Muhammad H Zaman
Affiliation: Massachusetts Institute of Technology
- Computational model for cell migration in three-dimensional matricesMuhammad H Zaman
Whitehead Institute for Biomedical Research, Biological Engineering Division, Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, 02142, USA
Biophys J 89:1389-97. 2005..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...
- Misfolding dynamics of human prion proteinMuhammad H Zaman
Whitehead Institute and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Mol Cell Biomech 2:179-90. 2005....
- Microarchitecture of three-dimensional scaffolds influences cell migration behavior via junction interactionsBrendan A C Harley
Department of Mechanical Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Biophys J 95:4013-24. 2008..Strut junction interactions affect local directional persistence as well as cell speed at and away from the junctions, providing a new biophysical mechanism for the governance of cell motility by the extracellular microstructure...
- Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysisMuhammad H Zaman
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 103:10889-94. 2006..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...
- Interplay of active processes modulates tension and drives phase transition in self-renewing, motor-driven cytoskeletal networksMichael Mak
Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Nat Commun 7:10323. 2016..The consequence is versatile functionality, from dynamic steady-state prestress to large, pulsed constrictions. ..
- How flexible is alpha-actinin's rod domain?Muhammad H Zaman
Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
Mech Chem Biosyst 1:291-302. 2004..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...
- Multiscale mechanobiology: computational models for integrating molecules to multicellular systemsMichael Mak
Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
Integr Biol (Camb) 7:1093-108. 2015..Here we review recent advances in these models along with supporting and emerging experimental findings. ..
- Impact of dimensionality and network disruption on microrheology of cancer cells in 3D environmentsMichael Mak
Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
PLoS Comput Biol 10:e1003959. 2014..Our computational results and modeling show that motor-induced active stress fluctuations are enhanced in 2D, leading to increased local intracellular particle fluctuations and apparent fluid-like behavior. ..
- A high-throughput migration assay reveals HER2-mediated cell migration arising from increased directional persistenceNeil Kumar
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Biophys J 91:L32-4. 2006..Observed consistent increases in persistence associated with HER2 overexpression indicate a prospective mechanism for invasiveness previously documented in HER2-overexpressing human breast tumors...
- Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptidesMuhammad H Zaman
Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
J Mol Biol 331:693-711. 2003..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...
- Understanding effects of matrix protease and matrix organization on directional persistence and translational speed in three-dimensional cell migrationMuhammad H Zaman
Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
Ann Biomed Eng 35:91-100. 2007..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...
- Free energy landscape of receptor-mediated cell adhesionTianyi Yang
Department of Physics, The University of Texas at Austin, Austin, Texas 78712, USA
J Chem Phys 126:045103. 2007..The authors' results not only provide a fundamental understanding of adhesion at the molecular level but also suggest possible strategies for designing novel biomaterials...
- Dependence of invadopodia function on collagen fiber spacing and cross-linking: computational modeling and experimental evidenceHeiko Enderling
Center of Cancer Systems Biology, Caritas St Elizabeth s Medical Center, Tufts University School of Medicine, Boston, Massachusetts 02135, USA
Biophys J 95:2203-18. 2008..These results provide a novel framework for further studies on ECM structure and modifications that affect invadopodia and tissue invasion by cells...
- Cell adhesion to nanoligands: effects of ligand size and concentration in solutionTianyi Yang
Department of Physics, and Institute for Theoretical Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
Langmuir 24:11819-27. 2008..Our calculations provide insights into understanding cell-matrix interactions at a fundamental level as well as to identify potential avenues for fabrication of nanoligands for therapeutic and biotechnological purposes...
- Computer simulations in connective tissue research: successes and challengesMuhammad H Zaman
Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
Connect Tissue Res 49:162-4. 2008....
- A multiscale probabilisitic framework to model early steps in tumor metastasisMuhammad H Zaman
Department of Biomedical Engineering and Institute of Theoretical Chemistry, The University of Texas at Austin, Austin 78712, USA
Mol Cell Biomech 4:133-41. 2007..The model is first of its kind in capturing the essential early features of metastasis in a single simulation and shows good agreement with recent experimental studies...
- Understanding the molecular basis for differential binding of integrins to collagen and gelatinMuhammad H Zaman
Biophys J 92:L17-9. 2007..Our simulations provide a possible explanation of the molecular specificity in integrin binding and suggest new targets for regulating integrin-mediated invasion and metastasis...
- Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil libraryAbhishek K Jha
Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
Biochemistry 44:9691-702. 2005..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...
- Entropic benefit of a cross-link in protein associationMuhammad H Zaman
Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
Proteins 48:341-51. 2002..Thus, tethering results in significant stabilization for systems with millimolar or stronger dissociation constants...