arXiv subjects

Trinh X. Hoang

Publications and source records attributed to Trinh X. Hoang.

23 records · Page 2Linked to original sources

arXiv2012

Protein sequence and structure: Is one more fundamental than the other?

We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a sequence-independent free energy landscape with relatively few low energy minima with funnel-like character. The choice of a sequence that fits well into one of these predetermined structures facilitates rapid and cooperative folding. Our model calculations show that this novel phase facilitates the formation of an efficient route for sequence design starting from random peptides.

q-bio.BM↗

arXiv2007

Symmetry, shape, and order

Packing problems have been of great interest in many diverse contexts for many centuries. The optimal packing of identical objects has been often invoked to understand the nature of low temperature phases of matter. In celebrated work, Kepler conjectured that the densest packing of spheres is realized by stacking variants of the face-centered cubic lattice and has a packing fraction of $π/(3\sqrt{2}) \sim 0.7405$. Much more recently, an unusually high density packing of approximately 0.770732 was achieved for congruent ellipsoids. Such studies are relevant for understanding the structure of crystals, glasses, the storage and jamming of granular materials, ceramics, and the assembly of viral capsid structures. Here we carry out analytical studies of the stacking of close-packed planar layers of systems made up of truncated cones possessing uniaxial symmetry. We present examples of high density packing whose order is characterized by a {\em broken symmetry} arising from the shape of the constituent objects. We find a biaxial arrangement of solid cones with a packing fraction of $π/4$. For truncated cones, there are two distinct regimes, characterized by different packing arrangements, depending on the ratio $c$ of the base radii of the truncated cones with a transition at $c^*=\sqrt{2}-1$.

cond-mat.stat-mech↗

arXiv2007

Structural motifs of biomolecules

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularityfree self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.

q-bio.BM↗

arXiv2006

Geometry of proteins: hydrogen bonding, sterics and marginally compact tubes

The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for understanding the common character of globular proteins.We argue that a recent critique of the tube idea is not well founded.

q-bio.BM↗

arXiv2005

Geometrical model for the native-state folds of proteins

We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and the role played by hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as broad competing minima in the free energy landscape even for a homopolymer. Here we show how the introduction of sequence heterogeneity using a simple scheme of just two types of amino acids, hydrophobic (H) and polar (P), and sequence design allows a selected putative native fold to become the free energy minimum at low temperature. The folding transition exhibits thermodynamic cooperativity, if one neglects the degeneracy between two different low energy conformations sharing the same fold topology.

q-bio.BM↗