Biomedical subjects

Muhammad H Zaman

Publications and source records attributed to Muhammad H Zaman.

10 recordsLinked to original sources

PubMed2006

Understanding the molecular basis for differential binding of integrins to collagen and gelatin.

Integrin-mediated cell adhesion plays a central role in cell migration and signaling. Overexpression of integrins is also associated with cancer invasion and metastasis. Although a number of problems in integrin-matrix interactions have been studied in detail, the molecular specificity, which increases integrin adhesion to native collagen but results in poor integrin-gelatin interaction, is not understood. In this report, we study the role of individual amino acids in integrin-collagen and integrin-gelatin interactions using long-term (>100 ns) molecular simulations. The results, which are force-field independent, show that denatured collagen induces helical conformations in integrin amino acids and significantly reduces the poly-proline II content, which stabilizes the integrin-collagen interactions. Our simulations provide a possible explanation of the molecular specificity in integrin binding and suggest new targets for regulating integrin-mediated invasion and metastasis.

Binding Sites↗

PubMed2006

Understanding effects of matrix protease and matrix organization on directional persistence and translational speed in three-dimensional cell migration.

Recent studies have shown significant differences in migration mechanisms between two- and three-dimensional environments. While experiments have suggested a strong dependence of in vivo migration on both structure and proteolytic activity, the underlying biophysics of such dependence has not been studied adequately. In addition, the existing models of persistent random walk migration are primarily based on two-dimensional movement and do not account for the effect of proteolysis or matrix inhomogeneity. Using lattice Monte Carlo methods, we present a model to study the role of matrix metallo-proteases (MMPs) on directional persistence and speed. The simulations account for a given cell's ability to deform as well as to digest the matrix as the cell moves in three dimensions. Our results show a bimodal dependence of speed and persistence on matrix pore size and suggest high sensitivity on MMP activity, which is in very good agreement with experimental studies carried out in 3D matrices.

Cell Movement↗

PubMed2006

Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis.

Cell migration on 2D surfaces is governed by a balance between counteracting tractile and adhesion forces. Although biochemical factors such as adhesion receptor and ligand concentration and binding, signaling through cell adhesion complexes, and cytoskeletal structure assembly/disassembly have been studied in detail in a 2D context, the critical biochemical and biophysical parameters that affect cell migration in 3D matrices have not been quantitatively investigated. We demonstrate that, in addition to adhesion and tractile forces, matrix stiffness is a key factor that influences cell movement in 3D. Cell migration assays in which Matrigel density, fibronectin concentration, and beta1 integrin binding are systematically varied show that at a specific Matrigel density the migration speed of DU-145 human prostate carcinoma cells is a balance between tractile and adhesion forces. However, when biochemical parameters such as matrix ligand and cell integrin receptor levels are held constant, maximal cell movement shifts to matrices exhibiting lesser stiffness. This behavior contradicts current 2D models but is predicted by a recent force-based computational model of cell movement in a 3D matrix. As expected, this 3D motility through an extracellular environment of pore size much smaller than cellular dimensions does depend on proteolytic activity as broad-spectrum matrix metalloproteinase (MMP) inhibitors limit the migration of DU-145 cells and also HT-1080 fibrosarcoma cells. Our experimental findings here represent, to our knowledge, discovery of a previously undescribed set of balances of cell and matrix properties that govern the ability of tumor cells to migration in 3D environments.

Cell Adhesion↗

PubMed2006

A high-throughput migration assay reveals HER2-mediated cell migration arising from increased directional persistence.

Human epidermal growth factor receptor 2 (HER2) overexpression has been associated with increased invasiveness in mammalian breast cancer cell lines, but the effects of overexpression on key underlying cell migration properties such as translational speed and directional persistence are not understood. Moreover, the differential effect of HER2 activation through heterodimerization with epidermal growth factor receptor versus human epidermal growth factor receptor 3 (HER3) on cell speed and persistence has not been studied. To investigate these issues, we developed a high-throughput wound closure assay in which individual cell locomotion and wound closure kinetics were quantified in human mammary epithelial cells with varying levels of HER2 under epidermal growth factor or heregulin (a HER3 ligand) stimulation. Increasing levels of HER2 elevated wound closure with closure kinetics dependent on ligand treatment. Cell speed increased with HER2 levels under epidermal growth factor treatment, but decreased under heregulin treatment. In contrast, directional persistence increased with HER2 levels under both ligand treatments. Increasing persistence quantitatively accounted for observed elevated wound closure, as measured by the effective diffusion of the cells. Taken together, the data show that the HER2 overexpression mediates cell migration through differential control of translational speed and directional persistence dependent on epidermal growth factor receptor-HER2 versus HER2-HER3 heterodimerization. Observed consistent increases in persistence associated with HER2 overexpression indicate a prospective mechanism for invasiveness previously documented in HER2-overexpressing human breast tumors.

Biological Assay↗

PubMed2005

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library.

A central issue in protein folding is the degree to which each residue's backbone conformational preferences stabilize the native state. We have studied the conformational preferences of each amino acid when the amino acid is not constrained to be in a regular secondary structure. In this large but highly restricted coil library, the backbone preferentially adopts dihedral angles consistent with the polyproline II conformation rather than alpha or beta conformations. The preference for the polyproline II conformation is independent of the degree of solvation. In conjunction with a new masking procedure, the frequencies in our coil library accurately recapitulate both helix and sheet frequencies for the amino acids in structured regions, as well as polyproline II propensities. Therefore, structural propensities for alpha-helices and beta-sheets and for polyproline II conformations in unfolded peptides can be rationalized solely by local effects. In addition, these propensities are often strongly affected by both the chemical nature and the conformation of neighboring residues, contrary to the Flory isolated residue hypothesis.

Computational Biology↗

PubMed2005

Computational model for cell migration in three-dimensional matrices.

Although computational models for cell migration on two-dimensional (2D) substrata have described how various molecular and cellular properties and physiochemical processes are integrated to accomplish cell locomotion, the same issues, along with certain new ones, might contribute differently to a model for migration within three-dimensional (3D) matrices. To address this more complicated situation, we have developed a computational model for cell migration in 3D matrices using a force-based dynamics approach. This model determines an overall locomotion velocity vector, comprising speed and direction, for individual cells based on internally generated forces transmitted into external traction forces and considering a timescale during which multiple attachment and detachment events are integrated. Key parameters characterize cell and matrix properties, including cell/matrix adhesion and mechanical and steric properties of the matrix; critical underlying molecular properties are incorporated explicitly or implicitly. Model predictions agree well with experimental results for the limiting case of migration on 2D substrata as well as with recent experiments in 3D natural tissues and synthetic gels. Certain predicted features such as biphasic behavior of speed with density of matrix ligands for 3D migration are qualitatively similar to their 2D counterparts, but new effects generally absent in 2D systems, such as effects due to matrix sterics and mechanics, are now predicted to arise in many 3D situations. As one particular sample manifestation of these effects, the optimal levels of cell receptor expression and matrix ligand density yielding maximal migration are dependent on matrix mechanical compliance.

Animals↗

PubMed2005

Misfolding dynamics of human prion protein.

We report the results of longest to date simulation on misfolding of monomeric human prion protein (HuPrP). By comparing our simulation of a partially unfolded protein to the simulation of the native protein, we observe that the native protein as well as native regions in the partially unfolded protein remain in the native state, and the unfolded regions fold back with increased extended (sheet and PP-II) conformations. The misfolded regions show increased basin hopping from non-helical basins while the amino acids locked in the helical conformation tend to stay locked in that conformation. Our results also validate the hypothesis that denaturation of helices and formation of a partially unfolded intermediate is required for misfolding as the native protein stayed in native conformation for the entire simulation. Finally, we also observe that there is no correlation between misfolding and the chemical identity of amino acids, as both hydrophobic and hydrophilic amino acids showed equal probability of sampling extensively from non-native conformations.

Amino Acids↗

PubMed2004

How flexible is alpha-actinin's rod domain?

Alpha-actinin, an actin binding protein, plays a key role in cell migration, cross-links actin filaments in the Z-disk, and is a major component of contractile muscle apparatus. The flexibility of the molecule is critical to its function. The flexibility of various regions of the molecule, including the linker connecting central subunits is studied using constant force steered molecular dynamics simulations. The linker, whose structure has been a subject of debate, is predicted to be semi-flexible. The flexibility of the linker is compared to all possible segments of equal length throughout the molecule. The stretching profile of the molecule at different forces suggests that loops and regions adjacent to the loops are much more rigid than the helices in the protein. Amino acid composition analysis of most flexible and most rigid regions of the molecule reveals that the rigid regions are rich in Ser, Val and Ile whereas the flexible regions are rich in Ala, Leu and Glu.

Actins↗

PubMed2003

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides.

The populations and transitions between Ramachandran basins are studied for combinations of the standard 20 amino acids in monomers, dimers and trimers using an implicit solvent Langevin dynamics algorithm and employing seven commonly used force-fields. Both the basin populations and inter-conversion rates are influenced by the nearest neighbor's conformation and identity, contrary to the Flory isolated-pair hypothesis. This conclusion is robust to the choice of force-field, even though the use of different force-fields produces large variations in the populations and inter-conversion rates between the dominant helical, extended beta, and polyproline II basins. The computed variation of conformational and dynamical properties with different force-fields exceeds the difference between explicit and implicit solvent calculations using the same force-field. For all force-fields, the inter-basin transitions exhibit a directional dependence, with most transitions going through extended beta conformation, even when it is the least populated basin. The implications of these results are discussed in the context of estimates for the backbone entropy of single residues, and for the ability of all-atom simulations to reproduce experimental protein folding data.

Algorithms↗

PubMed2002

Entropic benefit of a cross-link in protein association.

We introduce a method to estimate the loss of configurational entropy upon insertion of a cross-link to a dimeric system. First, a clear distinction is established between the loss of entropy upon tethering and binding, two quantities that are often considered to be equivalent. By comparing the probability distribution of the center-to-center distances for untethered and cross-linked versions, we are able to calculate the loss of translational entropy upon cross-linking. The distribution function for the untethered helices is calculated from the probability that a given helix is closer to its partner than to all other helices, the "Nearest Neighbor" method. This method requires no assumptions about the nature of the solvent, and hence resolves difficulties normally associated with calculations for systems in liquids. Analysis of the restriction of angular freedom upon tethering indicates that the loss of rotational entropy is negligible. The method is applied in the context of the folding of a ten turn helical coiled coil with the tether modeled as a Gaussian chain or a flexible amino acid chain. After correcting for loop closure entropy in the docked state, we estimate the introduction of a six-residue tether in the coiled coil results in an effective concentration of the chain to be about 4 or 100 mM, depending upon whether the helices are denatured or pre-folded prior to their association. Thus, tethering results in significant stabilization for systems with millimolar or stronger dissociation constants.

Dimerization↗