arXiv subjects

Bartosz Rozycki

Publications and source records attributed to Bartosz Rozycki.

12 recordsLinked to original sources

arXiv2019

Binding and segregation of proteins in membrane adhesion: Theory, modelling, and simulations

The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes, which leads to an interplay between protein binding and membrane shape. In this article, we review current models of biomembrane adhesion and novel insights obtained from the models. Theory and simulations with elastic-membrane and coarse-grained molecular models of biomembrane adhesion indicate that the binding of proteins in membrane adhesion strongly depends on nanoscale shape fluctuations of the apposing membranes, which results in binding cooperativity. A length mismatch between protein complexes leads to repulsive interactions that are caused by membrane bending and act as a driving force for the length-based segregation of proteins during membrane adhesion.

q-bio.SC↗

arXiv2016

Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A

Cellulosomes are complex multi-enzyme machineries which efficiently degrade plant cell-wall polysaccharides. The multiple domains of the cellulosome proteins are often tethered together by intrinsically disordered regions. The properties and functions of these disordered linkers are not well understood. In this work, we study endoglucanase Cel8A, which is a relevant enzymatic component of the cellulosomes of Clostridium thermocellum. We use both all-atom and coarse-grained simulations to investigate how the equilibrium conformations of the catalytic domain of Cel8A are affected by the disordered linker at its C terminus. We find that when the endoglucanase is bound to its substrate, the effective stiffness of the linker can influence the distances between groups of amino-acid residues throughout the entire enzymatic domain. In particular, variations in the linker stiffness can lead to small changes in the geometry of the active-site cleft. We suggest that such geometrical changes may, in turn, have an effect on the catalytic activity of the enzyme.

q-bio.BM↗

arXiv2015

Unbinding and unfolding of adhesion protein complexes through stretching: Interplay between shear and tensile mechanical clamps

Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor on natural killer cells whereas CD48 is expressed on surfaces of various immune cells. So far, its mechanostability has not been assessed either experimentally or theoretically. We find that the dissociation processes strongly depend on the direction of pulling and may take place in several pathways. Interestingly, the CD48-2B4 interface can be divided into three distinct patches that act as units when resisting the pulling forces. At experimentally accessible pulling speeds, the characteristic mechanostability forces are in the range between 100 and 200 pN, depending on the pulling direction. These characteristic forces need not be associated with tensile forces involved in the act of separation of the complex because prior shear-involving unraveling within individual proteins may give rise to a higher force peak.

q-bio.BM↗

arXiv2015

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acids contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility and collective motions of the different forms of the enzyme.

q-bio.BM↗

arXiv2010

Segregation of receptor-ligand complexes in cell adhesion zones: Phase diagrams and role of thermal membrane roughness

The adhesion zone of immune cells, the 'immunological synapse', exhibits characteristic domains of receptor-ligand complexes. The domain formation is likely caused by a length difference of the receptor-ligand complexes, and has been investigated in experiments in which T cells adhere to supported membranes with anchored ligands. For supported membranes with two types of anchored ligands, MHCp and ICAM1, that bind to the receptors TCR and LFA1 in the cell membrane, the coexistence of domains of TCR-MHCp and LFA1-ICAM1 complexes in the cell adhesion zone has been observed for a wide range of ligand concentrations and affinities. For supported membranes with long and short ligands that bind to the same cell receptor CD2, in contrast, domain coexistence has been observed for a rather narrow ratio of ligand concentrations. In this article, we determine detailed phase diagrams for cells adhering to supported membranes with a statistical-physical model of cell adhesion. We find a characteristic difference between the adhesion scenarios in which two types of ligands in a supported membrane bind (i) to the same cell receptor or (ii) to two different cell receptors, which helps to explain the experimental observations. Our phase diagrams fully include thermal shape fluctuations of the cell membranes on nanometer scales, which lead to a critical point for the domain formation and to a cooperative binding of the receptors and ligands.

cond-mat.soft↗

arXiv2009

Adhesion of surfaces via particle adsorption: Exact results for a lattice of fluid columns

We present here exact results for a one-dimensional gas, or fluid, of hard-sphere particles with attractive boundaries. The particles, which can exchange with a bulk reservoir, mediate an interaction between the boundaries. A two-dimensional lattice of such one-dimensional gas `columns' represents a discrete approximation of a three-dimensional gas of particles between two surfaces. The effective particle-mediated interaction potential of the boundaries, or surfaces, is calculated from the grand-canonical partition function of the one-dimensional gas of particles, which is an extension of the well-studied Tonks gas. The effective interaction potential exhibits two minima. The first minimum at boundary contact reflects depletion interactions, while the second minimum at separations close to the particle diameter results from a single adsorbed particle that crosslinks the two boundaries. The second minimum is the global minimum for sufficiently large binding energies of the particles. Interestingly, the effective adhesion energy corresponding to this minimum is maximal at intermediate concentrations of the particles.

cond-mat.stat-mech↗

arXiv2009

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.

cond-mat.soft↗

arXiv2009

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.

cond-mat.soft↗

arXiv2008

Effective surface interactions mediated by adhesive particles

In biomimetic and biological systems, interactions between surfaces are often mediated by adhesive molecules, nanoparticles, or colloids dispersed in the surrounding solution. We present here a general, statistical-mechanical model for two surfaces that interact via adhesive particles. The effective, particle-mediated interaction potential of the surfaces is obtained by integrating over the particles' degrees of freedom in the partition function. Interestingly, the effective adhesion energy of the surfaces exhibits a maximum at intermediate particle concentrations, and is considerably smaller both at low and high concentrations. The effective adhesion energy corresponds to a minimum in the interaction potential at surface separations slightly larger than the particle diameter, while a secondary minimum at surface contact reflects depletion interactions. Our results can be generalized to surfaces with specific receptors for solute particles, and have direct implications for the adhesion of biomembranes and for phase transitions in colloidal systems.

cond-mat.soft↗

arXiv2008

Stable patterns of membrane domains at corrugated substrates

Multi-component membranes such as ternary mixtures of lipids and cholesterol can exhibit coexistence regions between two liquid phases. When such membranes adhere to a corrugated substrate, the phase separation process strongly depends on the interplay between substrate topography, bending rigidities, and line tension of the membrane domains as we show theoretically via energy minimization and Monte Carlo simulations. For sufficiently large bending rigidity contrast between the two membrane phases, the corrugated substrate truncates the phase separation process and leads to a stable pattern of membrane domains. Our theory is consistent with recent experimental observations and provides a possible control mechanism for domain patterns in biological membranes.

cond-mat.soft↗

arXiv2006

Membrane adhesion via competing receptor/ligand bonds

The adhesion of biological membranes is controlled by various types of receptor and ligand molecules. In this letter, we present a statistical-mechanical model for membranes that interact via receptor/ligand bonds of two different lengths. We show that the equilibrium phase behavior of the membranes is governed by an effective double-well potential. The depths of the two potential wells depend on the concentrations and binding energies of the receptors and ligands. The membranes are unbound for small, and bound for larger potential depths. In the bound state, the length mismatch of the receptor/ligand bonds can lead to lateral phase separation. We derive explicit scaling laws for the critical points of unbinding and phase separation, and determine the prefactors by comparison with Monte Carlo results.

cond-mat.soft↗

arXiv2005

Adhesion of membranes via actively switched receptors

We consider a theoretical model for membranes with adhesive receptors, or stickers, that are actively switched between two conformational states. In their 'on'-state, the stickers bind to ligands in an apposing membrane, whereas they do not interact with the ligands in their 'off'-state. We show that the adhesiveness of the membranes depends sensitively on the rates of the conformational switching process. This dependence is reflected in a resonance at intermediate switching rates, which can lead to large membrane separations and unbinding. Our results may provide insights into novel mechanisms for the controlled adhesion of biological or biomimetic membranes.

cond-mat.soft↗