Institute for Complex Systems - Sapienza - CNR

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ISC Sapienza Physics of Biopolymers

Physics of Biopolymers

Statistical mechanics approach to proteins and biopolymers: protein folding, functional dynamics, translocation.

Publications>> 

Protein molecules

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Biopolymers such as nucleic acids (DNA and RNA) and proteins have been charged by natural evolution with the task of storing, transmitting and transforming genetic information of living matter.
In particular proteins are the macromolecules which perform most of the biochemical and biomechanical activities of organisms. Proteins, for instance, provide the building blocks of cells and tissues, they are involved in control and regulation of cellular cycles, in enzymatic catalysis, proteins are at the basis of muscle contractions and constitute part of the immunitary defence, etc... The list of biological functions which proteins are involved in is extremely long and rapidly increasing with the research advances.
Biologists use to classify proteins in terms of primary structure (amino acid sequence), secondary structure (regions of alpha-helices, beta-sheets, coils and turns) tertiary structure (3-dimensional spatial arrangement of atoms).
Last Updated on Wednesday, 27 July 2011 12:41 Read more...

Protein functional dynamics

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All those movements and structural rearrangements which proteins undergo in their active state are generally referred to as functional dynamics since they are believed to be dependent on protein physiological functions. A quantitative characterization of mechanisms intertwining structure, chemistry, and dynamics with functions represent a challenge in molecular biology. For this reason normal mode analysis (NMA) has been a widely applied technique for reconstructing conformational changes of proteins from the knowledge of native structures.

Our activity aims to investigate the predictability of normal modes on the salient features of the dynamics even in regimes near folding transitions with the purpose to understand whether physiological-temperature NMA is justified at least in proteins with cooperative folding. We suggest how to identify several modes in order to eliminate the unpredictable temperature dependence of single-mode contributions to protein fluctuations.

Last Updated on Wednesday, 27 July 2011 12:42 Read more...

Protein Folding

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Protein Folding is a specific chemical and physical transition by which a linear sequence of aminoacids finds its functional (native) three dimensional structure. The theoretical study of protein folding represents perhaps one of the most challenging research with a marked interdisciplinary character, where biology, chemistry, physics, mathematics and computer science can fruitfully interact each other.

Our activity in this field concerns the prediction of folding mechanisms by the knowledge of tertiary structure only. This finds a strong justification on theColor representation of MyBPC C5-domein folding pathway widely recognised importance that native states have in stirring the folding processes.

In particular, we follow the approach combining molecular dynamics simulations, coarse-grained protein models and Statistical Mechanical methods which constitutes a viable framework to tackle this issue at convenient computational costs. In this philosophy the protein is assimilated to a polymer composed of its backbone of C-alpha carbons and the interactions among amino-acids are assigned via an potential energy which takes on a minimum on the native state.

Last Updated on Wednesday, 27 July 2011 12:42 Read more...