Bourne Laboratory
Projects (contact pbourne@ucsd.edu) –
Last Update January 2008
Rotation/PhD Projects: General Topic – Pharmaceutical Sciences - Competitive Binding of Major Pharmaceuticals.
We have recently developed a method to determine the geometric potential [1] which describes the ligand binding sites of 3-dimensional proteins. Subsequently we developed a fast approach to search for these sites in a high throughput mode [2] across the druggable proteome. The goal of the project is to use these tools to search for competitive binding of major pharmaceuticals which might explain observed side effects, reposition an existing drug, or ultimately point the way towards further lead optimization. So far we have been able to offer an explanation for the side effects observed using select estrogen receptor modularors (SERMS), for example tamoxifen [3] and potentially reposition an existing drug for use in the treatment of TB (experimental verification on-going).
A project exists to search for alternative binding sites for Nelfinavir an HIV-1 protease inhibitor which has been observed to be effective against a variety of tumor cell lines. Nelfinavir is known to inhibit the activation of Akt, a protein implicated in cancer development, but the exact target is unknown. See http://www.nih.gov/news/pr/sep2007/nci-01.htm for more details. The goal of this project is to seek out the alterative target(s) of Nelfinavir.
[1] L. Xie and P.E. Bourne 2007 A Robust and Efficient Algorithm for the Shape Description of Protein Structures and Its Application in Predicting Ligand Binding Sites BMC Bioinformatics, 8(Suppl 4):S9
[2] L. Xie and P.E. Bourne 2007
Detecting Evolutionary Linkages Across Fold and
Functional Space with Sequence Order Independent Profile-profile Alignments. PNAS,
Submitted
[3] L. Xie, J. Wang and P.E.Bourne 2007 In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators. PLoS Comp. Biol., 3(11) e217.
Primary Mentors: Phil Bourne & Lei Xie
Summer/Rotation/PhD Student Project: From
Physical Model of Nucleosome Organization towards
Genome Annotation
This
project is a part of an effort towards the development of an accurate model for
prediction of the nucleosome location on an arbitrary
strand of DNA.
Packaging DNA into nucleosome
affects DNA accessibility by transcription factors (TFs): while some TFs can
bind nucleosome-packed DNA (e.g., GR, Sp1, USF,
GAL4), the majority of TFs cannot bind nucleosome-packed
DNA. Knowledge of nucleosome positioning is essential
for understanding mechanisms of the regulation of gene expression in eukaryotic
cells; also, reliable prediction of nucleosome
positioning may facilitate wide-scale annotation of the genomes. [Read more…]
Primary Mentors: Julia
Ponomarenko and Apostol Gramada
Rotation/Summer/PhD
Projects: General Topic – Earth Sciences
Meets Life Sciences
There has been a variety of exciting work in the past few
years that relates geochemistry to genomics (see Cavalier-Smith 2006 Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29;361(1470):969-1006). This is important since it provides
new insights into evolutionary events and may provide insights into the
implications of human impact on our ecosystems as measured at the fundamental
level of
In a recent paper (Dupont et al. 2006 PNAS accepted) we have explored the impact of geochemical changes (environmental changes over evolutionary time scales) in metal ion concentration on the proteomes of modern day organisms and provide the first evidence for a strong correlation. Only through the disposition of protein structures known to bind metals across the three superkingdoms of life was this analysis possible. Looking at the impact on changing environment at the level of the superkingdom is a course grained study which sets the stage for more detailed analyses.
The following are projects that we are keen to see pursued that expands on this initial finding. They are based on a premise bought forward by Cavalier-Smith that there may be “megaevents” which in our case would imply the emergence of a new fold, domain combination or other structural event that led to new phenotypic variance with significant implications.
Rotation/Summer
Project: Exploring the Impact of Co and Mo Environments on Life
This is a follow on from the PNAS study which focused primarily on Fe and Zn.
Primary Mentor: Phil Bourne and Chris Dupont
Rotation/Summer/PhD
Project: Exploring the Flexibility versus Designability
of Protein Folds
Nature consists of a very limited number of protein folds - of the order of 1000 are known today. Each protein fold accommodates one or more families of proteins. The more families that a fold accommodates the more designable it is said to be.
Recently we have developed a method (Gu et al. 2006 PLoS Comp. Biol. 2(7) e90) which measures the flexibility of a protein from only its amino acid sequence. The approach uses the Gaussian Network Model and a normalization procedure to measure relative flexibility at each amino acid position. Training a support vector machine on sequences taken from known structures from which flexibility can be experimentally verified a generalized method of determining flexibility from sequence is obtained.
Hypothesis - Flexibility is correlated with designability. That is the more designable a protein the more flexible it will be. Certainly this is intuitively what one would expect. The more flexible the protein the more sequences it can be expected to accommodate.
Part of the project
will be to develop the appropriate experimental protocol to test this
hypothesis, but the basic intent is to use the existing methodology (and code)
to determine flexibility of a range of protein sequences which fall into given
folds of varying designability. The latter can be
taken directly from the
Primary
Rotation/Summer/PhD
Project: What Makes Some Introns’ Positions Ultra-conserved?
Appearance of spliceosomal introns is central to eukaryotic evolution; the origins and evolution of spliceosomal introns is still hotly debated and one of the most exciting topics of molecular evolution. A small subset of spliceosomal introns in eukaryotic genes exhibits strikingly high level of conservation across eukaryotic species in terms of their position and phase within the genes. These introns are particularly interesting as they are likely to be very old, dating back to or before last eukaryotic common ancestor (LECA).
We are interested in finding out what are the characteristic of genes and proteins with such ultra-conserved introns. Do these genes code for proteins that appear/expand in early eukaryotic evolution? Do these proteins have a specific subset of functions/structures? Are the splice-sites of ultra-conserved introns are different in any way from less conserved introns? Answering these questions will advance our understanding of early stages of evolution of spliceosomal introns.
We are currently working with Sm/lsm multi-gene family that contains many such ultra-conserved introns, but would like to extend this work further. A dataset with introns positions is available for 684 orthologous genes in 8 organisms (Rogozin et al. (2003) Current Biology 13;1512-1517), which we intend to use to address this problem.
Primary
Rotation/Summer/PhD
Project: Building a Meta-method for
Assignment of Structural Domains in Proteins.
Partitioning protein structures into domains is a prerequisite for many types of structure analysis. While many automatic methods for assigning structural domains exit, none of them is able to perform above 85% accuracy. The lack of complete success in domain assignment reflects the fundamental biological problem– the inconsistency of real biological data; thus ultimately it is impossible to construct an automatic method that will assign domains correctly 100% of the time. We have analyzed in-depth the properties and tendencies of different automatic methods for domain assignment and observed that different methods have complementary strengths and weaknesses (Veretnik et al. (2004) J Mol Biol 339:647-78; Holland et al. (2006) J Mol Biol. 361:562-90.). We are currently beginning the building of a meta-method, which will incorporate predictions of several existing methods. A consensus among methods will be sought, when no consensus exist, the method that performs best for give type of structure (based on the size of the protein and the sizes of assigned domains, the secondary structure of the protein as well as architecture and the topology of the protein) will be applied. If developed well, a meta-method will become a sorely needed tool for consistently and precisely partitioning any structure into domains..
Qualifications: good programming skills (C++ / Java/Perl) and basic understanding of protein structures.
Primary Mentors: Stella Veretnik and Phil Bourne
PhD Project: Looking for Correlation Between Protein and Gene Structure.
To what extend is the current repertoire of proteins built from a combinatorial assembly of small structural units? And to what extend are the structural units encoded by the individual exons within a gene? Clear evidence exists for recent proteins in which structural domains frequently co-inside with individual exons. The situation is much more blurry for older proteins due to intron gain and loss throughout evolution which masks the original correlation (if there was one).
We would like to approach this differently by looking at the smaller structural units and investigate whether there is correlation between individual subdomains (or motifs) and individual exons. Furthermore, we would like to look at structural units with internal symmetry/pseudo-symmetry and the correlation between symmetry unit and exons.
Analysis will be performed separately for proteins of different “ages”, giving a sense as to how ubiquitous exon shuffling was throughout eukaryotic evolution.
Qualifications: good programming skills in C++ , experience with databases, some knowledge of structural biology.
Primary Mentors: Stella Veretnik and Phil Bourne
Rotation/Summer Project: General Topic – Scholarly Communication.
Our laboratory is a strong supporter of open access (OA) to the scientific literature. OA affords opportunities to disseminate and comprehend science in news ways. We are working in two areas using OA content. First we are integrating OA literature with database content using PubMedCentral and the PDB as our test case (http://biolit.ucsd.edu). Second we are integrating video content with OA content as part of a video delivery site (http://www.scivee.tv) . See .L. Fink and P.E.Bourne 2007 Reinventing Scholarly Communication for the Electronic Age. CT Watch, 3(3) 26-31 [HTML] for further details. Projects are available in areas of programming and video production.
Primary Mentors: Lynn Fink and Phil Bourne