Barry J. Hardy

Molecular dynamics simulations and diffraction-based analysis of the native cellulose fibre: structural modelling of the I-α and I-β phases and their interconversion

Abstract In this report we describe the building of diffraction-based models of the two phases of cellulose I, which subsequently are subjected to molecular dynamics simulation. The models showed an interesting variety of behaviour, including glycosidic and exocyclic torsional motion and isomerization, hydrogen-bond breakage and formation, individual and collective chain motion, and sheet deformation in the non-hydrogen-bonding direction. The I-α phase exhibited a greater dynamic range of behaviour than the I-β phase, including considerable movement of glycosidic torsions away from initial diffraction-based positions and considerable relative motion of the chains. Based on motions observed in the simulations, we suggest a break-slip model for the I-α→I-β phase transition, which proposes that the transition is initiated by heating-induced hydroxymethyl and hydroxyl side-group torsional rotations accompanied by hydrogen-bond breakage. Chains of the I-α phase are hence freed for rotation and sliding into the more stable I-β morphology. This model was tested with molecular mechanics refinement of likely intermediate structures. The results suggested that a facile transformation path is available via such a mechanism.

THE GLYCOSIDIC LINKAGE FLEXIBILITY AND TIME-SCALE SIMILARITY HYPOTHESES

Abstract In this paper, the framework surrounding two hypotheses is described: 1. (1) that glycosidic linkages of carbohydrates can be inherently flexible and thus undergo significant torsional motions in solution; 2. (2) that internal and overall motions of disaccharides occur on similar time-scales. A brief summary is provided of the current position of the experimental and theoretical data with respect to these hypotheses. An analysis of glycosidic linkage conformational flexibility in terms of linkage density functions is presented. Statistical indices for the evaluation and ranking of linkage flexibility are developed. Conformational sampling of glycosidic linkages using Monte Carlo sampling based on linkage distributions is described. Time-scale similarity is examined by comparing interproton correlation functions with respect to the laboratory frame and different internal coordinate frames, and the relative dependence of the time-scales on the system temperature is analysed. Finally, it is suggested that, instead of the traditional “lock-and-key” viewpoint, we should consider the paradigm that carbohydrates may be viewed as a “bunch of keys”.

First Molecular Graphics and Modelling Society Electronic Conference

Abstract In this article we describe activities at the First Molecular Modelling and Graphics Society Electronic Conference (MGMS EC-1) which was held on the Internet and World Wide Web in October 1996.1 MGMS EC-1 involved the presentation and discussion of scientific research results in a virtual conferencing environment which incorporated virtual replicas of many activities usually observed at a physical conference in addition to features unique to the electronic medium. Highlights of the scientific programme and technical developments in the design and use of these facilities are briefly described. A second electronic conference is planned for October 1997. 2

Builder, an interactive molecular construction utility—structural modelling using virtual reality on the web

Abstract In this paper we discuss and show how virtual reality (VR) working over the World Wide Web (WWW) can be used by chemists and biochemists as an extremely powerful tool in analyzing data and disseminating information and for interactive learning. Examples are presented of how VR is being used to investigate and visualize otherwise complex data. The program Builder v1.2, which is an interactive WWW program that illustrates the integration of Web and VR technologies, is described. The VRML language is used to build these virtual realities and is an acronym for the Virtual Reality Modelling Language. VRML was developed originally by Gavin Bell, Anthony Parisi and Mark Pesce and is based upon Silicon Graphics, Inc. successful Open Inventor graphics language. It is used to describe scenes that are displayed within a VRML viewer. But VRML is not an ordinary graphics language because it was designed to work within the World Wide Web by including aspects of a hypertext language. Thus objects in a scene may be hyperlinks to other virtual worlds, WWW pages or MIME types, allowing the viewer to navigate the Internet in a virtual reality and it is this aspect that is explored here in relation to chemistry. Builder v1.2 is an on-line utility to create customized, 3-D models of membranes using a WWW forms interface and was one of the very first examples of interactive scene creation with VRML. The user may choose components to go in the membrane from a range of proteins, cholesterol or a glycoprotein and then specify their location in the membrane. The 3-D scene may be supplied at several levels of detail, including a full sphere representation suitable for high-end workstations, and a simple, minimum-rendering format ideal for PCs. The coordinates of the components may be downloaded in PDB format; the VRML scene has the components all hyperlinked to Web pages describing their function. In conclusion, VRML provides a medium through which data that is too difficult to portray in 2-D may be analyzed and published. This illustrates clearly the benefits of the Internet as a future scientific publishing medium and a repository for supplementary and enhanced material to traditional printed journal information.

Virtual resource development in the glycosciences

The development of Internet-based virtual resources is a relatively new area of scientific and technical activity that is currently undergoing rapid expansion. Major factors fuelling recent growth include the emergence of multimedia capabilities through the rapid evolution of the World Wide Web, the reduction in cost of high quality personal computers and graphics workstations and the provision of mass-marketed provider services. Prior to 1995 the presence of Internet resources in the glycosciences was virtually non-existent. Existing scientific knowledge was primarily made available on the Net through the provision of databases from gopher and ftp sites. A particular example in the glycosciences is the Carbbank database of biological carbohydrate sequences. We will describe here our efforts in 1994–95 in establishing The Glycoscience Network (TGN, http://bellatrix.pcl.ox.ac.uk/TGN/). These activities included the establishment of a newsgroup, mailing lists, Web resources and the running of the First Electronic Glycoscience Conference (EGC-1, http://bellatrix.pcl.ox.ac.uk/egc/). EGC-1 included many novel initiatives in the glycosciences including electronic posters and papers, a Virtual Conference Centre, a Web-based hyperglossary, Virtual Trade and Employment Centres, refereed electronic publishing, and the creation of a Virtual Reality Gallery. We would like to look towards the near future and discuss several initiatives in virtual resource creation that we believe will have significant scientific impact on the glycosciences including the development of bioinformatics-based servers, sophisticated interactive databases, and videoconferencing. Furthermore, we cherish the belief that these resources will foster international scientific collaboration and progress of an extent never previously possible. Finally, we indulge in speculation and make some suggestions on the form and long-term impact of Glycoscience Virtual Resources. We predict that their development may completely reconstruct the scientific environment that we work in as scientists and we reflect on the probable benefits and pitfalls to be encountered.