Postdoctoral Program - Energy landscapes of designed proteins: structure, dynamics and thermodynamics
Applications are invited for post-doctoral researchers to work on a unique four year collaborative project, which combines the landscape exploration expertise of Professor David Wales’ group in the Chemistry Department in Cambridge with the expertise on coarse-grained models and designed proteins in Dr. Shachi Gosavi’s group at the National Centre for Biological Sciences, Bangalore, India. Half of the postdoctoral tenure will be spent at Cambridge while the other half will be at NCBS.
This project will involve the theory and simulation of designed proteins using both coarse- grained and atomistic descriptions. Applications of designed proteins range from human health to nanotechnology. However, de novo protein design is not well understood and several attempts need to be made before a sequence that successfully folds to a target structure is found. One possible reason for the failures is that most protein design protocols target the final folded structure and do not attempt to sculpt the entire folding energy landscape. Natural or evolved proteins have funnel-shaped folding energy landscapes and these landscapes support folding on a biologically reasonable timescale, usually in an all-or-nothing fashion. It is known that the landscapes of several de novo designed proteins are frustrated, i.e., contain deep non-native traps, which allow the protein to sample misfolded states. Such misfolding is detrimental in the crowded environment of the cell, which is the usual milieu of biotechnological applications. The aims of this project are to understand the coarse-grained and atomistic folding energy landscapes of experimentally well characterized designed proteins, to compare these to the landscapes of similar natural proteins, and, using this comparison, attempt to redesign the sequence and in turn the landscapes. The broad goal of the project is to set up a computational framework that can be used to reduce frustration in the landscapes of designed proteins.
Applicants should have (or be about to receive) a PhD in theoretical chemistry or physics. Significant expertise in computer simulation and statistical mechanics is essential. A substantial part of the project involves implementing coarse-grained potentials in programs supported in the Wales group, and extensive experience with at least one compiled language, preferably fortran, and one scripting language is also essential.
The closing date for initial applications is 6th March. Applications should include a CV, publication list, and contact details for three professional referees. Candidates will first be invited for an in person or electronic interview at NCBS or Cambridge soon after. The selected candidate will then develop a two page proposal jointly with Dr Gosavi and Prof. Wales and will submit a complete application (proposal, CV and two letters of recommendation, including one from their Ph. D. thesis advisor) to the Bangalore-Cambridge selection committee by 20th March 2015. Candidates will present a talk and be interviewed by a panel in either Bangalore or Cambridge in the week commencing 28th March, 2016. Appointment decisions will be announced soon after.
Initial applications should be sent to Shachi Gosavi (firstname.lastname@example.org) and David Wales (via Sue Harding: email@example.com). Please mention NCBS-Cambridge postdoctoral fellowship in the subject line.