Biomedical subjects

J R Banavar

Publications and source records attributed to J R Banavar.

7 recordsLinked to original sources

PubMed1999

Size and form in efficient transportation networks.

Many biological processes, from cellular metabolism to population dynamics, are characterized by allometric scaling (power-law) relationships between size and rate. An outstanding question is whether typical allometric scaling relationships--the power-law dependence of a biological rate on body mass--can be understood by considering the general features of branching networks serving a particular volume. Distributed networks in nature stem from the need for effective connectivity, and occur both in biological systems such as cardiovascular and respiratory networks and plant vascular and root systems, and in inanimate systems such as the drainage network of river basins. Here we derive a general relationship between size and flow rates in arbitrary networks with local connectivity. Our theory accounts in a general way for the quarter-power allometric scaling of living organisms, recently derived under specific assumptions for particular network geometries. It also predicts scaling relations applicable to all efficient transportation networks, which we verify from observational data on the river drainage basins. Allometric scaling is therefore shown to originate from the general features of networks irrespective of dynamical or geometric assumptions.

Biological Transport↗

PubMed1999

Statistical mechanics of protein-like heteropolymers.

A strategy is outlined for obtaining the free energy of a typical designed heteropolymer. The design procedure considers the probability that the target conformation is occupied in comparison with all the other conformations that could house the given sequence. Numerical calculations on lattice heteropolymer models are presented to illustrate the key physical principles.

Animals↗

PubMed1998

Design of proteins with hydrophobic and polar amino acids.

A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of 20 single chain proteins. Strikingly, the percentage of successful identification of the nature of the residues benchmarked against naturally occurring proteins and their homologues is around 75%, independent of the complexity of the design procedure. Typically, the lowest success rate occurs for residues such as alanine that have a high secondary structure functionality. Using a simple lattice model, we argue that one possible shortcoming of the model studied may involve the coarse-graining of the 20 kinds of amino acids into just two effective types.

Algorithms↗

PubMed1998

Structure-based design of model proteins.

A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model.

Amino Acid Sequence↗

PubMed1998

Interaction potentials for protein folding.

We outline a general strategy for determining the effective coarse-grained interactions between the amino acids of a protein from the experimentally derived native-state structures. The method is, in principle, free from any adjustable or empirically determined parameters, and it is tested on simple models and compared with other existing approaches.

Amino Acids↗

PubMed1997

Cell dynamics of folding in two-dimensional model proteins.

BACKGROUND: Functionally useful proteins are sequences of amino acids that fold rapidly under appropriate conditions into their native states. It is believed that rapid folders are sequences for which the folding dynamics entail the exploration of restricted conformations-the phase space can be thought of as a folding funnel. While there are many experimentally accessible predictions pertaining to the existence of such funnels and a coherent picture of the kinetics of folding has begun to emerge, there have been relatively few simple studies in the controlled setting of well-characterized lattice models. RESULTS: We design rapidly folding sequences by assigning the strongest couplings to the contacts present in a target native state in a two-dimensional model of heteropolymers. Such sequences have large folding transition temperatures and low glass transition temperatures. The dependence of median folding times on temperature is investigated. The pathways to folding and their dependence on the temperature are illustrated via a study of the cell dynamics-a mapping of the dynamics into motion within the space of the maximally compact cells. CONCLUSIONS: Folding funnels can be defined operationally in a coarse-grained sense by mapping the states of the system into maximally compact conformations and then by identifying significant connectivities between them.

Models, Chemical↗

PubMed1995

Lattice model for rapidly folding protein-like heteropolymers.

Protein folding is a relatively fast process considering the astronomical number of conformations in which a protein could find itself. Within the framework of a lattice model, we show that one can design rapidly folding sequences by assigning the strongest attractive couplings to the contacts present in a target native state. Our protein design can be extended to situations with both attractive and repulsive contacts. Frustration is minimized by ensuring that all the native contacts are again strongly attractive. Strikingly, this ensures the inevitability of folding and accelerates the folding process by an order of magnitude. The evolutionary implications of our findings are discussed.

Biological Evolution↗