相关论文: Cooperativity in Protein Folding: From Lattice Mod…
We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. We find that in its low temperature phase…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
The asymmetry in the shapes of folded and unfolded states are probed using two parameters, one being a measure of the sphericity and the other that describes the shape. For the folded states, whose interiors are densely packed, the radii of…
In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed…
For the hard-core lattice gas model defined on independent sets weighted by an activity $\lambda$, we study the critical activity $\lambda_c(\mathbb{Z}^2)$ for the uniqueness/non-uniqueness threshold on the 2-dimensional integer lattice…
Many ternary mixtures composed of saturated and unsaturated lipids with cholesterol (Chol) exhibit a region of coexistence between liquid-disordered $(L_d)$ and liquid-ordered $(L_o)$ domains, bearing some similarities to lipid rafts in…
Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein…
A novel statistical model for the cooperative binding of monomeric ligands to a linear lattice is developed to study the interaction of ionic surfactant molecules with flexible polyion chain in dilute solution. Electrostatic binding of a…
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/T_F ~ N^-1, where T_F is the folding transition…
The BCS-BEC crossover in a lattice is a powerful paradigm to understand how a superconductor deviates from the Bardeen-Cooper-Schrieffer physics as the attractive interaction increases. Optical lattices loaded with binary mixtures of cold…
We investigate tunneling properties of a bound pair of Fermi atoms in an optical lattice, comparing with results obtained in an attractive Hubbard model. In the strong coupling regime of the Hubbard model, it has been predicted that the…
Native extracellular matrices (ECMs), such as those of the human brain and other neural tissues, exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
We introduce a multi-species lattice gas model for motor protein driven collective cargo transport on cellular filaments. We use this model to describe and analyze the collective motion of interacting vesicle cargoes being carried by…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
We investigate the addition of stiffness to the lattice model of hydrogen-bonded polymers in two and three dimensions. We find that, in contrast to polymers that interact via a homogeneous short-range interaction, the collapse transition is…
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…