scholarly journals Force-dependent facilitated dissociation can generate protein-DNA catch bonds

2019 ◽  
Author(s):  
K. Dahlke ◽  
J. Zhao ◽  
C.E. Sing ◽  
E. J. Banigan
Keyword(s):  
Dna Binding ◽  
Protein Concentration ◽  
Molecular Complexes ◽  
Dissociation Pathway ◽  
Extrinsic Factor ◽  
Catch Bond ◽  
Interaction Kinetics ◽  
Protein Dissociation ◽  
Applied Forces ◽  
Catch Bonds

AbstractCellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via “slip bonds,” so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo “facilitated dissociation,” in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a “catch bond,” for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry, and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. These force-dependent kinetics are broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor – competitor proteins – rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.Statement of significanceMechanotransduction regulates chromatin structure and gene transcription. Forces may be transduced via biomolecular interaction kinetics, particularly, how molecular complexes dissociate under stress. Typically, molecules form “slip bonds” that dissociate more rapidly under tension, but some form “catch bonds” that dissociate more slowly under tension due to their internal structure. We develop a model for a distinct type of catch bond that emerges via an extrinsic factor: protein concentration in solution. Underlying this extrinsic catch bond is “facilitated dissociation,” whereby competing proteins from solution accelerate protein-DNA unbinding by invading the DNA binding site. Forces may suppress invasion, inhibiting dissociation, as for catch bonds. Force-dependent facilitated dissociation can thus govern the kinetics of proteins sensitive to local DNA conformation and mechanical state.

scholarly journals Effect of loading conditions on the dissociation behaviour of catch bond clusters

2011 ◽  
Vol 9 (70) ◽  
pp. 928-937 ◽  
Author(s):  
L. Sun ◽  
Q. H. Cheng ◽  
H. J. Gao ◽  
Y. W. Zhang
Keyword(s):  
Multiple Bond ◽  
Tensile Load ◽  
Load Sharing ◽  
Loading Conditions ◽  
Bond Behaviour ◽  
Catch Bond ◽  
Linear Load ◽  
Bond System ◽  
Bond Mechanism ◽  
Catch Bonds

Under increasing tensile load, the lifetime of a single catch bond counterintuitively increases up to a maximum and then decreases exponentially like a slip bond. So far, the characteristics of single catch bond dissociation have been extensively studied. However, it remains unclear how a cluster of catch bonds behaves under tensile load. We perform computational analysis on the following models to examine the characteristics of clustered catch bonds: (i) clusters of catch bonds with equal load sharing, (ii) clusters of catch bonds with linear load sharing, and (iii) clusters of catch bonds in micropipette-manipulated cell detachment. We focus on the differences between the slip and catch bond clusters, identifying the critical factors for exhibiting the characteristics of catch bond mechanism for the multiple-bond system. Our computation reveals that for a multiple-bond cluster, the catch bond behaviour could only manifest itself under relatively uniform loading conditions and at certain stages of decohesion, explaining the difficulties in observing the catch bond mechanism under real biological conditions.

Sliding-Rebinding Mechanism Governs Glycoprotein Ib/von Willebrand Factor Catch Bonds.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3723-3723
Author(s):  
Jizhong Lou ◽  
Cheng Zhu
Keyword(s):  
Crystal Structure ◽  
Von Willebrand Factor ◽  
Bottom Surface ◽  
Dissociation Pathway ◽  
Glycoprotein Ib ◽  
New Interactions ◽  
Von Willebrand ◽  
Willebrand Factor ◽  
Β Sheet ◽  
Catch Bonds

Abstract The interaction of platelet receptor Glycoprotein Ib (GPIb) and the plasma protein von Willebrand factor (VWF) initiates platelet adhesion and agglutination at the site of vascular injury. The binding sites of GPIb and vWF have been mapped to be the N-terminal domain of GPIb α subunit (GPIbαN) and the A1 domain of VWF respectively. The co-crystal structure of wild-type GPIbαN and VWF-A1 complex is solved and two separated binding interfaces have been identified. One is between the β-switch region of GPIbαN and the central β sheet of A1, another is between the β-finger region of GPIbαN and the loops on the bottom of A1. It has been demonstrated that flow enhances GPIb-VWF binding. Moreover, recent single-molecule experiments with atomic force microscopy (AFM) have shown that GPIb forms catch bonds with VWF. Using GPIbαN/VWF-A1 crystal structure, we studied the dissociation of GPIbαN from VWF-A1 with steered molecular dynamics (SMD) simulations. Our results show that the sliding-rebinding mechanism we proposed previously for selectin/ligand catch bonds also operates for the GPIb/VWF system. When force is applied to GPIbαN/VWF-A1 complex, the interactions between GPIbαN β switch and A1 central β sheet dissociate first, this may lead to the sliding of GPIbαN β finger on the A1 bottom surface to allow new interactions formation. The sliding and forming new interactions will in turn enhance the rebinding of GPIbαN β switch and A1 central β sheet and prolong bond lifetime. The N- and C- terminal flanking sequence of A1 serves as a flexible hinge to regulate catch bonds. As shown in the crystal structure, the A1 N-terminal residue D506 interacts with R543 and R687. The presence of these interactions favors the fast-dissociation pathway, while their dissociation signifies the transition to the sliding pathway. Our results have provided an explanation for the AFM experimental data showing that catch bonds were eliminated by two A1 gain-of-function mutants R543Q and R687E, because these single residue replacements eliminate their interaction with D506, making the transition to occur at much lower forces and prolonging bond lifetime at low forces. R543Q mutant naturally occurs in some patients with type 2B von Willebrand disease (VWD) and R687E mutant also exhibits type 2B VWD phenotype. Our results may provide an explanation for type 2B VWD based on the mechanically regulated nonequilibrium structure-function relationship of GPIb/VWF interaction.

scholarly journals Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome

2016 ◽  
Vol 198 (12) ◽  
pp. 1735-1742 ◽  
Author(s):  
Nastaran Hadizadeh ◽  
Reid C. Johnson ◽  
John F. Marko
Keyword(s):  
Gene Regulation ◽  
Dna Binding ◽  
Protein Concentration ◽  
Model Systems ◽  
Bacterial Chromosome ◽  
Regulatory Function ◽  
Content Type ◽  
E Coli ◽  
Dna Double Helix

ABSTRACTOff-rates of proteins from the DNA double helix are widely considered to be dependent only on the interactions inside the initially bound protein-DNA complex and not on the concentration of nearby molecules. However, a number of recent single-DNA experiments have shown off-rates that depend on solution protein concentration, or “facilitated dissociation.” Here, we demonstrate that this effect occurs for the majorEscherichia colinucleoid protein Fis on isolated bacterial chromosomes. We isolatedE. colinucleoids and showed that dissociation of green fluorescent protein (GFP)-Fis is controlled by solution Fis concentration and exhibits an “exchange” rate constant (kexch) of ≈104M−1s−1, comparable to the rate observed in single-DNA experiments. We also show that this effect is strongly salt dependent. Our results establish that facilitated dissociation can be observedin vitroon chromosomes assembledin vivo.IMPORTANCEBacteria are important model systems for the study of gene regulation and chromosome dynamics, both of which fundamentally depend on the kinetics of binding and unbinding of proteins to DNA. In experiments on isolatedE. colichromosomes, this study showed that the prolific transcription factor and chromosome packaging protein Fis displays a strong dependence of its off-rate from the bacterial chromosome on Fis concentration, similar to that observed inin vitroexperiments. Therefore, the free cellular DNA-binding protein concentration can strongly affect lifetimes of proteins bound to the chromosome and must be taken into account in quantitative considerations of gene regulation. These results have particularly profound implications for transcription factors where DNA binding lifetimes can be a critical determinant of regulatory function.

scholarly journals Demonstration of catch bonds between an integrin and its ligand

2009 ◽  
Vol 185 (7) ◽  
pp. 1275-1284 ◽  
Author(s):  
Fang Kong ◽  
Andrés J. García ◽  
A. Paul Mould ◽  
Martin J. Humphries ◽  
Cheng Zhu
Keyword(s):  
Active Conformation ◽  
Integrin Α5β1 ◽  
Catch Bond ◽  
Force Microscopy ◽  
Atomic Force ◽  
Force Range ◽  
Integrin Ligand ◽  
Single Bonds ◽  
Catch Bonds ◽  
Bond Region

Binding of integrins to ligands provides anchorage and signals for the cell, making them prime candidates for mechanosensing molecules. How force regulates integrin–ligand dissociation is unclear. We used atomic force microscopy to measure the force-dependent lifetimes of single bonds between a fibronectin fragment and an integrin α5β1-Fc fusion protein or membrane α5β1. Force prolonged bond lifetimes in the 10–30-pN range, a counterintuitive behavior called catch bonds. Changing cations from Ca2+/Mg2+ to Mg2+/EGTA and to Mn2+ caused longer lifetime in the same 10–30-pN catch bond region. A truncated α5β1 construct containing the headpiece but not the legs formed longer-lived catch bonds that were not affected by cation changes at forces <30 pN. Binding of monoclonal antibodies that induce the active conformation of the integrin headpiece shifted catch bonds to a lower force range. Thus, catch bond formation appears to involve force-assisted activation of the headpiece but not integrin extension.

scholarly journals Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands

2017 ◽  
Author(s):  
Jacob Peacock ◽  
James B. Jaynes
Keyword(s):  
Dna Binding ◽  
Complex Formation ◽  
Ternary Complex ◽  
Dissociation Constants ◽  
Cooperative Binding ◽  
List Type ◽  
Improved Method ◽  
Binding Behavior ◽  
Ternary Complex Formation ◽  
Protein Dissociation

ABSTRACTBACKGROUNDThe affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations.METHODSWe use standard computational and mathematical methods, and develop novel methods as described in Results.RESULTSWe explore some complexities of cooperative binding, and develop an improved method for relating in vitro measurements to in vivo function, based on ternary complex formation. We derive expressions for the equilibria among the various complexes, and explore the limitations of binding experiments that model the system using a single parameter. We describe how to use single-ligand binding and ternary complex formation in tandem to determine parameters that have thermodynamic relevance. We develop an improved method for finding both single-ligand dissociation constants and concentrations simultaneously. We show how the cooperativity factor can be found when only one of the single-protein dissociation constants can be measured.CONCLUSIONSThe methods that we develop constitute an optimized approach to accurately model cooperative binding.GENERAL SIGNIFICANCEThe expressions and methods we develop for modeling and analyzing DNA binding and cooperativity are applicable to most cases where multiple ligands bind to distinct sites on a common substrate. The parameters determined using these methods can be fed into models of higher-order cooperativity to increase their predictive power.HIGHLIGHTSHill plots remain prominent in biology, but can mask cooperativityEffective modeling of binding by two ligands requires the use of 3 parametersWe develop novel ways to find these parameters for two cooperating ligandsWe show how they can be used to enhance the power of established methodsWe describe how this framework can be extended to multiple cooperating ligands

scholarly journals Mechanical feedback enables catch bonds to selectively stabilize scanning microvilli at T-cell surfaces

2019 ◽  
Author(s):  
Robert H. Pullen ◽  
Steven M. Abel
Keyword(s):  
T Cells ◽  
Single Molecule ◽  
Physical Mechanism ◽  
Dependent Manner ◽  
Receptor Ligand ◽  
Active Motion ◽  
Bond Behavior ◽  
Applied Forces ◽  
Antigen Presenting ◽  
Catch Bonds

AbstractT cells use microvilli to search the surfaces of antigen-presenting cells for antigenic ligands. The active motion of scanning microvilli provides a force-generating mechanism that is intriguing in light of single-molecule experiments showing that applied forces on stimulatory receptor-ligand bonds increase their lifetimes (catch-bond behavior). In this work, we introduce a theoretical framework to explore the motion of a microvillus tip above an antigen-presenting surface when receptors on the tip stochastically bind to ligands on the surface and dissociate from them in a force-dependent manner. Forces on receptor-ligand bonds impact the motion of the microvillus, leading to feedback between binding and microvillar motion. We use computer simulations to show that the average microvillus velocity varies in a ligand-dependent manner, that catch bonds generate responses in which some microvilli almost completely stop while others move with a broad distribution of velocities, and that the frequency of stopping depends on the concentration of stimulatory ligands. Typically, a small number of catch bonds initially immobilize the microvillus, after which additional bonds accumulate and increase the cumulative receptor-engagement time. Our results demonstrate that catch bonds can selectively slow and stabilize scanning microvilli, suggesting a physical mechanism that may contribute to antigen discrimination by T cells.

scholarly journals Mechanical feedback enables catch bonds to selectively stabilize scanning microvilli at T-cell surfaces

2019 ◽  
Vol 30 (16) ◽  
pp. 2087-2095 ◽  
Author(s):  
Robert H. Pullen ◽  
Steven M. Abel
Keyword(s):  
T Cells ◽  
Single Molecule ◽  
Physical Mechanism ◽  
Dependent Manner ◽  
Receptor Ligand ◽  
Active Motion ◽  
Bond Behavior ◽  
Applied Forces ◽  
Antigen Presenting ◽  
Catch Bonds

T-cells use microvilli to search the surfaces of antigen-presenting cells for antigenic ligands. The active motion of scanning microvilli provides a force-generating mechanism that is intriguing in light of single-molecule experiments showing that applied forces increase the lifetimes of stimulatory receptor–ligand bonds (catch-bond behavior). In this work, we introduce a theoretical framework to explore the motion of a microvillar tip above an antigen-presenting surface when receptors on the tip stochastically bind to ligands on the surface and dissociate from them in a force-dependent manner. Forces on receptor-ligand bonds impact the motion of the microvillus, leading to feedback between binding and microvillar motion. We use computer simulations to show that the average microvillar velocity varies in a ligand-dependent manner; that catch bonds generate responses in which some microvilli almost completely stop, while others move with a broad distribution of velocities; and that the frequency of stopping depends on the concentration of stimulatory ligands. Typically, a small number of catch bonds initially immobilize the microvillus, after which additional bonds accumulate and increase the cumulative receptor-engagement time. Our results demonstrate that catch bonds can selectively slow and stabilize scanning microvilli, suggesting a physical mechanism that may contribute to antigen discrimination by T-cells.

Albumin-Induced Endocytic Vacuoles in Tetrahymena Pyrijormis

1975 ◽  
Vol 33 ◽  
pp. 694-695
Author(s):  
L. J. Brenner ◽  
D. G. Osborne ◽  
B. L. Schumaker
Keyword(s):  
Electron Microscopy ◽  
Bovine Serum Albumin ◽  
Bovine Serum ◽  
Protein Concentration ◽  
Tetrahymena Pyriformis ◽  
Sequence Of Events ◽  
Cytoplasmic Bodies ◽  
Food Vacuoles ◽  
Mouse Ascites ◽  
Normal Human

Exposure of the ciliate, Tetrahymena pyriformis, strain WH6, to normal human or rabbit sera or mouse ascites fluids induces the formation of large cytoplasmic bodies. By electron microscopy these (LB) are observed to be membrane-bounded structures, generally spherical and varying in size (Fig. 1), which do not resemble the food vacuoles of cells grown in proteinaceous broth. The possibility exists that the large bodies represent endocytic vacuoles containing material concentrated from the highly nutritive proteins and lipoproteins of the sera or ascites fluids. Tetrahymena mixed with bovine serum albumin or ovalbumin solutions having about the same protein concentration (7g/100 ml) as serum form endocytic vacuoles which bear little resemblance to the serum-induced LB. The albumin-induced structures (Fig. 2) are irregular in shape, rarely spherical, and have contents which vary in density and consistency. In this paper an attempt is made to formulate the sequence of events which might occur in the formation of the albumin-induced vacuoles.

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