesting zinc enzyme that promotes the t... more Protein farnesyltransferase (FTase) is a particularly interesting zinc enzyme that promotes the transfer of a 15-carbons isoprenoid farnesyl group from farnesyl diphosphate (FPP) to a number of peptide substrates with a typical-CAAX motif at the carboxyl-terminus, where C represents the cysteine residue that is farnesylated. This enzyme has been the subject of great attention in anticancer research, as several proteins known to be involved in human cancer development are thought to serve as substrates for FTase and to require farnesylation for proper biological activity. Several FTase inhibitors have advanced into clinical testing. However, despite the progress in the field several functional and mechanistic doubts on the FTase catalytic activity have persisted. This work describes the application of molecular dynamics simulations using specifically designed molecular mechanical parameters to the four key-intermediate states formed during the FTase catalytic mechanism-FTase resting state, binary complex (FTase-FPP), ternary complex (FTase-FPP-Peptide), and product complex (FTase-Product). The study involves a comparative analysis of several important molecular aspects for which are vital not only motion but also the conformational sampling of both enzyme and substrate as well as their interaction, and especially the effect of the solvent. These include the radial distribution function of the water molecules around the catalytically important zinc metal atom, the conformations of the substrate and product molecules and the corresponding RMSF values, critical hydrogen bonds and several catalytically relevant distances. These results are discussed in light of recent experimental and computational evidence, yielding new insights into the elusive catalytic mechanism of this enzyme.
Alternative vectors to deliver viable cells of probiotics, to those conferring limited resistance... more Alternative vectors to deliver viable cells of probiotics, to those conferring limited resistance to gastrointestinal conditions, still need to be sought. Therefore the main goal of the study was to develop tablets able to protect entrapped probiotic bacteria from gastric acidity, thus providing an easily manufacturing scale-up dosage form to deliver probiotics to the vicinity of the human colon. Whey protein concentrate microparticles with Lactobacillus paracasei L26 were produced by spray-drying and incorporated in tablets with cellulose acetate phthalate and sodium croscarmellose. The viability of L. paracasei L.26 throughout tableting as well as its gastric resistance and release from the tablets were evaluated. Storage stability of L. paracasei L26 tablets was also performed by evaluation of viable cells throughout 60 days at 23°C and 33% relative humidity. A decrease of approximately one logarithmic cycle was observed after the acid stage and the release of L. paracasei L26 from the tablets occurred only after 4 h in the conditions tested. Microencapsulated L. paracasei L26 in tablets revealed some susceptibility to the storage conditions tested since the number of viable cells decreased 2 log cycles after 60 days of storage. However, the viability of L. paracasei L26 after 45 days of storage did not reveal significant susceptibility upon exposure to simulated gastrointestinal conditions. The developed probiotic tablets revealed to be potential vectors for delivering viable cells of L. paracasei L26 and probably other probiotics to persons/patients who might benefit from probiotic therapy.
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.
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
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.
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
During the last decade, Virtual Screening (VS) has definitively established itself as an importan... more During the last decade, Virtual Screening (VS) has definitively established itself as an important part of the drug discovery and development process. VS involves the selection of likely drug candidates from large libraries of chemical structures by using computational methodologies, but the generic definition of VS encompasses many different methodologies. This chapter provides an introduction to the field by reviewing a variety of important aspects, including the different types of virtual screening methods, and the several steps required for a successful virtual screening campaign within a state-of-the-art approach, from target selection to postfilter application. This analysis is further complemented with a small collection important VS success stories.
... The CHARMM energy function also includes an UreyBradley term to describe 1,3-non-bonded inte... more ... The CHARMM energy function also includes an UreyBradley term to describe 1,3-non-bonded interac-tions. ... where Kb, KUB, Kθ, Kχ, and Kimp are the bond, UreyBradley, angle, dihedral angle, and improper dihedral angle force constants, respectively; b, S, θ, χ and ' are the ...
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.
The decomposition of three complexes involving the alkali metal cations Li ? , Na ? and K ? and a... more The decomposition of three complexes involving the alkali metal cations Li ? , Na ? and K ? and a potentially octadentate polyethylene-glycol-type podand(1,2-bis-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-benzene, hereafter b33) in dichloromethane was studied by steered molecular dynamics (SMD). This technique proved applicable to the problem. Analysis of the resulting trajectories allowed phenomenological descriptions of the decomposition processes. Use of the Jarzynski identity allowed the estimation of the corresponding free energies, which in turn allowed the estimation of the complex formation free energies in dichloromethane. These are very similar to the experimental values determined by liquid-liquid extraction, as long as a strong reduction of the podand denticity is considered, possibly due to the presence of competing water molecules. To the best of our knowledge, the present study is the first to use SMD to address the problem of determination of the free energies involved in the complexation of alkali cations by an extraction agent (here a podand), in a bulk solvent (here dichloromethane).
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.
Proteins: Structure, Function, and Bioinformatics, 2006
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;66:205-218. V V C 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.
Farnesyltransferase (FTase) is an enzyme composed by a 48 kDa α-subunit and a 46 kDa β-subunit th... more Farnesyltransferase (FTase) is an enzyme composed by a 48 kDa α-subunit and a 46 kDa β-subunit that contains a catalytically relevant zinc ion in its composition 14. This enzyme catalyzes the addition of an isoprenoid farnesyl group from farnesyl diphosphate (FPP), to a ...
Protein farnesyltransferase (FTase) is a particularly interesting zinc enzyme that promotes the t... more Protein farnesyltransferase (FTase) is a particularly interesting zinc enzyme that promotes the transfer of a 15-carbons isoprenoid farnesyl group from farnesyl diphosphate (FPP) to a number of peptide substrates with a typical-CAAX motif at the carboxyl-terminus, where C represents the cysteine residue that is farnesylated. This enzyme has been the subject of great attention in anticancer research, as several proteins known to be involved in human cancer development are thought to serve as substrates for FTase and to require farnesylation for proper biological activity. Several FTase inhibitors have advanced into clinical testing. However, despite the progress in the field several functional and mechanistic doubts on the FTase catalytic activity have persisted. This work describes the application of molecular dynamics simulations using specifically designed molecular mechanical parameters to the four key-intermediate states formed during the FTase catalytic mechanism-FTase resting state, binary complex (FTase-FPP), ternary complex (FTase-FPP-Peptide), and product complex (FTase-Product). The study involves a comparative analysis of several important molecular aspects for which are vital not only motion but also the conformational sampling of both enzyme and substrate as well as their interaction, and especially the effect of the solvent. These include the radial distribution function of the water molecules around the catalytically important zinc metal atom, the conformations of the substrate and product molecules and the corresponding RMSF values, critical hydrogen bonds and several catalytically relevant distances. These results are discussed in light of recent experimental and computational evidence, yielding new insights into the elusive catalytic mechanism of this enzyme.
Alternative vectors to deliver viable cells of probiotics, to those conferring limited resistance... more Alternative vectors to deliver viable cells of probiotics, to those conferring limited resistance to gastrointestinal conditions, still need to be sought. Therefore the main goal of the study was to develop tablets able to protect entrapped probiotic bacteria from gastric acidity, thus providing an easily manufacturing scale-up dosage form to deliver probiotics to the vicinity of the human colon. Whey protein concentrate microparticles with Lactobacillus paracasei L26 were produced by spray-drying and incorporated in tablets with cellulose acetate phthalate and sodium croscarmellose. The viability of L. paracasei L.26 throughout tableting as well as its gastric resistance and release from the tablets were evaluated. Storage stability of L. paracasei L26 tablets was also performed by evaluation of viable cells throughout 60 days at 23°C and 33% relative humidity. A decrease of approximately one logarithmic cycle was observed after the acid stage and the release of L. paracasei L26 from the tablets occurred only after 4 h in the conditions tested. Microencapsulated L. paracasei L26 in tablets revealed some susceptibility to the storage conditions tested since the number of viable cells decreased 2 log cycles after 60 days of storage. However, the viability of L. paracasei L26 after 45 days of storage did not reveal significant susceptibility upon exposure to simulated gastrointestinal conditions. The developed probiotic tablets revealed to be potential vectors for delivering viable cells of L. paracasei L26 and probably other probiotics to persons/patients who might benefit from probiotic therapy.
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.
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
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.
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
During the last decade, Virtual Screening (VS) has definitively established itself as an importan... more During the last decade, Virtual Screening (VS) has definitively established itself as an important part of the drug discovery and development process. VS involves the selection of likely drug candidates from large libraries of chemical structures by using computational methodologies, but the generic definition of VS encompasses many different methodologies. This chapter provides an introduction to the field by reviewing a variety of important aspects, including the different types of virtual screening methods, and the several steps required for a successful virtual screening campaign within a state-of-the-art approach, from target selection to postfilter application. This analysis is further complemented with a small collection important VS success stories.
... The CHARMM energy function also includes an UreyBradley term to describe 1,3-non-bonded inte... more ... The CHARMM energy function also includes an UreyBradley term to describe 1,3-non-bonded interac-tions. ... where Kb, KUB, Kθ, Kχ, and Kimp are the bond, UreyBradley, angle, dihedral angle, and improper dihedral angle force constants, respectively; b, S, θ, χ and ' are the ...
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.
The decomposition of three complexes involving the alkali metal cations Li ? , Na ? and K ? and a... more The decomposition of three complexes involving the alkali metal cations Li ? , Na ? and K ? and a potentially octadentate polyethylene-glycol-type podand(1,2-bis-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-benzene, hereafter b33) in dichloromethane was studied by steered molecular dynamics (SMD). This technique proved applicable to the problem. Analysis of the resulting trajectories allowed phenomenological descriptions of the decomposition processes. Use of the Jarzynski identity allowed the estimation of the corresponding free energies, which in turn allowed the estimation of the complex formation free energies in dichloromethane. These are very similar to the experimental values determined by liquid-liquid extraction, as long as a strong reduction of the podand denticity is considered, possibly due to the presence of competing water molecules. To the best of our knowledge, the present study is the first to use SMD to address the problem of determination of the free energies involved in the complexation of alkali cations by an extraction agent (here a podand), in a bulk solvent (here dichloromethane).
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.
Proteins: Structure, Function, and Bioinformatics, 2006
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;66:205-218. V V C 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.
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Papers by Sergio Sousa