Line Tension and Stability of Domains in Cell-Adhesion Zones Mediated by Long and Short Receptor-Ligand Complexes

Submicron scale domains of membrane-anchored receptors play an important role in cell signaling. Central questions concern the stability of these microdomains, and the mechanisms leading to the domain formation. In immune-cell adhesion zones, microdomains of short receptor-ligand complexes form next to domains of significantly longer receptor-ligand complexes. The length mismatch between the receptor-ligand complexes leads to membrane deformations and has been suggested as a possible cause of the domain formation. The domain formation is a nucleation and growth process that depends on the line tension and free energy of the domains. Using a combination of analytical calculations and Monte Carlo simulations, we derive here general expressions for the line tension between domains of long and short receptor-ligand complexes and for the adhesion free energy of the domains. We argue that the length mismatch of receptor-ligand complexes alone is sufficient to drive the domain formation, and obtain submicron-scale minimum sizes for stable domains that are consistent with the domain sizes observed during immune-cell adhesion

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior

A major component of ex vivo amyloid plaques of patients with dialysis-related amyloidosis (DRA) is a cleaved variant of β2-microglobulin (ΔN6) lacking the first six N-terminal residues. Here we perform a computational study on ΔN6, which provides clues to understand the amyloidogenicity of the full-length β2-microglobulin. Contrary to the wild-type form, ΔN6 is able to efficiently nucleate fibrillogenesis in vitro at physiological pH. This behavior is enhanced by a mild acidification of the medium such as that occurring in the synovial fluid of DRA patients. Results reported in this work, based on molecular simulations, indicate that deletion of the N-terminal hexapeptide triggers the formation of an intermediate state for folding and aggregation with an unstructured strand A and a native-like core. Strand A plays a pivotal role in aggregation by acting as a sticky hook in dimer assembly. This study further predicts that the detachment of strand A from the core is maximized at pH 6.2 resulting into higher aggregation efficiency. The structural mapping of the dimerization interface suggests that Tyr10, His13, Phe30 and His84 are hot-spot residues in ΔN6 amyloidogenesis

Binding cooperativity of membrane adhesion receptors

The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is typically quantified by the binding equilibrium constant K3D in the linear relation [RL] = K3D [R][L] between the volume concentration [RL] of bound complexes and the volume concentrations [R] and [L] of unbound molecules. For membrane-anchored molecules, it is often assumed by analogy that the area concentration of bound complexes [RL] is proportional to the product [R][L] of the area concentrations for the unbound receptor and ligand molecules. We show here (i) that this analogy is only valid for two planar membranes immobilized on rigid surfaces, and (ii) that the thermal roughness of flexible membranes leads to cooperative binding of receptors and ligands. In the case of flexible membranes, the area concentration [RL] of receptor-ligand bonds is proportional to the square of [R][L] for typical lengths and concentrations of receptors and ligands in cell adhesion zones. The cooperative binding helps to understand why different experimental methods for measuring the binding affinity of membrane-anchored molecules have led to values differing by several orders of magnitude.Comment: 9 pages, 4 figures; to appear in Soft Matte

Adhesion of membranes via receptor-ligand complexes: Domain formation, binding cooperativity, and active processes

Cell membranes interact via anchored receptor and ligand molecules. Central questions on cell adhesion concern the binding affinity of these membrane-anchored molecules, the mechanisms leading to the receptor-ligand domains observed during adhesion, and the role of cytoskeletal and other active processes. In this review, these questions are addressed from a theoretical perspective. We focus on models in which the membranes are described as elastic sheets, and the receptors and ligands as anchored molecules. In these models, the thermal membrane roughness on the nanometer scale leads to a cooperative binding of anchored receptor and ligand molecules, since the receptor-ligand binding smoothens out the membranes and facilitates the formation of additional bonds. Patterns of receptor domains observed in Monte Carlo simulations point towards a joint role of spontaneous and active processes in cell adhesion. The interactions mediated by the receptors and ligand molecules can be characterized by effective membrane adhesion potentials that depend on the concentrations and binding energies of the molecules.Comment: Review article, 13 pages, 9 figures, to appear in Soft Matte

How determinant is N-terminal to C-terminal coupling for protein folding?

This work investigates the role of N- to C- termini coupling in the folding transition of small, single domain proteins via extensive Monte Carlo simulations of both lattice and off-lattice models. The reported results provide compelling evidence that the existence of native interactions between the terminal regions of the polypeptide chain (i.e. termini coupling) is a major determinant of the height of the free energy barrier that separates the folded from the denatured state in a two-state folding transition, therefore being a critical modulator of protein folding rates and thermodynamic cooperativity. We further report that termini interactions are able to substantially modify the kinetic behavior dictated by the full set of native interactions. Indeed, a native structure of high contact order with ‘‘switched-off’’ termini-interactions actually folds faster than its circular permutant of lowest CO

Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches

<div><p>Deciphering the effects of nonsynonymous mutations on protein structure is central to many areas of biomedical research and is of fundamental importance to the study of molecular evolution. Much of the investigation of protein evolution has focused on mutations that leave a protein’s folded structure essentially unchanged. However, to evolve novel folds of proteins, mutations that lead to large conformational modifications have to be involved. Unraveling the basic biophysics of such mutations is a challenge to theory, especially when only one or two amino acid substitutions cause a large-scale conformational switch. Among the few such mutational switches identified experimentally, the one between the G_A all-α and G_B α+β folds is extensively characterized; but all-atom simulations using fully transferrable potentials have not been able to account for this striking switching behavior. Here we introduce an explicit-chain model that combines structure-based native biases for multiple alternative structures with a general physical atomic force field, and apply this construct to twelve mutants spanning the sequence variation between G_A and G_B. In agreement with experiment, we observe conformational switching from G_A to G_B upon a single L45Y substitution in the GA98 mutant. In line with the latent evolutionary potential concept, our model shows a gradual sequence-dependent change in fold preference in the mutants before this switch. Our analysis also indicates that a sharp G_A/G_B switch may arise from the orientation dependence of aromatic π-interactions. These findings provide physical insights toward rationalizing, predicting and designing evolutionary conformational switches.</p></div

Rationalization of the G_A/G_B switch and model prediction of incremental stabilization of the alternate fold.

<p>(a) Free energy landscapes as a function of the progress variables Q_A and Q_B are simulated in our hybrid model (ε_B = −0.37). The Q_A/Q_B scale (bottom-left axes for GBwt) is identical for all GA/GB variants. Free energy, in units of <i>k</i>_B<i>T</i>, is the negative natural logarithm of the sampled population (<i>Methods</i>). For each sequence, this quantity is computed for points on a ~100×100 grid at the sequence’s melting temperature <i>T</i>_m. The free energies for the grid points are plotted according to the color code on the right, with the lowest free energy on the grid normalized to zero for each sequence. Note that all resulting free energy values ≥ 6 are shown in the same color. (b) Free energy differences ΔF(G_A-G_B). (c) Comparing sequence-dependent <i>T</i>_ms from experiment and simulation, each normalized to the range defined by GA77 (set to 1) and GB98 (set to 0). The <i>T</i>_m values in (c) are in an arbitrary unit for a non-absolute temperature scale. (d) Scatter plot between absolute melting temperatures in simulation (model unit) and in experiment (in K). The experimental <i>T</i>_ms used in the comparison in (c) and (d) are from refs. [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004960#pcbi.1004960.ref019" target="_blank">19</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004960#pcbi.1004960.ref020" target="_blank">20</a>].</p

Effect of a rudimentary π-π potential for Phe (F) and Tyr (Y) residues on the G_A/G_B switch.

<p>(a) Three geometric variables are used to characterize the relative position and orientation of a pair of aromatic rings in F or Y: center-to-center distance <i>r</i> (spatial separation between the centers of the two rings), planar tilt angle <i>θ</i>, and center dislocation angle <i>φ</i>. (b) PDB statistics for F-F, Y-Y, and F-Y contacts were used to derive an interaction strength of the π-π potential as a function of <i>r</i>, <i>θ</i>, and <i>φ</i>. The vertical variable here corresponds to |<i>E</i>_ππ(<i>r</i>, <i>θ</i>, <i>φ</i>)/<i>ε</i>_ππ| defined in <i>Methods</i>. (c) Difference landscape for the L45Y mutation. Free energy of GB98 minus free energy of GA98 as a function of Q_A and Q_B computed in our hybrid model with two different transferrable components: the original Lund potential (left), and the modified potential (right) that incorporates the F,Y potential with interaction strengths given in (b) and <i>ε</i>_ππ = 1.5.</p

Volumetric Physics of Polypeptide Coil–Helix Transitions

Volumetric properties of proteins bear directly on their biological functions in hyperbaric environments and are useful in general as a biophysical probe. To gain insight into conformation-dependent protein volume, we developed an implicit-solvent atomic chain model that transparently embodies two physical origins of volume: (1) a fundamental geometric term capturing the van der Waals volume of the protein and the particulate, finite-size nature of the water molecules, modeled together by the volume encased by the protein’s molecular surface, and (2) a physicochemical term for other solvation effects, accounted for by empirical proportionality relationships between experimental partial molar volumes and solvent-accessible surface areas of model compounds. We tested this construct by Langevin dynamics simulations of a 16-residue polyalanine. The simulated trajectories indicate an average volume decrease of 1.73 ± 0.1 ų/residue for coil–helix transition, ∼80% of which is caused by a decrease in geometric void/cavity volume, and a robust positive activation volume for helical hydrogen bond formation originating from the transient void created by an approaching donor–acceptor pair and nearby atoms. These findings are consistent with prior experiments with alanine-rich peptides and offer an atomistic analysis of the observed overall volume changes. The results suggest, in general, that hydrostatic pressure likely stabilizes helical conformations of short peptides but slows the process of helix formation. In contrast, hydrostatic pressure is more likely to destabilize natural globular proteins because of the void volume entrapped in their folded structures. The conceptual framework of our model thus affords a coherent physical rationalization for experiments

Free energy landscapes of additional switch sequences in the G_A/G_B system.

<p>Plotted in the same style as that in <b><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004960#pcbi.1004960.g005" target="_blank">Fig 5</a></b>. (a) GB98-T25I (PDB:2LHG). (b) GB98-T25I,L20A (PDB:2LHE). PDB structures in (a) and (b) are depicted by the ribbon diagrams. (c) Predicted switch sequence “S1” prefers G_B whereas (d) sequence “S2” prefers G_A [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004960#pcbi.1004960.ref066" target="_blank">66</a>]. The arrows mark the global minimum in each of the energy landscapes.</p