Related papers: Multiple scales and phases in discrete chains with…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
This article focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid-liquid…
Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion, from a relatively small number of components. Here we propose to identify the…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified from the aa sequence alone for the amyloid 770 aa precursor protein A4.…
The formation and dynamics of a wide variety of binary two-dimensional ordered structures and superlattices are investigated through a phase field crystal model with sublattice ordering. Various types of binary ordered phases, the phase…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
Algorithms that detect covariance between pairs of columns in multiple sequence alignments are commonly employed to predict functionally important residues and structural contacts. However, the assumption that co-variance only occurs…
Proteins are an example of heteropolymers able to self-assemble in specific target structures. The self-assembly of designed artificial heteropolymers is still, to the best of our knowledge, not possible with control over the single chain…
This research paper comprehensively explores the effects of molecular weight and chain architecture on the interfacial and thermodynamic properties of cyclic and linear polymer blends. Utilizing the Kremer-Grest bead-spring model, the study…