Wilfred W. Li

MEME Suite: tools for motif discovery and searching

The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms—MAST, FIMO and GLAM2SCAN—allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm Tomtom. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and Tomtom), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.

Avian influenza virus subtype H5N1 is a potential pandemic threat with human-adapted strains resistant to antiviral drugs. Although virtual screening (VS) against a crystal or relaxed receptor structure is an established method to identify potential inhibitors, the more dynamic changes within binding sites are neglected. To accommodate full receptor flexibility, we use AutoDock4 to screen the NCI diversity set against representative receptor ensembles extracted from explicitly solvated molecular dynamics simulations of the neuraminidase system. The top hits are redocked to the entire nonredundant receptor ensemble and rescored using the relaxed complex scheme (RCS). Of the 27 top hits reported, half ranked very poorly if only crystal structures are used. These compounds target the catalytic cavity as well as the newly identified 150- and 430-cavities, which exhibit dynamic properties in electrostatic surface and geometric shape. This ensemble-based VS and RCS approach may offer improvement over existing strategies for structure-based drug discovery.

Web servers and services for electrostatics calculations with APBS and PDB2PQR

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal‐enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.

Induction of the mammalian GRP78/BiP gene by Ca2+ depletion and formation of aberrant proteins: activation of the conserved stress-inducible grp core promoter element by the human nuclear factor YY1.

Previously, we have identified a constitutive nuclear factor, p70CORE, from HeLa cell nuclear extract which interacts specifically with the stress-inducible change region (SICR) of the grp78 promoter. Here we report that p70CORE is identical to YY1, a member of the GLI zinc finger family, by criteria of biochemical properties including apparent molecular weight, binding site homology, immunoreactivity, and affinity purification. Recombinant YY1 binds the double-stranded SICR with high specificity but has no affinity for its single-stranded form. In cotransfection studies, YY1 specifically enhanced the transcriptional activation of the grp78 promoter under a variety of stress conditions: depletion of the endoplasmic reticulum calcium stores, protein glycosylation block, and formation of aberrant proteins by azetidine treatment. In contrast, YY1 has minimal effect on the stress induction of the hsp70 promoter. YY1 enhancement of the grp78 stress response is dependent on its DNA-binding domain, with little effect on the basal expression of the promoter. The effect of YY1 transactivation may be mediated by the highly conserved grp78 core element. This is the first example of the ubiquitous factor YY1 involved in regulating inducible gene expression and its involvement in mediating stress signals generated from the endoplasmic reticulum to the nucleus.

Calcium-sensitive Transcriptional Activation of the Proximal CCAAT Regulatory Element of the grp78/BiP Promoter by the Human Nuclear Factor CBF/NF-Y

Transcription of the gene encoding GRP78/BiP, a calcium-binding molecular chaperone localized in the endoplasmic reticulum, is induced in mammalian cells through gradual depletion of the intracellular calcium stores. The multimeric CCAAT binding factor, CBF/NF-Y, binds to the most proximal CCAAT regulatory element (C1) of the grp78 promoter required for both basal level expression and stress response. Using an in vitro transcription system, we show through factor competition and immunodepletion that the grp78 C1-mediated enhancement of transcription requires primarily CBF. Correlating with the previous observation that CBF binding to the 78C1 site is enhanced by EGTA and EDTA, these divalent cation chelators specifically stimulate 78C1-directed transcription. In contrast, increasing amounts of calcium ions are inhibitory. These results provide evidence that CBF is functionally important in transactivating the grp78 C1 transcriptional activity, and suggest a possible mechanism by which grp78 transcription is stimulated by calcium depletion. We further discovered that in addition to binding CBF, both the 78C1 element and the CBF binding site of the α2(I) collagen promoter interact weakly with the multifunctional transcription factor YY1. Our studies show that the binding sites for CBF and YY1 are distinct for the two promoter sites, suggesting that YY1 and other interacting factors could exert differential effects on individual promoters bearing the same CBF site.

Emerging Methods for Ensemble-Based Virtual Screening

Ensemble based virtual screening refers to the use of conformational ensembles from crystal structures, NMR studies or molecular dynamics simulations. It has gained greater acceptance as advances in the theoretical framework, computational algorithms, and software packages enable simulations at longer time scales. Here we focus on the use of computationally generated conformational ensembles and emerging methods that use these ensembles for discovery, such as the Relaxed Complex Scheme or Dynamic Pharmacophore Model. We also discuss the more rigorous physics-based computational techniques such as accelerated molecular dynamics and thermodynamic integration and their applications in improving conformational sampling or the ranking of virtual screening hits. Finally, technological advances that will help make virtual screening tools more accessible to a wider audience in computer aided drug design are discussed.

Opal: SimpleWeb Services Wrappers for Scientific Applications

The grid-based infrastructure enables large-scale scientific applications to be run on distributed resources and coupled in innovative ways. However, in practice, grid resources are not very easy to use for the end-users who have to learn how to generate security credentials, stage inputs and outputs, access grid-based schedulers, and install complex client software. There is an imminent need to provide transparent access to these resources so that the end-users are shielded from the complicated details, and free to concentrate on their domain science. Scientific applications wrapped as Web services alleviate some of these problems by hiding the complexities of the back-end security and computational infrastructure, only exposing a simple SOAP API that can be accessed programmatically by application-specific user interfaces. However, writing the application services that access grid resources can be quite complicated, especially if it has to be replicated for every application. In this paper, we present Opal which is a toolkit for wrapping scientific applications as Web services in a matter of hours, providing features such as scheduling, standards-based grid security and data management in an easy-to-use and configurable manner

Multiscale modeling: physiome project standards, tools, and databases

The Physiome Projects markup languages and associated tools leverage the CellML and FieldML model databases published in peer-reviewed journals. As these tools mature, researchers can check models for conformance to underlying physics laws, using them to develop complex physiological models from separately validated components

Design and Evaluation of Opal2: A Toolkit for Scientific Software as a Service

Grid computing provides mechanisms for making large-scale computing environments available to the masses. In recent times, with the advent of Cloud computing, the concepts of Software as a Service (SaaS), where vendors provide key software products as services over the internet that can be accessed by users to perform complex tasks, and Service as Software (SaS), where customizable and repeatable services are packaged as software products that dynamically meet the demands of individual users, have become increasingly popular. Both SaaS and SaS models are highly applicable to scientific software and users alike. Opal2 is a toolkit for wrapping scientific applications as Web services on Grid and cloud computing resources. It provides a mechanism for scientific application developers to expose the functionality of their codes via simple Web service APIs, abstracting out the details of the back-end infrastructure. Services may be combined via customized workflows for specific research areas and distributed as virtual machine images. In this paper, we describe the overall philosophy and architecture of the Opal2 framework, including its new plug-in architecture and data handling capabilities. We analyze its performance in typical cluster and Grid settings, and in a cloud computing environment within virtual machines, using Amazons Elastic Computing Cloud (EC2).

Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective.

Hemagglutinins (HA’s) from duck, swine, and human influenza viruses have previously been shown to prefer avian and human glycan receptor analogues with distinct topological profiles, pentasaccharides LSTa (α-2,3 linkage) and LSTc (α-2,6 linkage), in comparative molecular dynamics studies. On the basis of detailed analyses of the dynamic motions of the receptor binding domains (RBDs) and interaction energy profiles with individual glycan residues, we have identified ∼30 residue positions in the RBD that present distinct profiles with the receptor analogues. Glycan binding constrained the conformational space sampling by the HA. Electrostatic steering appeared to play a key role in glycan binding specificity. The complex dynamic behaviors of the major SSE and trimeric interfaces with or without bound glycans suggested that networks of interactions might account for species specificity in these low affinity and high avidity (multivalent) interactions between different HA and glycans. Contact frequency, energetic decomposition, and H-bond analyses revealed species-specific differences in HA−glycan interaction profiles, not readily discernible from crystal structures alone. Interaction energy profiles indicated that mutation events at the set of residues such as 145, 156, 158, and 222 would favor human or avian receptor analogues, often through interactions with distal asialo-residues. These results correlate well with existing experimental evidence, and suggest new opportunities for simulation-based vaccine and drug development.