Giorgio Colombo

Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water

The formation of amyloid fibrils is associated with major human diseases. Nevertheless, the molecular mechanism that directs the nucleation of these fibrils is not fully understood. Here, we used molecular dynamics simulations to study the initial self‐assembly stages of the NH2‐NFGAIL‐COOH peptide, the core‐recognition motif of the type II diabetes associated islet amyloid polypeptide. The simulations were performed using multiple replicas of the monomers in explicit water, in a confined box starting from a random distribution of the peptides at T = 300 K and T = 340 K. At both temperatures the formation of unique clusters was observed after a few nanoseconds. Structural analysis of the clusters clearly suggested the formation of “flat” ellipsoid‐shaped clusters through a preferred locally parallel alignment of the peptides. The unique assembly is facilitated by a preference for an extended conformation of the peptides and by intermolecular aromatic interactions. Taken together, our results may provide a description of the molecular recognition determinants involved in fibril formation, in terms of the atomic detailed structure of nascent aggregates. These observations may yield information on new ways to control this process for either materials development or drug design. Proteins 2005.

Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories

Molecular dynamics simulations of the RN24 peptide, which includes a diverse set of structurally heterogeneous states, are carried out in explicit solvent. Two approaches are employed and compared directly under identical simulation conditions. Specifically, we examine sampling by two individual long trajectories (microsecond timescale) and many shorter (MS) uncoupled trajectories. Statistical analysis of the structural properties indicates a qualitative agreement between these approaches. Microsecond timescale sampling gives large uncertainties on most structural metrics, while the shorter timescale of MS simulations results in slight structural memory for beta‐structure starting states. Additionally, MS sampling detects numerous transitions on a relatively short timescale that are not observed in microsecond sampling, while long simulations allow for detection of a few transitions on significantly longer timescales. A correlation between the complex free energy landscape and the kinetics of the equilibrium is highlighted by principal component analysis on both simulation sets. This report highlights the increased precision of the MS approach when studying the kinetics of complex conformational change, while revealing the complementary insight and qualitative agreement offered by far fewer individual simulations on significantly longer timescales.

Interplay between hydrophobic cluster and loop propensity in β-hairpin formation: A mechanistic study

We investigated the structural determinants of the stability of a designed β‐hairpin containing a natural hydrophobic cluster from the protein GB1 and a D‐Pro‐Gly turn forming sequence. The results of our simulations shed light on the factors leading to an ordered secondary structure in a model peptide: in particular, the importance of the so‐called diagonal interactions in forming a stable hydrophobic nucleus in the β‐hairpin, together with the more obvious lateral interactions, is examined. With the use of long timescale MD simulations in explicit water, we show the role of diagonal interactions in driving the peptide to the correct folded structure (formation of the hydrophobic core with Trp 2, Tyr 4, and Phe 9 in the first stages of refolding) and in keeping it in the ensemble of folded conformations. The combination of the stabilizing effects of the D‐Pro‐Gly turn sequence and of the hydrophobic nucleus formation thus favors the attainment of an ordered secondary structure compatible with the one determined experimentally. Moreover, our data underline the importance of the juxtapositions of the side chains of amino acids not directly facing each other in the three‐dimensional structure. The combination of these interactions forces the peptide to sample a nonrandom portion of the conformational space, as can be seen in the rapid collapse to an ordered structure in the refolding simulation, and shows that the unfolded state can be closely correlated to the folded ensemble of structures, at least in the case of small model peptides.

Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides

Electrostatic interactions play a fundamental role in determining the structure and dynamics of biomolecules in solution. However the accurate representation of electrostatics in classical mechanics based simulation approaches such as molecular dynamics (MD) is a challenging task. Given the growing importance that MD simulation methods are taking on in the study of protein folding, protein stability and dynamics, and in structure prediction and design projects, it is important to evaluate the influence that different electrostatic schemes have on the results of MD simulations. In this paper we performed long timescale simulations (500 ns) of two peptides, beta3 and RN24 forming different secondary structures, using for each peptide four different electrostatic schemes (namely PME, reaction field correction, and cut-off schemes with and without neutralizing counterions) for a total of eight 500 ns long MD runs. The structural and conformational features of each peptide under the different conditions were evaluated in terms of the time dependence of the flexibility, secondary structure evolution, hydrogen-bonding patterns, and several other structural parameters. The degree of sampling for each simulation as a function of the electrostatic scheme was also critically evaluated. Our results suggest that, while in the case of the short peptide RN24 the performances of the four methods are comparable, PME and RF schemes perform better in maintaining the structure close to the native one for the β-sheet peptide beta3, in which long range contacts are mostly responsible for the definition of the native structure.

Deforestation and the Structure of Frog Communities in the Humedale Terraba-Sierpe, Costa Rica

Loss of tropical forests is a major cause of biodiversity loss worldwide. Although drastic modification of the habitat has been shown to negatively affect amphibians, we are far from a complete understanding of the response of amphibian communities to deforestation. We studied frog assemblages in a gradient of forest modification in a humid area of Costa Rica, where the primary forest has been partially converted into pasture. The study area is a mosaic of primary palm forest, abandoned pasture covered by secondary forest, and pasture. Species richness was assessed by randomized walk surveys and audio strip transects. We also measured ecological features to evaluate the relationship between landscape alteration and amphibian distribution. The study area hosted a large number of amphibian species. We focused our monitoring on six anurans: Leptodactylus labialis, Eleutherodactylus fitzingeri, E. diastema, Hyla rosenbergi, H. microcephala, and Cochranella granulosa. Three species (L. labialis, H. rosenbergi, and H. microcephala) were most abundant in pasture areas with livestock presence, while E. fitzingeri, E. diastema, and C. granulosa were associated with primary forest. Most of the variation in community structure was explained by the joint effect of forest alteration and presence of livestock. Whereas forest specialists suffer direct negative effect from deforestation, generalist species can take advantage of forest alteration and the presence of farm animals. Species that are able to take advantage of the new environmental characteristics associated with human modifications of landscapes will come to prevail in the new communities.

Assessing the value of secondary forest for amphibians: Eleutherodactylus frogs in a gradient of forest alteration

Secondary forests constitute a growing portion of forested areas worldwide. They might have a substantial role for the conservation of biodiversity in tropical areas, but there is little information on their potential to support forest species and the recovery of faunal communities. We studied two forest frogs (Eleutherodactylus diastema and E. fitzingeri) in an area of Costa Rica composed of a mosaic of primary forest, young secondary forest and pasture, and we compared the density of calling males in areas with different forest alteration. Autoregressive models were used to compensate for potentially undesired effects of spatial autocorrelation and pseudoreplication. Both species were most abundant in riparian, primary forest. However, E. fitzingeri was also abundant in riparian secondary forests, and its density far from the river was similar in primary and secondary forest, suggesting that river proximity can influence the recovery of secondary forest for amphibians. Conversely, the density of E. diastema was similar in secondary forest and pasture, stressing interspecific differences for recovery rate. These frogs have a keystone role in nutrient cycling and food webs, and their prompt recovery might represent an important step for the functional recovery of forests. Nevertheless, the strong interspecific differences stress the complexity of these processes.

Simulation of carbohydrate-protein interactions: Computer-aided design of a second generation GM1 mimic

The oligosaccharide of ganglioside GM1 [Galβ1-3GalNAcβ1-4(NeuAcα2-3)Galβ1-4Glcβ1-1Cer] is the cellular target of two bacterial enterotoxins: the cholera toxin (CT) and the heat-labile toxin of E.coli (LT). We recently reported that the pseudosaccharide 2[Galβ1-3GalNAcβ1-4(NeuAcα2-3)DCCHD] is a high-affinity ligand for CT, and thus a functional mimic of GM1 (Bernardi, A., Checchia, A., Brocca, P., Sonnino, S. and Zuccotto, F., J. Am. Chem. Soc., 121 (1999) 2032–2036). In this paper we describe the design of a second-generation mimic, formally obtained from 2 by inverting the configuration of a single stereocenter, thus transforming a N-acetyl galactosamine into a N-acetyl glucosamine. The design process involved modeling of the free ligand and its LT complex, followed by qualitative and quantitative comparison with the corresponding structures of 2. The protocol employed relied on both conformational search and molecular dynamics methodologies to account for the flexibility of both the ligand and the protein receptor. The conformational search of the LT:inhibitor complex showed that, compared to 2, the new compound can insert one more hydroxy group within the protein binding site. Molecular dynamics simulations showed that, in turn, this may trigger a series of rearrangements and reorientations of side chains and crystallographic water molecules in the toxin, leading to new H-bond contacts which may result in enhanced affinity of the new inhibitor. FEP calculations were performed by mutating the structure of 2 in solution and in the protein complex, and the prediction was made that the second-generation mimic should be a stronger binder than its parent compound.

Enzymatic and Inhibition Mechanism of Human Aromatase (CYP19A1) Enzyme. A Computational Perspective from QM/MM and Classical Molecular Dynamics Simulations.

The enzyme human aromatase (HA), a member of the cytochrome P450 family, catalyses in a highly specific and peculiar manner the conversion of estrogens to androgens. Thus, this enzyme is a relevant target for inhibitor design for the treatment of breast cancer and currently there are several HA inhibitors employed in clinical practice. The HA crystal structure was solved only in 2009 and, since then, several studies have been done to characterize a variety of its structural, dynamical and mechanistic properties. In the last decade, the predictive power and the accuracy of computer simulations techniques, either relying on force field or on ab initio description of the system, has enormously increased. This was mainly due to the development of more accurate algorithms, which allow accelerating the time-scale accessible by simulations techniques, and to the increase of computer power. Hence, computer simulations can now accurately paint an atomistic picture to the molecular mechanism of biomolecules providing also an estimate of the kinetic and thermodynamic properties of the enzyme at increasingly quantitative level. In this review, on the basis of selected examples taken from our work, we summarize current active research topics concerning HA enzyme, with a focus on computational studies. In particular, we will illustrate current results and novel hypothesis concerning the final (rate-determining) aromatization step promoted by this enzyme, on how the structural/dynamics/functional properties of HA are modulated in a membrane lipophilic environment, and finally on novel possible (allosteric) inhibition mechanisms which may modulate estrogen production in HA.

Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors

Abstractβ-Lactamases are bacterial enzymes conferring resistance to β-lactam antibiotics in clinically-relevant pathogens, and represent relevant drug targets. Recently, the identification of new boronic acids (i.e. RPX7009) paved the way to the clinical application of these molecules as potential drugs. Here, we screened in silico a library of ~1400 boronic acids as potential AmpC β-lactamase inhibitors. Six of the most promising candidates were evaluated in biochemical assays leading to the identification of potent inhibitors of clinically-relevant β-lactamases like AmpC, KPC-2 and CTX-M-15. One of the selected compounds showed nanomolar Ki value with the clinically-relevant KPC-2 carbapenemase, while another one exhibited broad spectrum inhibition, being also active on Enterobacter AmpC and the OXA-48 class D carbapenemase.

Short- vs long-course antibiotic therapy for pneumonia: a comparison of systematic reviews and guidelines for the SIMI Choosing Wisely Campaign

Reduction of the inappropriate use of antibiotics in clinical practice is one of the main goals of the Società Italiana di Medicina Interna (SIMI) choosing wisely campaign. We conducted a systematic review of secondary studies (systematic reviews and guidelines) to verify what evidence is available on the duration of antibiotic treatment in Pneumonia. A literature systematic search was performed to identify all systematic reviews and the three most cited and recent guidelines that address the duration of antibiotic therapy in pneumonia. Moreover, a meta-analysis of non-duplicate data from randomized controlled trials (RCTs) considered in the enrolled systematic reviews was performed together with a trial sequential analysis to identify the need for further studies. Two systematic reviews on antibiotic duration in community-acquired pneumonia (CAP) for a total of 17 RCTs (2764 patients) were enrolled in our study. Meta-analysis of non-duplicate RCTs show a non-significant difference in rate of treatment failure between short (≤u20097xa0days) and long (>u20097xa0days) antibiotic treatment course: RR 1.05 (95% CI, 0.82–1.36). The trial sequential analysis suggests that further data would not affect current evidence or become clinically relevant. Selected guidelines suggest consideration of a short course, with a low grade of evidence and without citing the already published systematic reviews. Antibiotic treatment of CAP foru2009≤u20097xa0days is not associated with a higher rate of treatment failure than longer courses and should thus be taken in consideration. Guidelines should upgrade the evidence on this topic.