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Volume 10, Issue 8 (Suppl)

J Proteomics Bioinform, an open access journal

ISSN: 0974-276X

Structural Biology 2017

September 18-20, 2017

International Conference on

Structural Biology

September 18-20, 2017 Zurich, Switzerland

Structural and molecular dynamics analysis of the super secondary motifs fromTIM barrel proteins:

Implications for folding and engineering of foldable building blocks for the assembly of TIMS

Ramakrishna Vadrevu

Birla Institute of Technology and Science, India

Statement of the Problem:

The acquired complex three-dimensional structure of proteins is a culmination of simple structural

fragments like

α,

β-β,

-β and β-

units. Thus, tertiary structures can be seen as a combination of basic building block

motifs implying that all complex protein structures have evolved from the assembly of small independently folding super

secondary structures. The TIM barrel proteins are made up of a regular repeating β

β motif resulting in the strands and helices

in an alternating repetitive pattern. Experimental and theoretical studies have revealed that β

β unit acts as a minimal unit of

stability. The success of designing super secondary motifs that fold in isolation underscores the prospects of designing and or

identification of independently folding motifs from the existing protein structures. However, intriguingly, naturally occurring

β sequences from proteins that fold independently have not been identified. In our attempts, we addressed the finding of

‘needles in hay stick’ scenario by an exhaustive sequence and structural space search of the β

β units from the TIM barrels.

Methodology & Theoretical Orientation:

The search approach implemented in this work considered features such as alpha

helical propensity, loop length, loop dynamics, residue preferences in loops, long range side chain main chain interactions etc.,

to shortlist β

β units with strong propensity to fold in isolation. The prospective β

β candidates thus shortlisted from the TIM

barrels have been further subjected to structure forming tendency employing a combination of Monte Carlo and Molecular

dynamics simulations to assess their foldability and stability.

Conclusion & Significance:

The prediction of some independently folding β

β candidates from TIMs are enabling us to

experimentally asses their folding and stability. The identification and analysis of independently folding β

β units that exist

naturally will not only provide substantial information on nature’s design strategies and evolution of protein conformations but

also help to design/engineer novel proteins.

Biography

Ramakrishna Vadrevu received his Master’s degree in Physical Chemistry and his PhD degree in Biophysical Chemistry. He spent few years at the Pennsylvania

State University and later at University of Massachusetts Medical School as a Postdoctoral Fellow with Prof. C. Robert Mathews. Since 2008 he has been a faculty

at the Birla Institute of Technology and Science-Pilani, Hyderabad Campus in the department of Biological Sciences. His research focuses on understanding the

role cellular environment on protein stability and folding. His research interests include: protein design and engineering, amyloid material and its applications.

vrk@hyderabad.bits-pilani.ac.in

Ramakrishna Vadrevu et al., J Proteomics Bioinform 2017, 10:8(Suppl)

DOI: 10.4172/0974-276X-C1-0100