Biomedical subjects

Piercarlo Fantucci

Publications and source records attributed to Piercarlo Fantucci.

At least 19 recordsLinked to original sources

PubMed2007

Insights into the mechanism of electrocatalytic hydrogen evolution mediated by Fe2(S2C3H6)(CO)6: the simplest functional model of the Fe-hydrogenase active site.

The di-iron complex Fe2(S2C3H6)(CO)6 (a), one of the simplest functional models of the Fe-hydrogenases active site, is able to electrocatalyze proton reduction. In the present study, the H2 evolving path catalyzed by a has been characterized using density functional theory. It is showed that, in the early stages of the catalytic cycle, a neutral mu-H adduct is formed; monoelectron reduction and subsequent protonation can give rise to a diprotonated neutral species (a-muH-SH), which is characterized by a mu-H group, a protonated sulfur atom, and a CO group bridging the two iron centers, in agreement with experimental IR data indicating the formation of a long-lived mu7-CO species. H2 release from a-muH-SH, and its less stable isomer a-H2 is kinetically unfavorable, while the corresponding monoanionic compounds (a-muH-SH- and a-H2-) are more reactive in terms of dihydrogen evolution, in agreement with experimental data. The key species involved in electrocatalysis have structural features different from the hypothetical intermediates recently proposed to be involved in the enzymatic process, an observation that is possibly correlated with the reduced catalytic efficiency of the biomimetic di-iron assembly.

Binding Sites↗

PubMed2006

Time-dependent density functional theory study of Fe2(CO)9 low-lying electronic excited states.

The valence electronic excited states of Fe2(CO)9 have been studied using the time-dependent density functional theory (TDDFT). Both tribridged D3h and monobridged C2v structures have been considered, and the structure of selected low-lying singlet and triplet excited states have been optimized on the basis of the TDDFT analytical gradient. Optimized excited-state geometries are used to obtain an insight into certain aspects of the Fe2(CO)9 photochemistry. The Fe2(CO)9 (D3h) first triplet and second singlet excited states are unbound with respect to dibridged Fe2(CO)8 + CO, and the first two monobridged Fe2(CO)9 (C2v) singlet states are unbound with respect to the Fe(CO)5 + Fe(CO)4 dissociation. These results are discussed in light of the experimental data available.

Electrons↗

PubMed2006

Computational and experimental approaches for assessing the interactions between the model calycin beta-lactoglobulin and two antibacterial fluoroquinolones.

Norfloxacin and levofloxacin, two fluoroquinolones of different bulk, rigidity and hydrophobicity taken as model ligands, were docked to one apo and two holo crystallographic structures of bovine beta-lactoglobulin (BLG) using different computational approaches. BLG is a member of the lipocalin superfamily. Lipocalins show a typical b-barrel structure encompassing an internal cavity where small hydrophobic molecules are usually bound. Our studies allowed the identification of two putative binding sites in addition to the calyx. The rigid docking approximation resulted in strong repulsive forces when the ligands were docked into the calyx of the apo form. On the contrary, hindrance was not experienced in flexible docking protocols whether on the apo or on the holo BLG forms, due to allowance for side chain rearrangement. K(i) between 10(-7) and 10(-6) M were estimated for norfloxacin at pH 7.4, smaller than 10(-5) M for levofloxacin. Spectroscopic and electrophoretic techniques experimentally validated the occurrence of an interaction between norfloxacin and BLG. Changes in chemical shift and dynamic parameters were observed between the (19)F NMR spectra of the complex and of the ligand. A K(i) (ca 10(-7) M) comparable with the docking results was estimated through a NMR relaxation titration. Stabilization against unfolding was demonstrated by denaturant gradient gel electrophoresis on the complex versus apo BLG. NMR experimental evidence points to a very loose interaction for ofloxacin, the racemic mixture containing levofloxacin. Furthermore, we were able to calculate in silico K(i)'s comparable to the published experimental values for the complexes of palmitic and retinoic acid with BLG.

Animals↗

PubMed2006

Insight into the catalytic mechanism of vanadium haloperoxidases. DFT investigation of vanadium cofactor reactivity.

Density functional theory (DFT) has been used to investigate the catalytic properties of the isolated vanadium cofactor found in vanadium haloperoxidases, with a particular emphasis on the steps going from the resting form of the cofactor to the peroxo complex. Computation of transition states, intermediate species, and UV-vis spectra, as well as comparison of reaction energies, demonstrated the important role of protonation in cofactor activation. This illustrates that the resting form of the vanadium cofactor reacts with hydrogen peroxide according to a mechanism that implies formation of an aqua complex, release of the apical water molecule according to a dissociative pathway, and binding of hydrogen peroxide to vanadium. This process leads to a side-on peroxo species corresponding to the peroxo form observed in the enzyme. In addition, it appears that an acid-base catalysts strongly accelerates the conversion to the side-on peroxo form. The comparison of computed and experimental UV-vis spectra corroborated the proposed reaction pathway and allowed us to explain the effects of the vanadium ligands on the electronic properties of the cofactor.

Catalysis↗

PubMed2006

Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family.

Molecular dynamics simulations of representative mesophilic and psycrophilic elastases have been carried out at different temperatures to explore the molecular basis of cold adaptation inside a specific enzymatic family. The molecular dynamics trajectories have been compared and analyzed in terms of secondary structure, molecular flexibility, intramolecular and protein-solvent interactions, unravelling molecular features relevant to rationalize the efficient catalytic activity of psychrophilic elastases at low temperature. The comparative molecular dynamics investigation reveals that modulation of the number of protein-solvent interactions is not the evolutionary strategy followed by the psycrophilic elastase to enhance catalytic activity at low temperature. In addition, flexibility and solvent accessibility of the residues forming the catalytic triad and the specificity pocket are comparable in the cold- and warm-adapted enzymes. Instead, loop regions with different amino acid composition in the two enzymes, and clustered around the active site or the specificity pocket, are characterized by enhanced flexibility in the cold-adapted enzyme. Remarkably, the psycrophilic elastase is characterized by reduced flexibility, when compared to the mesophilic counterpart, in some scattered regions distant from the functional sites, in agreement with hypothesis suggesting that local rigidity in regions far from functional sites can be beneficial for the catalytic activity of psychrophilic enzymes.

Acclimatization↗

PubMed2006

Proton reduction and dihydrogen oxidation on models of the [2Fe]H cluster of [Fe] hydrogenases. A density functional theory investigation.

Density functional theory was used to compare reaction pathways for H2 formation and H+ reduction catalyzed by models of the binuclear cluster found in the active site of [Fe] hydrogenases. Terminal H+ binding to an Fe(I)-Fe(I) form, followed by monoelectron reduction and protonation of the di(thiomethyl)amine ligand, can conveniently lead to H2 formation and release, suggesting that this mechanism could be operative within the enzyme active site. However, a pathway that implies the initial formation of Fe(II)-Fe(II) mu-H species and release of H2 from an Fe(II)-Fe(I) form is characterized by only slightly less favored energy profiles. In both cases, H2 formation becomes less favored when taking into account the competition between CN and amine groups for H+ binding, an observation that can be relevant for the design of novel synthetic catalysts. H2 cleavage can take place on Fe(II)-Fe(II) redox species, in agreement with previous proposals [Fan, H.-J.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828] and, in complexes characterized by terminal CO groups, does not need the involvement of an external base. The step in H2 oxidation characterized by larger energy barriers corresponds to the second H+ extraction from the cluster, both considering Fe(II)-Fe(II) and Fe(II)-Fe(III) species. A comparison of the different reaction pathways reveals that H2 formation could involve only Fe(I)-Fe(I), Fe(II)-Fe(I), and Fe(II)-Fe(II) species, whereas Fe(III)-Fe(II) species might be relevant in H2 cleavage.

Journal Article↗

PubMed2005

In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1.

BACKGROUND: Histones are short proteins involved in chromatin packaging; in eukaryotes, two H2a-H2b and H3-H4 histone dimers form the nucleosomal core, which acts as the fundamental DNA-packaging element. The double histone fold is a rare globular protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus originating a histone pseudodimer. This fold is included in a few prokaryotic histones and in the regulatory region of guanine nucleotide exchange factors of the Sos family. For the prokaryotic histones, there is no direct structural counterpart in the nucleosomal core particle, while the pseudodimer from Sos proteins is very similar to the dimer formed by histones H2a and H2b. RESULTS: The absence of a H3-H4-like histone pseudodimer in the available structural databases prompted us to search for proteins that could assume such fold. The application of several secondary structure prediction and fold recognition methods allowed to show that the viral protein gi|22788712 is compatible with the structure of a H3-H4-like histone pseudodimer. Further in silico analyses revealed that this protein module could retain the ability of mediating protein-DNA interactions, and could consequently act as a DNA-binding domain. CONCLUSION: Our results suggest a possible functional role in viral pathogenicity for this novel double histone fold domain; thus, the computational analyses here reported will be helpful in directing future biochemical studies on gi|22788712 protein.

Algorithms↗

PubMed2005

The isolated catalytic hairpin of the Ras-specific guanine nucleotide exchange factor Cdc25Mm retains nucleotide dissociation activity but has impaired nucleotide exchange activity.

Cdc25Mm is a mammalian Ras-specific guanine nucleotide exchange factor (GEF). By homology modeling we show that it shares with Sos-GEF the structure of the putative catalytic HI hairpin where the dominant negative T1184E mutation is located. Similarly to Cdc25MmT1184E, the isolated wild-type and mutant hairpins retain the ability to displace Ras-bound nucleotide, originate a stable Ras/GEF complex and downregulate the Ras pathway in vivo. These results indicate that nucleotide re-entry and Ras/GEF dissociation--final steps in the GEF catalytic cycle--require GEF regions different from the HI hairpin. GEF down-sizing could lead to development of novel Ras inhibitors.

Amino Acid Sequence↗

PubMed2005

Tailoring transition metal complexes for nonlinear optics applications. 2. A theoretical investigation of the second-order nonlinear optical properties of M(CO)(5)L complexes (M = Cr, W; L = Py, PyCHO, Pyz, PyzBF(3), BPE, BPEBF(3)).

In this work, we report an ab initio investigation of second-order nonlinear optical (NLO) properties and absorption electronic spectra of push-pull transition metal chromophores of the formula [M(CO)(5)L] (M = Cr, W; L = pyridine (Py), 4-formyl-pyridine (PyCHO), pyrazine (Pyz), trans-1,2-bis(4-pyridyl)ethylene (BPE)). Pyz and BPE are considered either with one nitrogen atom free or interacting with the strong acceptor BF(3). All of the molecular properties have been calculated using two different and methodologically independent approaches: the time dependent and coupled perturbed density functional theories (TDDFT and CPDFT) and the sum-over-states (SOS) approach, where the excited states are obtained via the single configuration interaction (SCI) ab initio method. DFT results are in acceptable agreement with the experimental energy values of electronic transitions (with the exception of chromophores with the large pi-delocalization, like BPE); SCI calculations overestimate excitation energies and produce an inversion in the order of d(M) --> pi(L) and d(M) --> pi(CO) transitions. The SCI-SOS approach gives first-order hyperpolarizabilities, basically in agreement as trend and values with the experiments and seems to be a tool generally suitable for the evaluation of these properties also for transition metal complexes. On the other hand, the first-order hyperpolarizabilities computed using the CPDFT approach are consistently overestimated in comparison with the experimental results, especially in the case of a ligand with large pi-delocalization. We also show that the "two-level" approximation taking into account only the lowest energy charge transfer excitation (e.g., d(M) --> pi(L)) is not applicable to chromophores with the extended pi-delocalized ligand (BPE) coordinated to a transition metal, due to significant contributions originating from intraligand pi(L) --> pi(L) transitions. This study reports a detailed analysis and comparison of electronic NLO effects of transition metal complexes computed with DFT and ab initio SCI-SOS methodology.

Chromium↗

PubMed2005

Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation.

The three-dimensional (3D) structure of the catalytic domain of Gas1p, a protein belonging to the only family of beta-(1,3)-glucan transferases so far identified in yeasts and some pathogenic fungi (family GH-72), has been predicted by combining results derived from threading methods, multiple sequence alignments and secondary-structure predictions. The 3D model has allowed the identification of several residues that are predicted to play a crucial role in structural integrity, substrate recognition and catalysis. In particular, the model of the catalytic domain can be useful for designing site-directed mutagenesis experiments and for developing inhibitors of Gas1p enzymatic activity.

Binding Sites↗

PubMed2005

DFT Investigation of H2 activation by [M(NHPnPr3)('S3')] (M = Ni, Pd). Insight into key factors relevant to the design of hydrogenase functional models.

Density functional theory has been used to investigate the reaction between H(2) and [Ni(NHPnPr(3))('S3')] or [Pd(NHPnPr(3))('S3')], where 'S3' = bis(2-sulfanylphenyl)sulfide(2-), which are among the few synthetic complexes featuring a metal coordination environment similar to that observed in the [NiFe] hydrogenase active site and capable of catalyzing H(2) heterolytic cleavage. Results allowed us to unravel the reaction mechanism, which is consistent with an oxidative addition-hydrogen migration pathway for [Ni(NHPnPr(3))('S3')], whereas metathesis is also possible with [Pd(NHPnPr(3))('S3')]. Unexpectedly, H(2) binding and activation implies structural reorganization of the metal coordination environment. It turns out that the structural rearrangement in [Ni(NHPnPr(3))('S3')] and [Pd(NHPnPr(3))('S3')] can take place due to the peculiar structural features of the Ni and Pd ligands, explaining the remarkable catalytic properties. However, the structural reorganization is the most unfavorable step along the H(2) cleavage pathway (DeltaG > 100 kJ mol(-1)), an observation that is relevant for the design and synthesis of novel biomimetic catalysts.

Computer Simulation↗

PubMed2005

2-Arylpropionic CXC chemokine receptor 1 (CXCR1) ligands as novel noncompetitive CXCL8 inhibitors.

The CXC chemokine CXCL8/IL-8 plays a major role in the activation and recruitment of polymorphonuclear (PMN) cells at inflammatory sites. CXCL8 activates PMNs by binding the seven-transmembrane (7-TM) G-protein-coupled receptors CXC chemokine receptor 1 (CXCR1) and CXC chemokine receptor 2 (CXCR2). (R)-Ketoprofen (1) was previously reported to be a potent and specific noncompetitive inhibitor of CXCL8-induced human PMNs chemotaxis. We report here molecular modeling studies showing a putative interaction site of 1 in the TM region of CXCR1. The binding model was confirmed by alanine scanning mutagenesis and photoaffinity labeling experiments. The molecular model driven medicinal chemistry optimization of 1 led to a new class of potent and specific inhibitors of CXCL8 biological activity. Among these, repertaxin (13) was selected as a clinical candidate drug for prevention of post-ischemia reperfusion injury.

Animals↗

PubMed2005

The yeast cyclin-dependent kinase inhibitor Sic1 and mammalian p27Kip1 are functional homologues with a structurally conserved inhibitory domain.

In Saccharomyces cerevisiae, Sic1, an inhibitor of Cdk (cyclin-dependent kinase), blocks the activity of S-Cdk1 (Cdk1/Clb5,6) kinase that is required for DNA replication. Deletion of Sic1 causes premature DNA replication from fewer origins, extension of the S phase and inefficient separation of sister chromatids during anaphase. Despite the well-documented relevance of Sic1 inhibition of S-Cdk1 for cell cycle control and genome instability, the molecular mechanism by which Sic1 inhibits S-Cdk1 activity remains obscure. In this paper, we show that Sic1 is functionally and structurally related to the mammalian Cki (Cdk inhibitor) p27Kip1 of the Kip/Cip family. A molecular model of the inhibitory domain of Sic1 bound to the Cdk2-cyclin A complex suggested that the yeast inhibitor might productively interface with the mammalian Cdk2-cyclin A complex. Consistent with this, Sic1 is able to bind to, and strongly inhibit the kinase activity of, the Cdk2-cyclin A complex. In addition, comparison of the different inhibitory patterns obtained using histone H1 or GST (glutathione S-transferase)-pRb (retinoblastoma protein) fusion protein as substrate (the latter of which recognizes both the docking site and the catalytic site of Cdk2-cyclin A) offers interesting suggestions for the inhibitory mechanism of Sic1. Finally, overexpression of the KIP1 gene in vivo in Saccharomyces cerevisiae, like overexpression of the related SIC1 gene, rescues the cell cycle-related phenotype of a sic1Delta strain. Taken together, these findings strongly indicate that budding yeast Sic1 and mammalian p27(Kip1) are functional homologues with a structurally conserved inhibitory domain.

Amino Acid Sequence↗

PubMed2005

Mutations in the "lid" region affect chain length specificity and thermostability of a Pseudomonas fragi lipase.

The cold-adapted Pseudomonas fragi lipase (PFL) displays highest activity on short-chain triglyceride substrates and is rapidly inactivated at moderate temperature. Sequence and structure comparison with homologous lipases endowed with different substrate specificity and stability, pointed to three polar residues in the lid region, that were replaced with the amino acids conserved at equivalent positions in the reference lipases. Substitutions at residues T137 and T138 modified the lipase chain-length preference profile, increasing the relative activity towards C8 substrates. Moreover, mutations conferred to PFL higher temperature stability. On the other hand, replacement of the serine at position 141 by glycine destabilized the protein.

Amino Acid Sequence↗

PubMed2005

Reactivity of peroxo forms of the vanadium haloperoxidase cofactor. A DFT investigation.

Density functional theory has been used to investigate structural, electronic and reactivity properties of complexes related to the peroxo forms of vanadium haloperoxidases (VHPO). In particular, the reactivity of the cofactor as a function of protonation state and environment, which are two factors thought to be crucial in modulating the activity of the enzyme, has been examined. In full agreement with experimental data, results highlight the role of protonation in the activation of the peroxo-vanadium complexes and show that the oxo-transfer step involves the unprotonated axial peroxo oxygen atom, which is easily accessible to substrates in the peroxo form of the enzyme. The role of Lys353, which in the X-ray structure of the peroxide-bound form of vanadium chloroperoxidase is hydrogen bonded to the equatorial oxygen atom of the peroxo group, has been also explored. It is concluded that Lys353 can play a role similar to a H+ in the activation of the peroxo form of the cofactor.

Ascomycota↗

PubMed2005

Dissecting the intimate mechanism of cyanation of {2Fe3S} complexes related to the active site of all-iron hydrogenases by DFT analysis of energetics, transition states, intermediates and products in the carbonyl substitution pathway.

A bridging carbonyl intermediate with key structural elements of the diiron sub-site of all-iron hydrogenase has been experimentally observed in the CN/CO substitution pathway of the {2Fe3S} carbonyl precursor, [Fe(2)(CO)(5){MeSCH(2)C(Me)(CH(2)S)(2)}]. Herein we have used density functional theory (DFT) to dissect the overall substitution pathway in terms of the energetics and the structures of transition states, intermediates and products. We show that the formation of bridging CO transitions states is explicitly involved in the intimate mechanism of dicyanation. The enhanced rate of monocyanation of {2Fe3S} over the {2Fe2S} species [Fe(2)(CO)(6){CH(2)(CH(2)S)(2)}] is found to rest with the ability of the thioether ligand to both stabilise a mu-CO transition state and act as a good leaving group. In contrast, the second cyanation step of the {2Fe3S} species is kinetically slower than for the {2Fe2S} monocyanide because the Fe2 atom is deactivated by coordination of the electron-donating thioether group. In addition, hindered rotation and the reaction coordinate of the approaching CN(-) group, are other factors which explain reactivity differences in {2Fe2S} and {2Fe3S} systems. The intermediate species formed in the second cyanation step of {2Fe3S} species is a mu-CO species, confirming the structural assignment made on the basis of FT-IR data (S. J. George, Z. Cui, M. Razavet, C. J. Pickett, Chem. Eur. J. 2002, 8, 4037-4046). In support of this we find that computed and experimental IR frequencies of structurally characterised {2Fe3S} species and those of the bridging carbonyl intermediate are in excellent agreement. In a wider context, the study may provide some insight into the reactivity of dinuclear systems in which neighbouring group on-off coordination plays a role in substitution pathways.

Binding Sites↗

PubMed2004

A theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site.

We have applied density functional theory, using both pure (BP86) and hybrid (B3LYP and B3LYP*) functionals, to investigate structural parameters and reaction energies for nickel(II)-sulfur coordination compounds, as well as for small cluster models of the Ni-SI and Ni-R redox state of [NiFe] hydrogenases. Results obtained investigating experimentally well-characterized complexes show that BP86 is well suited to describe the structural features of this class of compounds. However, the singlet-triplet energy splitting and even the computed ground state are strongly dependent on the applied functional. Results for the cluster models of [NiFe] hydrogenases lead to the conclusion that in the reduced protein structures characterized by X-ray diffraction a hydride bridges the two metal centres. The energy splitting of the singlet and triplet states in Ni-R and Ni-SI models is calculated to be very small and may be overcome at room temperature to allow a spin crossover. Moreover, the relative stability of the Ni-SI and Ni-R structures adopted in the present investigation is fully compatible with their involvement in the reversible heterolytic cleavage of H(2).

Binding Sites↗

PubMed2004

Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase.

Density functional theory has been used to investigate structural and electronic properties of complexes related to the resting form of the active site of vanadium haloperoxidase as a function of environment and protonation state. Results obtained by studying models of varying size and complexity highlight the influence of environment and protonation state on the structure and stability of the metal cofactor. The study shows that, in the trigonal bipyramidal active site, where one axial position is occupied by a key histidine, the trans position cannot contain a terminal oxo group. Further, a highly negatively charged vanadate unit is not stable. Protonation of at least one equatorial oxo ligand appears necessary to stabilize the metal cofactor. The study also indicates that, while at rest within the protein, the vanadate unit is most likely an anion with an axial hydroxide and an equatorial plane containing two oxos and a hydroxide. For the neutral, protonated state of the vanadate unit, there were two minima found. The first structure is characterized by an axial water with two oxo and one hydroxo group in the equatorial plane. The second structure contains an axial hydroxo group and an equatorial plane composed of one oxo and two hydroxo oxygen atoms. These two species are not significantly different in energy, indicating that either form may be important during the catalytic cycle. These data support the initial crystallographic assignment of an axially bound hydroxide, but an axial water is also a possibility. This study also shows that the protonation state of the vanadate ion is most likely greater than previously proposed.

Binding Sites↗