Chirality and Protein Folding

There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are established, i.e. whether the interacting amino acids come closer than some characteristic distance. We use Go-like models of proteins and show that such simple criteria may prompt one to declare folding even though fragments of the resulting conformations have a wrong sense of chirality. We propose that a better condition of folding should augment the simple criteria with the requirement that most of the local values of the chirality should be nearly native. The kinetic discrepancy between the simple and compound criteria can be substantially reduced in the Go-like models by providing the Hamiltonian with a term which favors native values of the local chirality. We study the effects of this term as a function of its amplitude and compare it to other models such as with the side groups and with the angle-dependent potentials.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

DOMAIN WALLS IN THE QUANTUM TRANSVERSE ISING MODEL

We discuss several problems concerning domain walls in the spin $S$ Ising model at zero temperature in a magnetic field, $H/(2S)$, applied in the $x$ direction. Some results are also given for the planar ($y$-$z$) model in a transverse field. We treat the quantum problem in one dimension by perturbation theory at small $H$ and numerically over a large range of $H$. We obtain the spin density profile by fixing the spins at opposite ends of the chain to have opposite signs of $S_z$. One dimension is special in that there the quantum width of the wall is proportional to the size $L$ of the system. We also study the quantitative features of the `particle' band which extends up to energies of order $H$ above the ground state. Except for the planar limit, this particle band is well separated from excitations having energy $J/S$ involving creation of more walls. At large $S$ this particle band develops energy gaps and the lowest sub-band has tunnel splittings of order $H2^{1-2S}$. This scale of energy gives rise to anomalous scaling with respect to a) finite size, b) temperature, or c) random potentials. The intrinsic width of the domain wall and the pinning energy are also defined and calculated in certain limiting cases. The general conclusion is that quantum effects prevent the wall from being sharp and in higher dimension would prevent sudden excursions in the configuration of the wall.Comment: 40 pages and 13 figures, Phys. Rev. B, to be publishe

Coarse grained description of the protein folding

We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of the effective states. The first method is based on the steepest descent mapping of states to underlying local energy minima and the other involves an additional projection to maximally compact conformations. Both methods generate connectivity patterns that allow to distinguish between the good and bad folders. Connectivity graphs corresponding to the folding funnel have few loops and are thus tree-like. The Arrhenius law for the median folding time of a 16-monomer sequence is established and the corresponding barrier is related to easily identifiable kinetic trap states.Comment: REVTeX, 9 pages, 15 EPS figures, to appear in Phys. Rev.

Energy landscapes, supergraphs, and "folding funnels" in spin systems

Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph which represents the energy landscape of the system. The resulting supergraph describes both dynamics and statics of the system in a unified coarse-grained sense. We give examples of the supergraphs for several two dimensional spin and protein-related systems. We demonstrate that disordered ferromagnets have supergraphs akin to those of model proteins whereas spin glasses behave like random sequences of aminoacids which fold badly.Comment: REVTeX, 9 pages, two-column, 13 EPS figures include

Scaling of folding properties in simple models of proteins

Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with the system size. The corresponding exponents are not universal. Scaling of the thermodynamic stability also indicates size-related deterioration of the folding properties.Comment: REVTeX, 4 pages, 4 EPS figures, PRL (in press

Localization and Interaction Effects in Strongly Underdoped La2-xSrxCuO4

The in-plane magnetoresistance (MR) in La2-xSrxCuO4 films with 0.03 < x < 0.05 has been studied in the temperature range 1.6 K to 100 K, and in magnetic fields up to 14 T, parallel and perpendicular to the CuO2 planes. The behavior of the MR is consistent with a predominant influence of interaction effects at high temperatures, switching gradually to a regime dominated by spin scattering at low T. Weak localization effects are absent. A positive orbital MR appears close to the boundary between the antiferromagnetic and the spin-glass phase, suggesting the onset of Maki-Thompson superconducting fluctuations deep inside the insulating phase.Comment: 4 pages, 3 figures, to appear in Phys. Rev. Letter

Folding in two-dimenensional off-lattice models of proteins

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 determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that the rank-ordering-based scheme of the assignment of contact energies typically fails in off-lattice models even though it generates high stability of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in which the interaction potentials are restricted to the native contacts in a target shape, gives rise to good folding properties. Involving other contacts deteriorates these properties.Comment: REVTeX, 9 pages, 8 EPS figure

Delineation of the Native Basin in Continuum Models of Proteins

We propose two approaches for determining the native basins in off-lattice models of proteins. The first of them is based on exploring the saddle points on selected trajectories emerging from the native state. In the second approach, the basin size can be determined by monitoring random distortions in the shape of the protein around the native state. Both techniques yield the similar results. As a byproduct, a simple method to determine the folding temperature is obtained.Comment: REVTeX, 6 pages, 5 EPS figure

Boundary conditions at a fluid - solid interface

We study the boundary conditions at a fluid-solid interface using molecular dynamics simulations covering a broad range of fluid-solid interactions and fluid densities, and both simple and chain-molecule fluids. The slip length is shown to be independent of the type of flow, but rather is related to the fluid organization near the solid, as governed by the fluid-solid molecular interactions.Comment: REVtex, to appear in Physical Review Letter

Selective function-blocking monoclonal human antibody highlights the important role of membrane type-1 matrix metalloproteinase (MT1-MMP) in metastasis.

The invasion-promoting MT1-MMP is a cell surface-associated collagenase with a plethora of critical cellular functions. There is a consensus that MT1-MMP is a key protease in aberrant pericellular proteolysis in migrating cancer cells and, accordingly, a promising drug target. Because of high homology in the MMP family and a limited success in the design of selective small-molecule inhibitors, it became evident that the inhibitor specificity is required for selective and successful MT1-MMP therapies. Using the human Fab antibody library (over 1.25×109 individual variants) that exhibited the extended, 23-27 residue long, VH CDR-H3 segments, we isolated a panel of the inhibitory antibody fragments, from which the 3A2 Fab outperformed others as a specific and potent, low nanomolar range, inhibitor of MT1-MMP. Here, we report the in-depth characterization of the 3A2 antibody. Our multiple in vitro and cell-based tests and assays, and extensive structural modeling of the antibody/protease interactions suggest that the antibody epitope involves the residues proximal to the protease catalytic site and that, in contrast with tissue inhibitor-2 of MMPs (TIMP-2), the 3A2 Fab inactivates the protease functionality by binding to the catalytic domain outside the active site cavity. In agreement with the studies in metastasis by others, our animal studies in acute pulmonary melanoma metastasis support a key role of MT1-MMP in metastatic process. Conversely, the selective anti-MT1-MMP monotherapy significantly alleviated melanoma metastatic burden. It is likely that further affinity maturation of the 3A2 Fab will result in the lead inhibitor and a proof-of-concept for MT1-MMP targeting in metastatic cancers