Tag Archives: LBL

Peppytides: Molecular Models of the Future

Peppytide assembly in action

A new physical model of peptide and protein folding has been published in PNAS highlighting innovative work from graduate student researcher Promita Chakraborty and LBNL senior scientist and Molecular Foundry Biological Nanostructures Facility Director Dr. Ron Zuckermann. This recent work highlights an elegant strategy to design, construct, and test a novel scaled model of polypeptide chains, dubbed Peppytides.

These Peppytides are a novel tactile interface to the complicated world of protein folding. They boast dynamic, flexible chains that can fold into secondary and tertiary structures while retaining the key biophysical parameters of the parent proteins and peptides. The models are highly intuitive and understandable while preserving the inherent complexity of the twists, turns, and folds that underlie protein folding. In a word, Peppytides are not the stuff your sophomore year biochemistry model set was made out of. Rather, these models represent the cutting edge of kinesthetic molecular visualization for molecules with a large number of atoms packaged into a system that is equally useful and accessible for a classroom as it is for a research laboratory.

The Peppytide strategy is achieved by using remarkable care in designing each element of the model to ensure accuracy in conveying the parameters that are relevant to protein folding and chain interactions. Via clever and scientifically driven design strategies, a peppytide consists of a generic polypeptide constructed with some critical  constraints that allow it to fold into all existing secondary structures possible in its biological counterpart. Precisely positioned magnetized bonds allow for reproducing torsion angles and long range H-bonding interactions. A 3D printer allows for high-throughput production of ultralight building blocks highlighting a peptide bond and alpha-carbon disconnection approach that includes adaptors for installation of all mechanical components.

Piper Promotes: Molecular Foundry Call for Proposals Due July 15, 2012

The Molecular Foundry at Lawrence Berkeley National Laboratory (LBNL) has a Call for Proposals with a submission deadline of Sunday, July 15, 2012. The projected award date for selected proposals will be October 1, 2012.

The Molecular Foundry is a Department of Energy-funded program providing support to researchers from around the world whose work can benefit from or contribute to nanoscience. Calls for Proposals allow users access to many scientists and instrumentation, including the Advanced Light Source (ALS), National Center for Electron Microscopy (NCEM), the Department of Energy (DOE) Joint Genomic Institute (JGI), and National Energy Research Science Computing Center (NERSC).

The Foundry is moving to a Spring/Autumn Call for Proposals next year, which means that there will be no Winter 2012 Call for Proposals. After the current Call for Proposals, the next call will not occur until Spring 2013.

Further information can be found at The Molecular Foundry Home Page, TMF Data-base Log in Page, and the Foundry Staff Scientists and Support Personnel. Questions should be directed to the User Program Manager (DABunzow@lbl.gov or 510-486-4674).

The 2012 Annual Users Meeting will be October 4 & 5, 2012.