Biomedical subjects

Michael Silberstein

Publications and source records attributed to Michael Silberstein.

5 recordsLinked to original sources

PubMed2005

Temporal exposure of cryptic collagen epitopes within ischemic muscle during hindlimb reperfusion.

Chronic limb-threatening ischemia is a devastating disease with limited surgical options. However, inducing controlled angiogenesis and enhancing reperfusion holds therapeutic promise. To gain a better understanding of the mechanisms that contribute to limb reperfusion, we examined the temporal biochemical and structural changes occurring within the extracellular matrix of ischemic skeletal muscle. Both the latent and active forms of MMP-2 and -9 significantly increased during the active phase of limb reperfusion. Moreover, small but significant alterations in tissue inhibitors of metalloproteinase levels also occurred during a similar time course, consistent with a net increase in extracellular matrix remodeling. This temporal increase in MMP activity coincided with enhanced exposure of the unique HU177 cryptic collagen epitope. Although the HUIV26 cryptic collagen epitope has been implicated in angiogenesis, little is known concerning such epitopes within ischemic muscle tissue. Here, we provide the first evidence that a functionally distinct cryptic collagen epitope (HU177) is temporally exposed in ischemic muscle tissue during the active phase of reperfusion. Interestingly, the exposure of the HU177 epitope was greatly diminished in MMP-9 null mice, corresponding with significantly reduced limb reperfusion. Therefore, the regulated exposure of a unique cryptic collagen epitope within ischemic muscle suggests an important role for collagen remodeling during the active phase of ischemic limb reperfusion.

Animals↗

PubMed2003

Identification of substrate binding sites in enzymes by computational solvent mapping.

Enzyme structures determined in organic solvents show that most organic molecules cluster in the active site, delineating the binding pocket. We have developed algorithms to perform solvent mapping computationally, rather than experimentally, by placing molecular probes (small molecules or functional groups) on a protein surface, and finding the regions with the most favorable binding free energy. The method then finds the consensus site that binds the highest number of different probes. The probe-protein interactions at this site are compared to the intermolecular interactions seen in the known complexes of the enzyme with various ligands (substrate analogs, products, and inhibitors). We have mapped thermolysin, for which experimental mapping results are also available, and six further enzymes that have no experimental mapping data, but whose binding sites are well characterized. With the exception of haloalkane dehalogenase, which binds very small substrates in a narrow channel, the consensus site found by the mapping is always a major subsite of the substrate-binding site. Furthermore, the probes at this location form hydrogen bonds and non-bonded interactions with the same residues that interact with the specific ligands of the enzyme. Thus, once the structure of an enzyme is known, computational solvent mapping can provide detailed and reliable information on its substrate-binding site. Calculations on ligand-bound and apo structures of enzymes show that the mapping results are not very sensitive to moderate variations in the protein coordinates.

Algorithms↗

PubMed2003

Algorithms for computational solvent mapping of proteins.

Computational mapping methods place molecular probes (small molecules or functional groups) on a protein surface to identify the most favorable binding positions by calculating an interaction potential. We have developed a novel computational mapping program called CS-Map (computational solvent mapping of proteins), which differs from earlier mapping methods in three respects: (i) it initially moves the ligands on the protein surface toward regions with favorable electrostatics and desolvation, (ii) the final scoring potential accounts for desolvation, and (iii) the docked ligand positions are clustered, and the clusters are ranked on the basis of their average free energies. To understand the relative importance of these factors, we developed alternative algorithms that use the DOCK and GRAMM programs for the initial search. Because of the availability of experimental solvent mapping data, lysozyme and thermolysin are considered as test proteins. Both DOCK and GRAMM speed up the initial search, and the combined algorithms yield acceptable mapping results. However, the DOCK-based approaches place the consensus site farther from its experimentally determined position than CS-Map, primarily because of the lack of a solvation term in the initial search. The GRAMM-based program also finds the correct consensus site for thermolysin. We conclude that good sampling is the most important requirement for successful mapping, but accounting for desolvation and clustering of ligand positions also help to reduce the number of false positives.

2-Propanol↗

PubMedDate not supplied

Improved mapping of protein binding sites.

Computational mapping methods place molecular probes--small molecules or functional groups--on a protein surface in order to identify the most favorable binding positions by calculating an interaction potential. Mapping is an important step in a number of flexible docking and drug design algorithms. We have developed improved algorithms for mapping protein surfaces using small organic molecules as molecular probes. The calculations reproduce the binding of eight organic solvents to lysozyme as observed by NMR, as well as the binding of four solvents to thermolysin, in good agreement with x-ray data. Application to protein tyrosine phosphatase 1B shows that the information provided by the mapping can be very useful for drug design. We also studied why the organic solvents bind in the active site of proteins, in spite of the availability of alternative pockets that can very tightly accommodate some of the probes. A possible explanation is that the binding in the relatively large active site retains a number of rotational states, and hence leads to smaller entropy loss than the binding elsewhere else. Indeed, the mapping reveals that the clusters of the ligand molecules in the protein's active site contain different rotational-translational conformers, which represent different local minima of the free energy surface. In order to study the transitions between different conformers, reaction path and molecular dynamics calculations were performed. Results show that most of the rotational states are separated by low free energy barriers at the experimental temperature, and hence the entropy of binding in the active site is expected to be high.

Animals↗

PubMedDate not supplied

Arterial injuries from femoral artery cannulation with port access cardiac surgery.

Although minimally invasive (MI) cardiac surgery reduces blood loss, hospital stay, and recovery time, some MI approaches require femoral arterial cannulation, which introduces a heretofore unknown risk of femoral arterial injury. This study was performed to examine the risk of femoral arterial injury after Port Access MI cardiac surgery (PA-MICS) with femoral cannulation. Data were prospectively obtained on 739 consecutive patients who had PA-MICS with femoral cannulation between June 1996 and April 2000, identifying any patient with new (<30 days postoperative) arterial insufficiency from the cannulation site. Patient characteristics (gender, age, height, weight, body surface area, smoking, peripheral vascular disease, diabetes) and operative variables (cannula size, cross-clamp time) were examined with univariate and multivariate analysis to identify risk factors for arterial injury. Injuries were defined and classified by radiologic and intraoperative assessment, and follow-up was obtained by patient examination and from the medical records. Femoral arterial occlusion (FAC) occurred in 0.68% (5/739) of patients (4 women, 1 man; age range 26-74 years). The risk of femoral injury was higher in women: 1.31% vs 0.23% (p = 0.07). One patient had intraoperative limb ischemia from iliofemoral dissection and was treated by axillopopliteal bypass. Four patients presented postoperatively with claudication. Three of these had iliofemoral arterial occlusion or localized iliofemoral dissection and were treated with iliofemoral bypass, and 1 patient had localized femoral artery stenosis treated by angioplasty. With a mean follow-up of 17.8 months (range 13-26 months) limb salvage was achieved in all patients. Secondary or tertiary interventions were required in 40% (2/5), both in patients with iliofemoral occlusion, and 1 patient (20% of femoral injuries, 0.135% of overall series) has chronic graft occlusion and long-term claudication. The risk of arterial injury after femoral arterial cannulation and perfusion for Port Access surgery was low (0.68%). This risk is increased in women and is unpredictable. Initial vascular repair has a significant failure rate, and secondary interventions are often necessary. Although the femoral cannulation and perfusion technique is safe overall, the risk must be clearly recognized.

Adult↗