NIAID’s Structural Genomics Centers Can Move You Forward
This is the latest in a series of articles highlighting resources for researchers from NIAID’s Division of Microbiology and Infectious Diseases (DMID).
Would knowing the 3-D atomic structure of a protein further your research?
If so, see if the structure of your protein is in a public database such as the Protein Data Bank. If it’s not, NIAID’s Structural Genomics Centers for Infectious Diseases may be able to determine the structure of your protein at no charge to you. Investigators in academia, not-for-profit organizations, industry, and government worldwide are welcome to request services.
Your protein has to play an important biological role, have potential as a target for vaccine and drug development, and relate to NIAID Category A, B, and C Priority Pathogens or Emerging and Re-emerging Infectious Diseases.
Go to Structural Genomics Centers for Infectious Diseases for details on assurances to users, data release guidelines, and the application, prioritization, and approval processes. Contact Valentina Di Francesco if you need more information about the program.
Visit Omics Research Tools and Technologies for links to other “Omics” resources and get in touch with Dr. Malu Polanski to discuss tapping their potential.
April 27, 2011
Posted in: Uncategorized
I am writing a proposal to the NASA NIAC solicitation due May 9. There is a need for the application of structural genomics methodology to a non-life domain. I have no experience in structural genomics. A summary of the proposal follows. Is there anyone out there who would be interested in providing some advice or guidance either before the proposal is submitted or afterward in case it is accepted? Thank you.
his proposal describes activities that serve as the introductory research into the Vehicle Genome Project. The Vehicle Genome Project envisions that complex aerospace vehicles can be designed by a process of evolution similar to that which has resulted in complex life forms. Of course, before we can expect to design complex vehicles, we must be able to use the evolutionary process to design very simple objects that perform very simple tasks.
As in the evolution of life, the process must start at a very basic and simple level. We will mimic the onset of life by using materials at a molecular or nano scale. The first step will be to generate simple objects, that behave in a specified manner or perform some specified task. In a sense, we could “reinvent the wheel,” in that we may specify that the new evolved object must roll. As the research progresses and more complex objects are designed, the process will almost certainly require the discovery of new materials that do not exist now.
The first goal of the research at this low TRL level is to discover a language analogous to the GCTA elements of life DNA and a means for translating codes written in that language to the physical characteristics of an object. A means for describing the environment that the object will inhabit is a key element toward determining the characteristics that the object will have. As with life, many objects may appear, but only those best adapted to the environment will survive, that is, be best suited to perform the desired task.
Mechanisms for translating the genome into physical characteristics, analogous to protein folding, must be discovered. “The challenge as a result of the genome mapping projects of the last and present decade,” says Charles Brooks of the Scripps Research Institute, “is to deduce protein function starting from genomic sequence.” This emerging field of activity is called “structural genomics.” Again, intense research is required, including investigations into leveraging from the research in computational biology such as the IBM Blue Gene project.
The proposed evolutionary process has an advantage over the actual life evolution in that self-replication of the objects is not required. The process will involve advanced computer modeling and simulation. No actual objects need be created until a useful design appears. However, as in actual life, a very large number of objects evolving over a very large number of generations will be required, even for simple cases. The project will make use of cloud computing to generate and analyze the evolving objects. The proposed project will also require the integration of the knowledge and experience of experts in the fields of design, nano-materials and structures, and structural genomics.
To summarize, the project will attempt to mimic the design capability of the evolution of life, the most successful designer of complex complex “vehicles” known to man. The primary goal is the proof of concept of a process of specifying the the basic genome, converting that genome into an object, and evaluating that object in a specified environment. There is no certainty that this goal can be met. But if such a process can be developed, it will have a startling effect on the design and development of all devices from the mundane (a better mousetrap) to the inspirational (a starship).
Having the ability to know the 3-D atomic structure of a protein would be very helpful for research. This is definitely a step in the right direction.
-Igor Purlantov