Globin-Coupled Sensors and Protoglobins
(PI: Maqsudul Alam)

Globin-coupled sensors (GCSs) are multi-domain proteins which have an N-terminal myoglobin-like domain linked to varying C-terminal transmitter domains. We identified the first globin-coupled sensors to be described: HemAT-Hs from Halobacterium salinarum and HemAT-Bs from Bacillus subtilis. Both proteins have an amino-terminal sensing domain that is homologous to myoglobin and a carboxy-terminal signaling domain characteristic of methyl-accepting chemotaxis proteins (MCPs). The HemAT transducers exhibit absorption spectra similar to myoglobin and reversibly bind oxygen. HemAT-Hs mediates an aerophobic response, whereas HemAT-Bs mediates an aerophilic response.

We designed a GCS sequence motif and used it to identify other GCSs from a variety of Bacteria and Archaea. Based on their C-terminal domains, the GCSs are classified as either aerotactic or gene regulating. The gene-regulating group can be further subdivided into three subgroups: protein-DNA, protein-protein and 2nd messenger pathways.

Classification of the globin-coupled sensors in relation to other biological heme-based sensors. 
Adapted from Freitas et al., 2007, Protoglobin and globin-coupled sensors, in Ghosh, A. (Ed.),
The smallest biomolecules: diatomics and their interactions with heme proteins, pp. 175-202. Click for expanded view

Our main goal is to determine the molecular signaling mechanism of the HemATs. In order to accomplish this, we plan to identify: the distal residues by monitoring the rates and/or affinities of ligand binding and their changes; the residues within the globin domain that are involved in propagating the oxygen-binding signal to the transmitter domain; and the residues in the linker region that are crucial for interdomain signaling. We also plan to investigate the HemAT-Hs and HemAT-Bs triggered aerotactic adaptation mechanisms.

We would also like to functionally characterize the gene-regulating GCSs. We will use resources and methods from bioinformatics, genetics, biophysics, and signal transduction to answer key questions about structure, function, regulation, and communication in the globin-coupled sensors.

An initial identification of all known GCSs motivated us to seek out and identify the globin ancestor (protoglobin) of these chimeric proteins. Using the experimentally determined globin domain length, proximal histidine and distal residue positions, and the chemical nature of the heme pocket, we identified protoglobins in both the Archaea and Bacteria. Protoglobins have demonstrated “flexibility,” with a broad ligand-binding range. Their sensitivity to oxygen predisposes them to functioning in low-oxygen environments. We plan to determine the physiological role of these protoglobins in their host organisms and investigate their evolutionary relationship with the GCSs.

Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB)
(Director: Maqsudul Alam)

The University of Hawaii’s aspiration is to become a member of the nation's research elite in the life and medical sciences. Thus, we are committed to establish the Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB), to support top tier researchers, to encourage cooperation and collaboration and to allow them to successfully complete in performing creative research while providing leadership and support for the University of Hawaii’s broader mission and goals. Hawaii has four unique reasons that will allow UH to become a major player in Genomics, Proteomics and Bioinformatics (GPB).

• The most heterogeneous population pool in the world
• Unequaled biological diversity including the endangered species capital of the world and 70-75% of the nation's coral reefs
• Ideal location for research in tropical medicine and agriculture
• Natural laboratory for the study of marine microbes and extremophiles

The opportunity in GPB research is great and the University of Hawaii (UH) is striving to take a leading role. The current objective is to create the UH Center for GPB to bring together multidisciplinary life and medical science teams to develop and apply high throughput genomic/proteomic-scale technologies with bioinformatic tools to compete successfully in performing cutting-edge research.

ASGPB as Lead Institute together with 85 researchers from 30 national and international teams have deciphered the genetic code of a disease-resistant
papaya, “Rainbow” variety.  The “Rainbow” papaya was developed in the 1990s by UH and Cornell University researchers as a fruit resistant to the ring spot virus that devastated island papaya crops during that decade.   The decoding of this Papaya Genome provides the foundation for revealing the basis of Papaya’s distinguishing medicinal and nutritional properties. It is a big step toward opening up consumer markets for this fruit in Japan and other Asian countries – and that, in turn, could significantly
improve the economic health of the papaya industry in Hawai`i.

Computational Proteomic Program
(PI: Maqsudul Alam)

A systems biology approach to computational proteomics emphasizes the integration of simple motif searches to complex high throughput protein folding. Complex data mining of diverse protein families can lead to an understanding of how proteins operate, including protein networks, protein clusters, protein folding, and protein three dimensional (3D) modeling and molecular dynamics simulation. Such studies rely on computational methods to analyze and integrate data, to construct models, and to simulate the activity of proteins. Such simulations give rise to predictions about changes in function when the protein is perturbed by mutation or lack of protein-protein interaction, which in turn leads to experimental testing of these hypotheses, refinement of these hypotheses, and further modeling and testing.

The Computational Proteomics program meets these objectives through the execution of the following three projects.

Exploring Oxygen, Nitric Oxide, and Carbon Monoxide Sensing of the Globin-Coupled Sensors (GCS) and Protoglobins from Diverse Microbial Family: Model for the Integration of Bioinformatics and Wet Lab Research

The collective evolution of hemoglobin, myoglobin, neuroglobin, and cytoglobin made life possible; whether by signal transduction, gene regulation, detoxification, sequestration, or transport, the inter- and intra-cellular balance of oxygen was key to the evolution of humans. Thus, it only seems logical that globins are found in most mammalian tissues and in the blood that bathes them. The globin descendents allowed higher organisms to evolve by maintaining their core function of oxygen homeostasis. Recently a novel DGC signaling pathway is mediated by a secondary messenger c-di- GMP in bacteria, which is linked to cell development of morphology, motility, virulence, biofilm, probably cell-cell communication, and even eukaryotic host cell cycle arrest. GCSs with globin domain and DGC domain haven’t been characterized yet.

Molecular Dynamics Studies (MDS) of homology models of the GCSs and protoglobins with three ligands O2, CO, and NO will be continued using the molecular dynamics package VMD/NAMD. As part of our protein modeling initiative and our commitment to efficiency and productivity, we plan to coordinate our bench top experiments around the results obtained from protein-ligand modeling studies.

DEN2 Envelope Protein: Molecular modeling, structure refinement and in silico high throughput compound library screening for potential antiviral drugs using high performance super computer environment

Dengue infection is re-emerging as a major global disease and is classified as a Category A priority pathogen. Dengue viruses are estimated to infect 50-100 million people annually and are considered to cause one of the most important arthropod-borne viral diseases in terms of human morbidity and mortality. Virus transmission occurs through the bite of the Aedes aegypti mosquito and half the world’s population is at risk for infection. There is presently no approved vaccine or antiviral drug that is effective against dengue viruses. The focus of this task is to combine the power of high performance computing with wet lab experiments for the discovery of novel antiviral drugs that can be used either to prevent or treat dengue virus infections by preventing viral entry.

We propose to use high performance supercomputer environment: molecular modeling and dynamics, ab initio molecular orbital computations, and ab initio molecular dynamics (AIMD)--in this case, Atom-Centered Density Matrix Propagation (ADMP) to study the crystallographic models of the DEN2 Envelope protein. High quality molecular dynamics runs will be performed using NAMD on the unliganded/liganded form as a monomer, then dimer, and finally trimer so that the ligand-binding pocket can be characterized accurately.

A University of Malaya team has discovered competitive inhibitors of NS2B/NS3 and dengue virus inhibitor from plants already in use in medicinal use in southeast Asia. These compounds were identified via in vitro experiments inhibiting growth of dengue virus. Their interaction with NS2B/NS3 protease has been studied kinetically, and some in silico docking studies to identify the pharmacophore have been undertaken.

Maui Institute of Molecular Medicine (MIMM) and High throughput genomic raw data generation and computational analysis

MIMM aims to utilize state-of-the-art genomics and proteomics technologies to rapidly carryout global analysis of the genome and proteome of selected extremeophiles. Sequencing of extremophiles genome is a critical step towards understanding the relationship between genome and function. Elucidating and characterization of the proteome validates the genome based predictions and provides an opportunity to identify new bioactive agents and proteins with unique enzymatic functions. This will enable the program to rapidly generate data and populate its databases with relevant proteomic information associated with extremophiles.