Mehdi Bagheri Hamaneh

Structure and function of the intracellular region of the plexin-b1 transmembrane receptor.

Members of the plexin family are unique transmembrane receptors in that they interact directly with Rho family small GTPases; moreover, they contain a GTPase-activating protein (GAP) domain for R-Ras, which is crucial for plexin-mediated regulation of cell motility. However, the functional role and structural basis of the interactions between the different intracellular domains of plexins remained unclear. Here we present the 2.4 Å crystal structure of the complete intracellular region of human plexin-B1. The structure is monomeric and reveals that the GAP domain is folded into one structure from two segments, separated by the Rho GTPase binding domain (RBD). The RBD is not dimerized, as observed previously. Instead, binding of a conserved loop region appears to compete with dimerization and anchors the RBD to the GAP domain. Cell-based assays on mutant proteins confirm the functional importance of this coupling loop. Molecular modeling based on structural homology to p120GAP·H-Ras suggests that Ras GTPases can bind to the plexin GAP region. Experimentally, we show that the monomeric intracellular plexin-B1 binds R-Ras but not H-Ras. These findings suggest that the monomeric form of the intracellular region is primed for GAP activity and extend a model for plexin activation.

EEG source imaging in epilepsy—practicalities and pitfalls

EEG source imaging (ESI) is a model-based imaging technique that integrates temporal and spatial components of EEG to identify the generating source of electrical potentials recorded on the scalp. Recent advances in computer technologies have made the analysis of ESI data less time-consuming, and have rekindled interest in this technique as a clinical diagnostic tool. On the basis of the available body of evidence, ESI seems to be a promising tool for epilepsy evaluation; however, the precise clinical value of ESI in presurgical evaluation of epilepsy and in localization of eloquent cortex remains to be investigated. In this Review, we describe two fundamental issues in ESI; namely, the forward and inverse problems, and their solutions. The clinical application of ESI in surgical planning for patients with medically refractory focal epilepsy, and its use in source reconstruction together with invasive recordings, is also discussed. As ESI can be used to map evoked responses, we discuss the clinical utility of this technique in cortical mapping—an essential process when planning resective surgery for brain regions that are in close proximity to eloquent cortex.

Insights into oncogenic mutations of plexin-B1 based on the solution structure of the Rho GTPase binding domain.

The plexin family of transmembrane receptors are important for axon guidance, angiogenesis, but also in cancer. Recently, plexin-B1 somatic missense mutations were found in both primary tumors and metastases of breast and prostate cancers, with several mutations mapping to the Rho GTPase binding domain (RBD) in the cytoplasmic region of the receptor. Here we present the NMR solution structure of this domain, confirming that the protein has both a ubiquitin-like fold and surface features. Oncogenic mutations T1795A and T1802A are located in a loop region, perturb the average structure locally, and have no effect on Rho GTPase binding affinity. Mutations L1815F and L1815P are located at the Rho GTPase binding site and are associated with a complete loss of binding for Rac1 and Rnd1. Both are found to disturb the conformation of the beta3-beta4 sheet and the orientation of surrounding side chains. Our study suggests that the oncogenic behavior of the mutants can be rationalized with reference to the structure of the RBD of plexin-B1.

Automated Removal of EKG Artifact From EEG Data Using Independent Component Analysis and Continuous Wavelet Transformation

The electrical potential produced by the cardiac activity sometimes contaminates electroencephalogram (EEG) recordings, resulting in spiky activities that are referred to as electrocardiographic (EKG) artifact. For a variety of reasons it is often desirable to automatically detect and remove these artifacts. Especially, for accurate source localization of epileptic spikes in an EEG recording from a patient with epilepsy, it is of great importance to remove any concurrent artifact. Due to similarities in morphology between the EKG artifacts and epileptic spikes, any automated artifact removal algorithm must have an extremely low false-positive rate in addition to a high detection rate. In this paper, an automated algorithm for removal of EKG artifact is proposed that satisfies such criteria. The proposed method, which uses combines independent component analysis and continuous wavelet transformation, uses both temporal and spatial characteristics of EKG related potentials to identify and remove the artifacts. The method outperforms algorithms that use general statistical features such as entropy and kurtosis for artifact rejection.

A Direct Coupling between Global and Internal Motions in a Single Domain Protein? MD Investigation of Extreme Scenarios

Proteins are not rigid molecules, but exhibit internal motions on timescales ranging from femto- to milliseconds and beyond. In solution, proteins also experience global translational and rotational motions, sometimes on timescales comparable to those of the internal fluctuations. The possibility that internal and global motions may be directly coupled has intriguing implications, given that enzymes and cell signaling proteins typically associate with binding partners and cellular scaffolds. Such processes alter their global motion and may affect protein function. Here, we present molecular dynamics simulations of extreme case scenarios to examine whether a possible relationship exists. In our model protein, a ubiquitin-like RhoGTPase binding domain of plexin-B1, we removed either internal or global motions. Comparisons with unrestrained simulations show that internal and global motions are not appreciably coupled in this single-domain protein. This lack of coupling is consistent with the observation that the dynamics of water around the protein, which is thought to permit, if not stimulate, internal dynamics, is also largely independent of global motion. We discuss implications of these results for the structure and function of proteins.

Sphenoidal electrodes significantly change the results of source localization of interictal spikes for a large percentage of patients with temporal lobe epilepsy.

Summary Although scalp EEG is a very useful tool for presurgical evaluation in epilepsy, the 10-20 system of electrodes in many cases fails to accurately localize the source of the epileptic seizures. One suggested solution to this problem is to use additional electrodes. Sphenoidal electrodes especially have been suggested to be helpful in identifying the irritative and seizure onset zones in patients with temporal lobe epilepsy. However, the value of these electrodes has been debated, and in many epilepsy centers they are not used. In this study, we investigate the impact of sphenoidal electrodes by comparing the results of EEG source localization with and without sphenoidal recordings. We retrospectively selected patients with temporal lobe epilepsy based on their clinical semiology and electrophysiologic data. For each patient, a prototype spike was used as a template for an automatic pattern search to find similar activities. The identified spikes were then averaged and analyzed by fitting a dipole to the data. The recordings from sphenoidal electrodes were then excluded and the analysis was repeated. It was found that in more than half of the patients inclusion of sphenoidal electrodes resulted in a shift of more than 2 cm in the location of the fitted dipole, and in some cases moved the dipole from the frontal lobe or the insula to the temporal lobe. Our results suggest that sphenoidal electrodes are helpful in the analysis of the EEG recordings of patients suspected of having temporal lobe epilepsy.

Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins.

A realistic representation of water molecules is important in molecular dynamics simulation of proteins. However, the standard method of solvating biomolecules, that is, immersing them in a box of water with periodic boundary conditions, is computationally expensive. The primary hydration shell (PHS) method, developed more than a decade ago and implemented in CHARMM, uses only a thin shell of water around the system of interest, and so greatly reduces the computational cost of simulations. Applying the PHS method, especially to larger proteins, revealed that further optimization and a partial reworking was required and here we present several improvements to its performance. The model is applied to systems with different sizes, and both water and protein behaviors are compared with those observed in standard simulations with periodic boundary conditions and, in some cases, with experimental data. The advantages of the modified PHS method over its original implementation are clearly apparent when it is applied to simulating the 82 kDa protein Malate Synthase G.

A method for the inclusion of sphenoidal electrodes in realistic EEG source imaging.

Summary: Although EEG source imaging (ESI) has become more popular over the last few years, sphenoidal electrodes (SPE) have never been incorporated in ESI using realistic head models. This is in part because of the true locations of these electrodes are not exactly known. In this study, we demonstrate the feasibility of determining the true locations of SPE and incorporating this information into realistic ESI. The impact of including these electrodes in ESI in mesial temporal lobe epilepsy is also discussed. Seventeen patients were retrospectively selected for this study. To determine the positions of SPE in each case, two orthogonal x-rays (sagittal and coronal) of the SPE needle stilette were taken in the presence of previously digitized scalp electrodes. An in-house computer program was then used to find the locations of the tip of the needle stilette relative to the surface electrodes. These locations were then incorporated in a realistic head model based on the finite element method. EEG source imaging was then performed using averaged spikes for included patients suspected of having mesial temporal lobe epilepsy. Including SPE significantly shifted the ESI result even in the presence of subtemporal electrodes, resulting in an inferior and mesial displacement.