All Publications


  • Regulation and dynamics of force transmission at individual cell-matrix adhesion bonds. Science advances Tan, S. J., Chang, A. C., Anderson, S. M., Miller, C. M., Prahl, L. S., Odde, D. J., Dunn, A. R. 2020; 6 (20): eaax0317

    Abstract

    Integrin-based adhesion complexes link the cytoskeleton to the extracellular matrix (ECM) and are central to the construction of multicellular animal tissues. How biological function emerges from the tens to thousands of proteins present within a single adhesion complex remains unclear. We used fluorescent molecular tension sensors to visualize force transmission by individual integrins in living cells. These measurements revealed an underlying functional modularity in which integrin class controlled adhesion size and ECM ligand specificity, while the number and type of connections between integrins and F-actin determined the force per individual integrin. In addition, we found that most integrins existed in a state of near-mechanical equilibrium, a result not predicted by existing models of cytoskeletal force transduction. A revised model that includes reversible cross-links within the F-actin network can account for this result and suggests one means by which cellular mechanical homeostasis can arise at the molecular level.

    View details for DOI 10.1126/sciadv.aax0317

    View details for PubMedID 32440534

    View details for PubMedCentralID PMC7228748

  • Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics JOURNAL OF CHEMICAL THEORY AND COMPUTATION Zerze, G. H., Miller, C. M., Granata, D., Mittal, J. 2015; 11 (6): 2776-2782
  • Role of solvation in pressure-induced helix stabilization JOURNAL OF CHEMICAL PHYSICS Best, R. B., Miller, C., Mittal, J. 2014; 141 (22)

    Abstract

    In contrast to the well-known destabilization of globular proteins by high pressure, recent work has shown that pressure stabilizes the formation of isolated α-helices. However, all simulations to date have obtained a qualitatively opposite result within the experimental pressure range. We show that using a protein force field (Amber03w) parametrized in conjunction with an accurate water model (TIP4P/2005) recovers the correct pressure-dependence and an overall stability diagram for helix formation similar to that from experiment; on the other hand, we confirm that using TIP3P water results in a very weak pressure destabilization of helices. By carefully analyzing the contributing factors, we show that this is not merely a consequence of different peptide conformations sampled using TIP3P. Rather, there is a critical role for the solvent itself in determining the dependence of total system volume (peptide and solvent) on helix content. Helical peptide structures exclude a smaller volume to water, relative to non-helical structures with both the water models, but the total system volume for helical conformations is higher than non-helical conformations with TIP3P water at low to intermediate pressures, in contrast to TIP4P/2005 water. Our results further emphasize the importance of using an accurate water model to study protein folding under conditions away from standard temperature and pressure.

    View details for DOI 10.1063/1.4901112

    View details for Web of Science ID 000346272800069

    View details for PubMedID 25494793

  • Disorder in Cholesterol-Binding Functionality of CRAC Peptides: A Molecular Dynamics Study JOURNAL OF PHYSICAL CHEMISTRY B Miller, C. M., Brown, A. C., Mittal, J. 2014; 118 (46): 13169-13174

    Abstract

    The cholesterol recognition/interaction amino acid consensus (CRAC) motif is a primary structure pattern used to identify regions that may be responsible for preferential cholesterol binding in many proteins. The leukotoxin LtxA, which is produced by a pathogenic bacterium, contains two CRAC seqences, only one of which is responsible for cholesterol binding, and the binding is required for cytotoxicity. The factors, in addition to the CRAC definition, that may be responsible for cholesterol-binding functionality and atomistic interactions between the CRAC region and cholesterol are as yet unknown. This study uses molecular dynamics simulations to identify structural characteristics and specific interactions of the two LtxA CRAC peptides with both pure phospholipid and binary cholesterol-phospholipid bilayers. We have identified changes in the secondary structure of these peptides that occur upon cholesterol binding, which are not seen when it is associated with a cholesterol-devoid membrane, and which show salient coupling of structural disorder and function. Additionally, the central tyrosine residue of the CRAC motif was found to play a significant role in cholesterol binding, though residues outside of the CRAC motif also influence membrane interactions and functionality of the CRAC region.

    View details for DOI 10.1021/jp5106423

    View details for Web of Science ID 000345468600015

    View details for PubMedID 25347282

  • Molecular Simulations Indicate Marked Differences in the Structure of Amylin Mutants, Correlated with Known Aggregation Propensity JOURNAL OF PHYSICAL CHEMISTRY B Miller, C., Zerze, G. H., Mittal, J. 2013; 117 (50): 16066-16075

    Abstract

    Human islet amyloid polypeptide (hIAPP), a 37-residue protein cosecreted with insulin by β-cells in the pancreas, is known to form amyloid fibrils in type II diabetes patients. This fibril formation is also associated with β-cell death. However, rat IAPP (rIAPP) does not aggregate into fibrils, nor is it associated with β-cell toxicity. Determining solution properties of hIAPP experimentally is difficult because it aggregates quickly. Our study uses molecular dynamics simulation to explore and compare in-solution characteristics of hIAPP and rIAPP, as well as two single-point hIAPP mutants, hIAPP I26P and hIAPP S20G, which exhibit observed differences from hIAPP in aggregation propensities. We find that all four polypeptide monomers sample structured states in solution. More importantly, differences in the helicity over residues 7-16 may play an important role in early aggregation, although this region is outside of commonly assumed amyloidogenic region 20-29. The long-range contacts, though unexpected of IDPs, cause variation in sampled conformations among four polypeptides within same amino acid sequence. Our results also yield evidence that previously determined structures bound to micelles are also transiently sampled in the solution state. In particular, similarities found in region 8-17 together with the helical differences that we observe in region 7-16 lead us to suggest that the region 7-16 is potentially responsible for amyloidogenic behavior of amylin peptides. Our results also provide support for the proposed mechanism of fibril formation based on experimentally observed transient helices in amyloidogenic peptides.

    View details for DOI 10.1021/jp409755y

    View details for Web of Science ID 000328920600015

    View details for PubMedID 24245879