Kinetic characterization of the critical step in HIV-1 protease maturation

HIV maturation requires multiple cleavage of long polyprotein chains into functional proteins that include the viral protease itself. Initial cleavage by the protease dimer occurs from within these precursors, and yet only a single protease monomer is embedded in each polyprotein chain. Self-activation has been proposed to start from a partially dimerized protease formed from monomers of different chains binding its own N termini by self-association to the active site, but a complete structural understanding of this critical step in HIV maturation is missing. Here, we captured the critical self-association of immature HIV-1 protease to its extended amino-terminal recognition motif using large-scale molecular dynamics simulations, thus confirming the postulated intramolecular mechanism in atomic detail. We show that self-association to a catalytically viable state requires structural cooperativity of the flexible β-hairpin “flap” regions of the enzyme and that the major transition pathway is first via self-association in the semiopen/open enzyme states, followed by enzyme conformational transition into a catalytically viable closed state. Furthermore, partial N-terminal threading can play a role in self-association, whereas wide opening of the flaps in concert with self-association is not observed. We estimate the association rate constant (k(on)) to be on the order of ∼1 × 10(4) s(−1), suggesting that N-terminal self-association is not the rate-limiting step in the process. The shown mechanism also provides an interesting example of molecular conformational transitions along the association pathway

Observations of an extreme storm in interplanetary space caused by successive coronal mass ejections

Space weather refers to dynamic conditions on the Sun and in the space environment of the Earth, which are often driven by solar eruptions and their subsequent interplanetary disturbances. It has been unclear how an extreme space weather storm forms and how severe it can be. Here we report and investigate an extreme event with multi-point remote-sensing and in-situ observations. The formation of the extreme storm showed striking novel features. We suggest that the in-transit interaction between two closely launched coronal mass ejections resulted in the extreme enhancement of the ejecta magnetic field observed near 1 AU at STEREO A. The fast transit to STEREO A (in only 18.6 hours), or the unusually weak deceleration of the event, was caused by the preconditioning of the upstream solar wind by an earlier solar eruption. These results provide a new view crucial to solar physics and space weather as to how an extreme space weather event can arise from a combination of solar eruptions.Comment: 23 pages, 7 figure

Variational Approach to Molecular Kinetics

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

Markov (state) models (MSMs) and related models of molecular kinetics have recently received a surge of interest as they can systematically reconcile simulation data from either a few long or many short simulations and allow us to analyze the essential metastable structures, thermodynamics, and kinetics of the molecular system under investigation. However, the estimation, validation, and analysis of such models is far from trivial and involves sophisticated and often numerically sensitive methods. In this work we present the opensource Python package PyEMMA (http://pyemma.org) that provides accurate and efficient algorithms for kinetic model construction. PyEMMA can read all common molecular dynamics data formats, helps in the selection of input features, provides easy access to dimension reduction algorithms such as principal component analysis (PCA) and time-lagged independent component analysis (TICA) and clustering algorithms such as k-means, and contains estimators for MSMs, hidden Markov models, and several other models. Systematic model validation and error calculation methods are provided. PyEMMA offers a wealth of analysis functions such that the user can conveniently compute molecular observables of interest. We have derived a systematic and accurate way to coarse-grain MSMs to few states and to illustrate the structures of the metastable states of the system. Plotting functions to produce a manuscript-ready presentation of the results are available. In this work, we demonstrate the features of the software and show new methodological concepts and results produced by PyEMMA

Practice of laparoscopic prolapse surgery in Europe - ESGE Survey.

peer reviewedSacrocolpopexy is considered as the "gold standard" for management of women with apical prolapse. Numerous technical variants are being practiced. The first aim of this survey was to determine the habits of practice of laparoscopic sacrocolpopexy (LSCP) in Europe. The second aim was to determine whether surgeons who perform laparoscopic pelvic organ prolapse (POP) repair are familiar with the practice of alternative techniques and with mesh-less laparoscopic treatment of prolapse. The questionnaire was designed by the Urogynaecology Special Interest Group of the European Society for Gynaecological Endoscopy (ESGE). All ESGE-members were invited by email to respond to this survey consisting of 54 questions divided in different categories. Following review of ESGE member's responses, we have highlighted the great heterogeneity concerning the practice of LSCP and important variability in performance of concomitant surgeries. Alternative techniques are rarely used in practice. Furthermore, the lack of standardisation of the many surgical steps of a laparoscopic sacrocolpopexy is mainly due to the lack of evidence. There is a need for training and teaching in both standard and newer innovative techniques as well as the reporting of medium and long-term outcomes of both standard laparoscopic sacrocolpopexy and any of its alternatives

The Free Energy Landscape of Small Molecule Unbinding

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding

Limits of Calcium Clearance by Plasma Membrane Calcium ATPase in Olfactory Cilia

BACKGROUND: In any fine sensory organelle, a small influx of Ca(2+) can quickly elevate cytoplasmic Ca(2+). Mechanisms must exist to clear the ciliary Ca(2+) before it reaches toxic levels. One such organelle has been well studied: the vertebrate olfactory cilium. Recent studies have suggested that clearance from the olfactory cilium is mediated in part by plasma membrane Ca(2+)-ATPase (PMCA). PRINCIPAL FINDINGS: In the present study, electrophysiological assays were devised to monitor cytoplasmic free Ca(2+) in single frog olfactory cilia. Ca(2+) was allowed to enter isolated cilia, either through the detached end or through membrane channels. Intraciliary Ca(2+) was monitored via the activity of ciliary Ca(2+)-gated Cl(-) channels, which are sensitive to free Ca(2+) from about 2 to 10 microM. No significant effect of MgATP on intraciliary free Ca(2+) could be found. Carboxyeosin, which has been used to inhibit PMCA, was found to substantially increase a ciliary transduction current activated by cyclic AMP. This increase was ATP-independent. CONCLUSIONS: Alternative explanations are suggested for two previous experiments taken to support a role for PMCA in ciliary Ca(2+) clearance. It is concluded that PMCA in the cilium plays a very limited role in clearing the micromolar levels of intraciliary Ca(2+) produced during the odor response

Validation of a low-cost virtual reality system for training street-crossing. A comparative study in healthy, neglected and non-neglected stroke individuals

Unilateral spatial neglect is a common consequence of stroke that directly affects the performance of activities of daily living. This impairment is traditionally assessed with paper-and-pencil tests that can lack correspondence to real life and are easily compensated. Virtual reality can immerse patients in more ecological scenarios, thus providing therapists with new tools to assess and train the effects of this impairment in simulated real tasks. This paper presents the clinical validation and convergent validity of a low-cost virtual reality system for training street-crossing in stroke patients with and without neglect. The performance of neglect patients was significantly worse than the performance of non-neglect and healthy participants. In addition, several correlations between the scores in the system and in the traditional scales were detected.This study was funded in part by Ministerio de Educacion y Ciencia Spain, Projects Consolider-C (SEJ2006-14301/PSIC), "CIBER of Physiopathology of Obesity and Nutrition, an initiative of ISCIII" and the Excellence Research Program PROMETEO (Generalitat Valenciana. Conselleria de Educacion, 2008-157).Navarro, MD.; Llorens Rodríguez, R.; Noé, E.; Ferri, J.; Alcañiz Raya, ML. (2013). Validation of a low-cost virtual reality system for training street-crossing. A comparative study in healthy, neglected and non-neglected stroke individuals. Neuropsychological Rehabilitation. 23(4):597-618. https://doi.org/10.1080/09602011.2013.806269S597618234Allegri, R. F. (2000). Atención y negligencia: bases neurológicas, evaluación y trastornos. Revista de Neurología, 30(05), 491. doi:10.33588/rn.3005.99645Appelros, P., Karlsson, G. M., Seiger, Åke, & Nydevik, I. (2002). Neglect and Anosognosia After First-Ever Stroke: Incidence and Relationship to Disability. Journal of Rehabilitation Medicine, 34(5), 215-220. doi:10.1080/165019702760279206Baheux, K., Yoshizawa, M., & Yoshida, Y. (2007). Simulating hemispatial neglect with virtual reality. Journal of NeuroEngineering and Rehabilitation, 4(1). doi:10.1186/1743-0003-4-27Boian, R. F., Burdea, G. C., Deutsch, J. E. and Winter, S. H. Street crossing using a virtual environment mobility simulator.Paper presented at 3rd Annual International Workshop on Virtual Reality. Lausanne, Switzerland.Broeren, J., Samuelsson, H., Stibrant-Sunnerhagen, K., Blomstrand, C., & Rydmark, M. (2007). Neglect assessment as an application of virtual reality. Acta Neurologica Scandinavica, 116(3), 157-163. doi:10.1111/j.1600-0404.2007.00821.xBuxbaum, L. J., Ferraro, M. K., Veramonti, T., Farne, A., Whyte, J., Ladavas, E., … Coslett, H. B. (2004). Hemispatial neglect: Subtypes, neuroanatomy, and disability. Neurology, 62(5), 749-756. doi:10.1212/01.wnl.0000113730.73031.f4Buxbaum, L. J., Palermo, M. A., Mastrogiovanni, D., Read, M. S., Rosenberg-Pitonyak, E., Rizzo, A. A., & Coslett, H. B. (2008). Assessment of spatial attention and neglect with a virtual wheelchair navigation task. Journal of Clinical and Experimental Neuropsychology, 30(6), 650-660. doi:10.1080/13803390701625821Castiello, U., Lusher, D., Burton, C., Glover, S., & Disler, P. (2004). Improving left hemispatial neglect using virtual reality. Neurology, 62(11), 1958-1962. doi:10.1212/01.wnl.0000128183.63917.02Conners, C. K., Epstein, J. N., Angold, A., & Klaric, J. (2003). Journal of Abnormal Child Psychology, 31(5), 555-562. doi:10.1023/a:1025457300409Folstein, M. F., Folstein, S. E., & McHugh, P. R. (1975). «Mini-mental state». Journal of Psychiatric Research, 12(3), 189-198. doi:10.1016/0022-3956(75)90026-6Fordell, H., Bodin, K., Bucht, G., & Malm, J. (2011). A virtual reality test battery for assessment and screening of spatial neglect. Acta Neurologica Scandinavica, 123(3), 167-174. doi:10.1111/j.1600-0404.2010.01390.xGupta, V., Knott, B. A., Kodgi, S., & Lathan, C. E. (2000). Using the «VREye» System for the Assessment of Unilateral Visual Neglect: Two Case Reports. Presence: Teleoperators and Virtual Environments, 9(3), 268-286. doi:10.1162/105474600566790Hartman-Maeir, A., & Katz, N. (1995). Validity of the Behavioral Inattention Test (BIT): Relationships With Functional Tasks. American Journal of Occupational Therapy, 49(6), 507-516. doi:10.5014/ajot.49.6.507Jannink, M. J. A., Aznar, M., de Kort, A. C., van de Vis, W., Veltink, P., & van der Kooij, H. (2009). Assessment of visuospatial neglect in stroke patients using virtual reality: a pilot study. International Journal of Rehabilitation Research, 32(4), 280-286. doi:10.1097/mrr.0b013e3283013b1cJehkonen, M., Laihosalo, M., & Kettunen, J. (2006). 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Quasi-continuous Interpolation Scheme for Pathways between Distant Configurations

A quasi-continuous interpolation (QCI) scheme is introduced for characterizing physically realistic initial pathways from which to initiate transition state searches and construct kinetic transition networks. Applications are presented for peptides, proteins, and a morphological transformation in an atomic cluster. The first step in each case involves end point alignment, and we describe the use of a shortest augmenting path algorithm for optimizing permutational isomers. The QCI procedure then employs an interpolating potential, which preserves the covalent bonding framework for the biomolecules and includes repulsive terms between unconstrained atoms. This potential is used to identify an interpolating path by minimizing contributions from a connected set of images, including terms corresponding to minima in the interatomic distances between them. This procedure detects unphysical geometries in the line segments between images. The most difficult cases, where linear interpolation would involve chain crossings, are treated by growing the structure an atom at a time using the interpolating potential. To test the QCI procedure, we carry through a series of benchmark calculations where the initial interpolation is coupled to explicit transition state searches to produce complete pathways between specified local minima.This work was supported by the Engineering and Physical Sciences Research Council [grant number EP/H042660/1]This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in the Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final edited and published work see http://dx.doi.org/10.1021/ct300483