Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimization of funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting for flexibility of the interface side chains. The method, called semi-definite programming-based underestimation (SDU), employs a general quadratic function to underestimate a set of local energy minima and uses the resulting underestimator to bias further sampling. While SDU effectively minimizes functions with funnel-shaped basins, its application to docking in the rotational and translational space SE(3) is not straightforward due to the geometry of that space. We introduce a strategy that uses separate independent variables for side-chain optimization, center-to-center distance of the two proteins, and five angular descriptors of the relative orientations of the molecules. The removal of the center-to-center distance turns out to vastly improve the efficiency of the search, because the five-dimensional space now exhibits a well-behaved energy surface suitable for underestimation. This algorithm explores the free energy surface spanned by encounter complexes that correspond to local free energy minima and shows similarity to the model of macromolecular association that proceeds through a series of collisions. Results for standard protein docking benchmarks establish that in this space the free energy landscape is a funnel in a reasonably broad neighborhood of the native state and that the SDU strategy can generate docking predictions with less than 5 � ligand interface Ca root-mean-square deviation while achieving an approximately 20-fold efficiency gain compared to Monte Carlo methods.

Nanostructured ferroelectric materials

Nanostructured materials are central to the evolution of future electronics and information technologies. Ferroelectrics have already been established as a dominant branch in the electronics sector because of their diverse application range such as ferroelectric memories, ferroelectric tunnel junctions, etc. The on-going dimensional downscaling of materials to allow packing of increased numbers of components onto integrated circuits provides the momentum for the evolution of nanostructured ferroelectric materials and devices. Nanoscaling of ferroelectric materials can result in a modification of their functionality, such as phase transition temperature or Curie temperature (TC), domain dynamics, dielectric constant, coercive field, spontaneous polarisation and piezoelectric response. Furthermore, nanoscaling can be used to form high density arrays of monodomain ferroelectric nanostructures, which is desirable for the miniaturisation of memory devices. This thesis details the use of various types of nanostructuring approaches to fabricate arrays of ferroelectric nanostructures, particularly non-oxide based systems. The introductory chapter reviews some exemplary research breakthroughs in the synthesis, characterisation and applications of nanoscale ferroelectric materials over the last decade, with priority given to novel synthetic strategies. Chapter 2 provides an overview of the experimental methods and characterisation tools used to produce and probe the properties of nanostructured antimony sulphide (Sb2S3), antimony sulpho iodide (SbSI) and lead titanate zirconate (PZT). In particular, Chapter 2 details the general principles of piezoresponse microscopy (PFM). Chapter 3 highlights the fabrication of arrays of Sb2S3 nanowires with variable diameters using newly developed solventless template-based approach. A detailed account of domain imaging and polarisation switching of these nanowire arrays is also provided. Chapter 4 details the preparation of vertically aligned arrays of SbSI nanorods and nanowires using a surface-roughness assisted vapour-phase deposition method. The qualitative and quantitative nanoscale ferroelectric properties of these nanostructures are also discussed. Chapter 5 highlights the fabrication of highly ordered arrays of PZT nanodots using block copolymer self-assembled templates and their ferroelectric characterisation using PFM. Chapter 6 summarises the conclusions drawn from the results reported in chapters 3, 4 and 5 and the future work.

The frequency of voluntary and involuntary autobiographical memories across the life span.

In the present study, ratings of the memory of an important event from the previous week on the frequency of voluntary and involuntary retrieval, belief in its accuracy, visual imagery, auditory imagery, setting, emotional intensity, valence, narrative coherence, and centrality to the life story were obtained from 988 adults whose ages ranged from 15 to over 90. Another 992 adults provided the same ratings for a memory from their confirmation day, when they were at about age 14. The frequencies of involuntary and voluntary retrieval were similar. Both frequencies were predicted by emotional intensity and centrality to the life story. The results from the present study-which is the first to measure the frequency of voluntary and involuntary retrieval for the same events-are counter to both cognitive and clinical theories, which consistently claim that involuntary memories are infrequent as compared with voluntary memories. Age and gender differences are noted.

Metazoan operons accelerate recovery from growth-arrested states.

Existing theories explain why operons are advantageous in prokaryotes, but their occurrence in metazoans is an enigma. Nematode operon genes, typically consisting of growth genes, are significantly upregulated during recovery from growth-arrested states. This expression pattern is anticorrelated to nonoperon genes, consistent with a competition for transcriptional resources. We find that transcriptional resources are initially limiting during recovery and that recovering animals are highly sensitive to any additional decrease in transcriptional resources. We provide evidence that operons become advantageous because, by clustering growth genes into operons, fewer promoters compete for the limited transcriptional machinery, effectively increasing the concentration of transcriptional resources and accelerating recovery. Mathematical modeling reveals how a moderate increase in transcriptional resources can substantially enhance transcription rate and recovery. This design principle occurs in different nematodes and the chordate C. intestinalis. As transition from arrest to rapid growth is shared by many metazoans, operons could have evolved to facilitate these processes.

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The 2001 World Trade Centre evacuation

The WTC evacuation of 11 September 2001 provides an unrepeatable opportunity to probe into and understand the very nature of evacuation dynamics and with this improved understanding, contribute to the design of safer, more evacuation efficient, yet highly functional, high rise buildings. Following 9/11 the Fire Safety Engineering Group (FSEG) of the University of Greenwich embarked on a study of survivor experiences from the WTC Twin Towers evacuation. The experiences were collected from published accounts appearing in the print and electronic mass media and are stored in a relational data base specifically developed for this purpose. Using these accounts and other available sources of information FSEG also undertook a series of numerical simulations of the WTC North Tower. This paper represents an overview of the results from both studies.

CONTRIBUTION OF A SPERM PROTEIN, PAWP, TO THE SIGNAL TRANSDUCT PATHWAY DURING VERTEBRATE FERTILIZATION

PAWP, postacrosomal sheath WW domain binding protein, is a novel sperm protein identified as a candidate sperm borne, oocyte-activating factor (SOAF). PAWP induces both early and later egg activation events including meiotic resumption, pronuclear formation and egg cleavage. Based on the fact that calcium increase is universally accepted as the sole requirement for egg activation, we hypothesized that PAWP is an upstream regulator of the calcium signaling pathway during fertilization. Intracellular calcium increase was detected by two-photon laser scanning fluorescence microscopy following microinjection of recombinant PAWP into Xenopus oocytes, bolstering our hypothesis and suggesting the involvement of a novel PAWP-mediated signaling pathway during fertilization. The N-terminal of PAWP shares a high homology to WW domain binding protein while the C-terminal half contains a functional PPXY motif, which allows it to interact with group I WW domain proteins. These structural considerations together with published data indicating that PPXY synthetic peptide derived from PAWP inhibits ICSI-induced fertilization led to the hypothesis that PAWP triggers egg activation by binding to a group I WW domain protein in the oocyte. By far-Western analysis of oocyte cytoplasmic fraction, PAWP was found to bind to a 52 kDa protein. The competitive inhibition studies with PPXY synthetic peptide, WW domain constructs, and their point mutants demonstrated that the interaction between PAWP and its binding partner is specifically via the PPXY-WW domain module. The 52 kDa protein band crossreacted with antibodies against group I WW domain protein YAP in Western blot assay, indicating that this 52 kDa PAWP binding partner is either YAP or a YAP-related protein. In addition, the far-Western competitive inhibition studies with recombinant GST fusion protein YAP and another WW domain-containing protein, TAZ, demonstrated that the binding of PAWP to its binding partner was significantly reduced by TAZ, providing evidence that TAZ could be the 52 kDa protein candidate. Mass spectrometry was employed to identify this PAWP binding partner candidate. However, due to the low abundance of the candidate protein and the complexity of the sample, several strategies are still needed to enrich this protein. This study correlates PAWP induced meiotic resumption and calcium efflux at fertilization and uncovers a 52 kDa candidate WW domain protein in the oocyte cytoplasm that most likely interacts with PAWP to trigger egg activation.

Experimentally elevated plasma testosterone levels do not influence singing behaviour of male blue tits (Parus caeruleus) during the early breeding season

Sexual selection theory suggests that females might prefer males on the basis of testosterone (T)-dependent secondary sexual traits such as song. Correlational studies have linked high plasma T-levels to high diurnal song output. This has been confirmed in experiments where T-levels were kept high at times when natural T-levels have decreased. However, surprisingly little is known about the relation between T-levels during the early breeding season and song. In many passerine birds males sing at a high rate at dawn early in the breeding season, referred to as the dawn chorus. In blue tits (Parus caeruleus), the dawn chorus coincides with the fertile period of the female, whereas diurnal song occurs throughout the breeding season. Previous studies on blue tits showed that characteristics of the dawn chorus correlate with male reproductive success. We experimentally elevated plasma T-levels in male blue tits during the pre-fertile and fertile period. Our aim was to test whether increased plasma T-levels affect dawn song characteristics and increase the amount of diurnal song. Although T-implants successfully raised circulating T-levels, we did not find any difference between T- and control males in temporal performance measures of dawn song or in diurnal song output. Our results suggest that either there is no direct causal link between song output or quality and individual T-levels, or experimental manipulations of T-levels using implants do not permit detection of such effects during the early breeding season. Although we cannot exclude that individual T-levels are causally linked to other (e.g. structural) song parameters, our results cast doubt on T-dependence as the mechanisms that enforces honesty on song as a sexually selected trait.