Biomedical subjects

David Perahia

Publications and source records attributed to David Perahia.

9 recordsLinked to original sources

PubMed2006

Conformational heterogeneity and low-frequency vibrational modes of proteins.

Molecular dynamics simulation and normal mode analysis are used to calculate the vibrational density of states of dihydrofolate reductase complexed with nicotinamide adenine dinucleotide phosphate at 120 K and the results are compared with the experimental spectrum derived from inelastic neutron scattering. The simulation results indicate that the experimental spectrum arises from an average over proteins trapped in different conformations with structural differences mainly in the loop regions, and that these conformations have significantly different low-frequency (<20 cm(-1)) spectra. Thus, the experimentally measured spectrum is an average over the vibrational modes of different protein conformations and is thus inhomogeneously broadened. The implications of this broadening for future neutron scattering experiments and ligand binding calculations are discussed.

Computer Simulation↗

PubMed2006

Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors.

We demonstrate the utility of normal mode analysis in correctly predicting the binding modes of inhibitors in the active sites of matrix metalloproteinases (MMPs). We show the accuracy in predicting the positions of MMP-3 inhibitors is strongly dependent on which structure is used as the target, especially when it has been energy minimized. This dependency can be overcome by using intermediate structures generated along one of the normal modes previously calculated for a given target. These results may be of prime importance for further in silico drug discovery.

Drug Design↗

PubMed2006

Odorant binding and conformational dynamics in the odorant-binding protein.

In mammals, the olfactory epithelium secretes odorant-binding proteins (OBPs), which are lipocalins found freely dissolved in the mucus layer protecting the olfactory neurons. OBPs may act as passive transporters of predominantly hydrophobic odorant molecules across the aqueous mucus layer, or they may play a more active role in which the olfactory neuronal receptor recognizes the OBP-ligand complex. To better understand the molecular events accompanying the initial steps in the olfaction process, we have performed molecular dynamics studies of rat and pig OBPs with the odorant molecule thymol. These calculations provide an atomic level description of conformational changes and pathway intermediates that remain difficult to study directly. A series of eight independent molecular dynamics trajectories of rat OBP permitted the observation of a consensus pathway for ligand unbinding and the calculation of the potential of mean force (PMF) along this path. Titration microcalorimetry confirmed the specific binding of thymol to this protein with a strong hydrophobic component. In both rat and pig OBPs we observed lipocalin strand pair opening in the presence of ligand, consistent with potential roles of these proteins in olfactive receptor recognition.

Animals↗

PubMed2006

Management of depression relapse: re-initiation of duloxetine treatment or dose increase.

Continuation of antidepressant therapy after patients have responded to medication has been shown to greatly reduce but not eliminate relapse. We evaluated response to reinstating or increasing drug doses in patients who relapsed during a long-term, randomized, double-blind, continuation phase study of duloxetine treatment for major depressive disorder (MDD). Patients with HAMD17 scores of >18 and CGI-Severity scores of >4 received duloxetine 60 mg QD for 12 weeks, responders then received 26 weeks of duloxetine 60 mg QD or placebo. The relapsing patients who started 12 weeks of rescue treatment received duloxetine 60 mg QD (if relapsing on placebo) or duloxetine 60 mg BID (if relapsing on duloxetine). In the continuation phase, 87 patients received duloxetine 60 mg QD (n=58) or 60 mg BID (n=29) as treatment for relapse. The percentage of patients who responded to treatment after relapse was 62% of those whose dose was increased from 60 mg QD to 60 mg BID, and 74% for those who switched from placebo to duloxetine 60 mg daily. By the end of the study, 32 patients taking duloxetine 60 mg QD were in remission (57%), compared with 11 patients taking duloxetine 60 mg BID (38%). There was significant improvement in HAMD17 and CGI-Severity scores for both groups at endpoint vs. start of treatment for relapse. Significant improvements were seen for all visual analog scale parameters in the 60 mg QD group, but only Interference with Daily Activities and Back Pain parameters showed significant improvement for patients receiving 60 mg BID. Significant within-group improvement from baseline was seen for both groups in Symptom Questionnaire-Somatic Subscale total and pain subscales. Treatment-emergent adverse events were mild/moderate in severity; no clinically significant changes were noted in laboratory results or vital signs. Reinstatement of duloxetine 60 mg QD was effective for patients who relapsed after discontinuing drug. Patients relapsing on duloxetine 60 mg QD benefited from an increase to 60 mg BID. These duloxetine doses were well tolerated and effective, and appear appropriate for MDD patients requiring treatment of relapse.

Adult↗

PubMed2006

A DFT study on the relative affinity for oxygen of the alpha and beta subunits of hemoglobin.

DFT calculations are carried out on computational models of the active center of the alpha and beta subunits of hemoglobin in both its oxygenated (R) and deoxygenated (T) states. The computational models are defined by the full heme group, including all porphyrin substituents, and the four amino acids closer to it. The role of the protein environment is introduced by freezing the position of the alpha carbon atom of each of the four amino acids to the positions they have in the available PDB structures. Oxygen affinity is then evaluated by computing the energy difference between the optimized structures of the oxygenated and deoxygenated forms of each model. The results indicate a higher affinity of the alpha subunits over the beta ones. Analysis of the computed structures points out to the strength of the hydrogen bond between the distal histidine and the oxygen molecule as a key factor in discriminating the different systems.

Computer Simulation↗

PubMed2005

Internal cavities and ligand passageways in human hemoglobin characterized by molecular dynamics simulations.

Molecular dynamics simulations of the unliganded T state of human hemoglobin showed the existence of a spontaneous, very wide cavity on the distal side of the alpha subunit. This cavity consists of three tunnels spreading from the vicinity of the iron atom (the ligand binding site) to the surface of the subunit, constituting possible passageways for the entrance of the ligand. A fourth passageway was characterized due to the trajectory of water molecules entering or leaving the heme pocket. Analogous passages were observed in the beta subunits. They all appear and disappear dynamically, although some parts of them are more persistent along the trajectories. The most persistent regions within these tunnels correspond to all the xenon docking sites of human cytoglobin and to some of those of sperm whale and horse heart myoglobins and group I truncated hemoglobins.

Binding Sites↗

PubMed2004

Integrating three views of Arf1 activation dynamics.

The proteins Arno and Gea2 of the Sec7 family can promote GDP-GTP exchange on Arf1, a small GTP-binding protein, which coordinates coated vesicle formation for protein transport within the cell. Crystal structures of the essential Sec7 domain (Sec7d) of Gea2 in the free and Arf1-bound forms suggest that conformational dynamics of the Sec7d as well as those of the G-protein play a role in nucleotide exchange. Starting from a set of complementary crystal structures, we compared the collective movements of unbound Gea2 and Arno Sec7 domains, Arf1-GDP, and the Arf1-Gea2(Sec7d) nucleotide-free complex using normal modes analyses. In all unbound Sec7d analyses, significant low-energy movements were found to lead to closure of the hydrophobic groove towards the form seen in the Arf1-Gea2(Sec7d) complex, suggesting that groove closure is a general feature of the Sec7 family. Low-energy movements in Arf1-GDP implicate critical switch 1 and 2 residues which are coupled to modifications in the myristoylated N-terminal-helix binding site at the other end of the "interswitch" beta hairpin. It is suggested that Sec7d groove closure upon docking of the two molecules may permit extraction of switch 1 from Arf1-GDP and prepare the complex for movement of the interswitch, which is central to the membrane-linked exchange activity. Large-scale collective movements in the Arf1-Sec7d complex appear to participate in the insertion of the Sec7d Glu finger into the GDP binding site to promote actual nucleotide release.

ADP-Ribosylation Factor 1↗

PubMed2002

New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations.

It is still difficult to obtain a precise structural description of the transition between the deoxy T-state and oxy R-state conformations of human hemoglobin, despite a large number of experimental studies. We used molecular dynamics with the Path Exploration with Distance Constraints (PEDC) method to provide new insights into the allosteric mechanism at the atomic level, by simulating the T-to-R transition. The T-state molecule in the absence of ligands was seen to have a natural propensity for dimer rotation, which nevertheless would be hampered by steric hindrance in the "joint" region. The binding of a ligand to the alpha subunit would prevent such hindrance due to the coupling between this region and the alpha proximal histidine, and thus facilitate completion of the dimer rotation. Near the end of this quaternary transition, the "switch" region adopts the R conformation, resulting in a shift of the beta proximal histidine. This leads to a sliding of the beta-heme, the effect of which is to open the beta-heme's distal side, increasing the accessibility of the Fe atom and thereby the affinity of the protein. Our simulations are globally consistent with the Perutz strereochemical mechanism.

Binding Sites↗

PubMed2002

Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101.

FixJ is a two-domain response regulator involved in nitrogen fixation in Sinorhizobium meliloti. Recent X-ray characterization of both the native (unphosphorylated) and the active (phosphorylated) states of the protein identify conformational changes of the beta4-alpha4 loop and the conserved residue Phe101 as the key switches in activation. These structures also allowed investigation of the transition between conformations of this two-component regulatory receiver domain by molecular dynamics simulations. The path for the conformational change was studied with a distance constraint directing the system from one state to the other. The simulations provide evidence for a correlation between the conformation of the beta4-alpha4 loop and the orientation of the residue Phe101. A model presenting the sequence of events during the activation/deactivation process is discussed.

Bacterial Proteins↗