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Nguyen AH, Kania S, Oztekin A, Webb EB. Predicting reaction behavior of tethered polymers in shear flow. J Chem Phys 2023; 159:174907. [PMID: 37929865 DOI: 10.1063/5.0168440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
Kinetics of force-mediated chemical reactions of end-tethered polymers with varying chain length N in varying shear rate flow γ̇ are explored via coarse-grained Brownian dynamics simulations. At fixed γ̇, force F along a polymer increases linearly with N as previously predicted; however, contrary to existing theory, the F(N) slope increases for N above a transition length that exhibits minimal dependence on γ̇. Force profiles are used in a stochastic model of a force-mediated reaction to compute the time for x percent of a polymer population to experience a reaction, tx. Observations are insensitive to the selected value of x in that tx data for varying N and γ̇ can be consistently collapsed onto a single curve via appropriate scaling, with one master curve for systems below the transition N (small N) and another for those above (large N). Different force scaling for small and large N results in orders of magnitude difference in force-mediated reaction kinetics as represented by the population response time. Data presented illustrate the possibility of designing mechano-reactive polymer populations with highly controlled response to flow across a range in γ̇.
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Affiliation(s)
- Anh Hung Nguyen
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Sagar Kania
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Edmund B Webb
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Csányi MC, Salamon P, Feller T, Bozó T, Hársfalvi J, Kellermayer MSZ. Structural hierarchy of mechanical extensibility in human von Willebrand factor multimers. Protein Sci 2023; 32:e4535. [PMID: 36478480 PMCID: PMC9798247 DOI: 10.1002/pro.4535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/04/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
The von Willebrand factor (VWF) is a multimeric glycoprotein composed of 80- to 120-nm-long protomeric units and plays a fundamental role in mediating platelet function at high shear. The exact nature of the shear-induced structural transitions have remained elusive; uncovering them requires the high-resolution quantitative analysis of gradually extended VWF. Here, we stretched human blood-plasma-derived VWF with molecular combing and analyzed the axial structure of the elongated multimers with atomic force microscopy. Protomers extended through structural intermediates that could be grouped into seven distinct topographical classes. Protomer extension thus progresses through the uncoiling of the C1-6 domain segment, rearrangements among the N-terminal VWF domains, and unfolding and elastic extension of the A2 domain. The least and most extended protomer conformations were localized at the ends and the middle of the multimer, respectively, revealing an apparent necking phenomenon characteristic of plastic-material behavior. The structural hierarchy uncovered here is likely to provide a spatial control mechanism to the complex functions of VWF.
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Affiliation(s)
- Mária Csilla Csányi
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary
| | - Pál Salamon
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary,Present address:
Department of BioengineeringSapientia Hungarian University of TransylvaniaMiercurea CiucRomania
| | - Tímea Feller
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary,Present address:
Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Tamás Bozó
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary
| | - Jolán Hársfalvi
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary
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Conformation of von Willebrand factor in shear flow revealed with stroboscopic single-molecule imaging. Blood 2022; 140:2490-2499. [PMID: 36040485 PMCID: PMC9837445 DOI: 10.1182/blood.2022016969] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 01/21/2023] Open
Abstract
von Willebrand factor (VWF) is a multimeric blood protein that acts as a mechanical probe, responding to changes in flow to initiate platelet plug formation. Previously, our laboratory tests had shown that using single-molecule imaging that shear stress can extend surface-tethered VWF, but paradoxically, we found that the required shear stress was higher than reported for free-in-flow VWF, an observation inconsistent with basic physical principles. To resolve this inconsistency critical to VWF's molecular mechanism, we measured free-VWF extension in shear flow using pulsed laser stroboscopic imaging of single molecules. Here, laser pulses of different durations are used to capture multiple images of the same molecule within each frame, enabling accurate length measurements in the presence of motion blur. At high shear stresses, we observed a mean shift in VWF extension of <200 nm, much shorter than the multiple-micron extensions previously reported with no evidence for the predicted sharp globule-stretch conformational transition. Modeling VWF with a Brownian dynamics simulation, our results were consistent with VWF behaving as an uncollapsed polymer rather than the theorized compact ball. The muted response of free VWF to high shear rates implies that the tension experienced by free VWF in physiological shear flow is lower than indicated by previous reports and that tethering to platelets or the vessel wall is required to mechanically activate VWF adhesive function for primary hemostasis.
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Nguyen AH, Kania S, Cheng X, Oztekin A, Zhang XF, Webb EB. Unraveling Kinetics of Collapsed Polymers in Extensional Flow. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Anh H. Nguyen
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sagar Kania
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Xuanhong Cheng
- Department of Material Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - X. Frank Zhang
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, United States
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Edmund B. Webb
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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Mechanical Forces Impacting Cleavage of Von Willebrand Factor in Laminar and Turbulent Blood Flow. FLUIDS 2021. [DOI: 10.3390/fluids6020067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Von Willebrand factor (VWF) is a large multimeric hemostatic protein. VWF is critical in arresting platelets in regions of high shear stress found in blood circulation. Excessive cleavage of VWF that leads to reduced VWF multimer size in plasma can cause acquired von Willebrand syndrome, which is a bleeding disorder found in some heart valve diseases and in patients receiving mechanical circulatory support. It has been proposed that hemodynamics (blood flow) found in these environments ultimately leads to VWF cleavage. In the context of experiments reported in the literature, scission theory, developed for polymers, is applied here to provide insight into flow that can produce strong extensional forces on VWF that leads to domain unfolding and exposure of a cryptic site for cleavage through a metalloproteinase. Based on theoretical tensile forces, laminar flow only enables VWF cleavage when shear rate is large enough (>2800 s−1) or when VWF is exposed to constant shear stress for nonphysiological exposure times (>20 min). Predicted forces increase in turbulence, increasing the chance for VWF cleavage. These findings can be used when designing blood-contacting medical devices by providing hemodynamic limits to these devices that can otherwise lead to acquired von Willebrand syndrome.
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Bortot M, Sharifi A, Ashworth K, Walker F, Cox A, Ruegg K, Clendenen N, Neeves KB, Bark D, Di Paola J. Pathologic Shear and Elongation Rates Do Not Cause Cleavage of Von Willebrand Factor by ADAMTS13 in a Purified System. Cell Mol Bioeng 2020; 13:379-390. [PMID: 32952737 PMCID: PMC7479076 DOI: 10.1007/s12195-020-00631-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 06/18/2020] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION Pathological flows in patients with severe aortic stenosis are associated with acquired von Willebrand syndrome. This syndrome is characterized by excessive cleavage of von Willebrand factor by its main protease, A Disintegrin and Metalloproteinase with a Thrombospondin Type 1 Motif, Member 13 (ADAMTS13) leading to decreased VWF function and mucocutaneous bleeding. Aortic valve replacement and correction of the flow behavior to physiological levels reverses the syndrome, supporting the association between pathological flow and acquired von Willebrand syndrome. We investigated the effects of shear and elongational rates on von Willebrand factor cleavage in the presence of ADAMTS13. METHODS We identified acquired von Willebrand syndrome in five patients with severe aortic stenosis. Doppler echography values from these patients were used to develop three computational fluid dynamic (CFD) aortic valve models (normal, mild and severe stenosis). Shear, elongational rates and exposure times identified in the CFD simulations were used as parameters for the design of microfluidic devices to test the effects of pathologic shear and elongational rates on the structure and function of von Willebrand factor. RESULTS The shear rates (0-10,000s-1), elongational rates (0-1000 s-1) and exposure times (1-180 ms) tested in our microfluidic designs mimicked the flow features identified in patients with aortic stenosis. The shear and elongational rates tested in vitro did not lead to excessive cleavage or decreased function of von Willebrand factor in the presence of the protease. CONCLUSIONS High shear and elongational rates in the presence of ADAMTS13 are not sufficient for excessive cleavage of von Willebrand Factor.
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Affiliation(s)
- Maria Bortot
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Alireza Sharifi
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523 USA
| | - Katrina Ashworth
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Faye Walker
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Allaura Cox
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Katherine Ruegg
- Hemophilia Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Nathan Clendenen
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Keith B. Neeves
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - David Bark
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523 USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523 USA
| | - Jorge Di Paola
- Department of Pediatrics, Washington University in St. Louis, 660 S. Euclid Avenue, Campus Box 8208, 5th floor MPRB, St. Louis, MO 63110 USA
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Dong C, Kania S, Morabito M, Zhang XF, Im W, Oztekin A, Cheng X, Webb EB. A mechano-reactive coarse-grained model of the blood-clotting agent von Willebrand factor. J Chem Phys 2019; 151:124905. [PMID: 31575216 DOI: 10.1063/1.5117154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The von Willebrand Factor (vWF) is a large blood glycoprotein that aids in hemostasis. Within each vWF monomer, the A2 domain hosts a cleavage site for enzyme ADAMTS13, which regulates the size of vWF multimers. This cleavage site can only be exposed when an A2 domain unfolds, and the unfolding reaction energy landscape is highly sensitive to the force conditions on the domain. Based on previous optical tweezer experimental results, we advance here a new activated A2 monomer model (AA2MM) for coarse-grained modeling of vWF that accurately represents the force-based probabilistic change between the unfolded/refolded states. A system of springs is employed to mimic the complex mechanical response of vWF monomers subject to pulling forces. AA2MM was validated by comparing monomer scale simulation results to data from prior pulling experiments on vWF monomer fragments. The model was further validated by comparing multimer scale Brownian dynamics simulation results to experiments using microfluidic chamber microscopy to visualize tethered vWF proteins subject to flow. The A2 domain unfolding reaction was studied in bulk flow simulations (pure shear and elongation flow), giving evidence that elongational flow drives the vWF size regulation process in blood. The mechanoreactive, coarse-grained AA2MM accurately describes the complex mechanical coupling between human blood flow conditions and vWF protein reactivity.
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Affiliation(s)
- Chuqiao Dong
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Sagar Kania
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Michael Morabito
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - X Frank Zhang
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Xuanhong Cheng
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Edmund B Webb
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Morabito MJ, Usta M, Cheng X, Zhang XF, Oztekin A, Webb EB. Prediction of Sub-Monomer A2 Domain Dynamics of the von Willebrand Factor by Machine Learning Algorithm and Coarse-Grained Molecular Dynamics Simulation. Sci Rep 2019; 9:9037. [PMID: 31227726 PMCID: PMC6588549 DOI: 10.1038/s41598-019-44044-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/15/2019] [Indexed: 11/09/2022] Open
Abstract
We develop a machine learning tool useful for predicting the instantaneous dynamical state of sub-monomer features within long linear polymer chains, as well as extracting the dominant macromolecular motions associated with sub-monomer behaviors of interest. We employ the tool to better understand and predict sub-monomer A2 domain unfolding dynamics occurring amidst the dominant large-scale macromolecular motions of the biopolymer von Willebrand Factor (vWF) immersed in flow. Results of coarse-grained Molecular Dynamics (MD) simulations of non-grafted vWF multimers subject to a shearing flow were used as input variables to a Random Forest Algorithm (RFA). Twenty unique features characterizing macromolecular conformation information of vWF multimers were used for training the RFA. The corresponding responses classify instantaneous A2 domain state as either folded or unfolded, and were directly taken from coarse-grained MD simulations. Three separate RFAs were trained using feature/response data of varying resolution, which provided deep insights into the highly correlated macromolecular dynamics occurring in concert with A2 domain unfolding events. The algorithm is used to analyze results of simulation, but has been developed for use with experimental data as well.
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Affiliation(s)
- Michael J Morabito
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, 18015, United States
| | - Mustafa Usta
- G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, United States
| | - Xuanhong Cheng
- Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA, 18015, United States.,Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, United States
| | - Xiaohui F Zhang
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, 18015, United States.,Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, United States
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, 18015, United States
| | - Edmund B Webb
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, 18015, United States.
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Wang Y, Morabito M, Zhang XF, Webb E, Oztekin A, Cheng X. Shear-Induced Extensional Response Behaviors of Tethered von Willebrand Factor. Biophys J 2019; 116:2092-2102. [PMID: 31103230 DOI: 10.1016/j.bpj.2019.04.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/03/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022] Open
Abstract
We perform single-molecule flow experiments using confocal microscopy and a microfluidic device for shear rates up to 20,000 s-1 and present results for the shear-induced unraveling and elongation of tethered von Willebrand factor (VWF) multimers. Further, we employ companion Brownian dynamics simulations to help explain details of our experimental observations using a parameterized coarse-grained model of VWF. We show that global conformational changes of tethered VWF can be accurately captured using a relatively simple mechanical model. Good agreement is found between experimental results and computational predictions for the threshold shear rate of extension, existence of nonhomogenous fluorescence distributions along unraveled multimer contours, and large variations in extensional response behaviors. Brownian dynamics simulations reveal the strong influence of varying chain length, tethering point location, and number of tethering locations on the underlying unraveling response. Through a complex molecule like VWF that naturally adopts a wide distribution of molecular size and has multiple binding sites within each molecule, this work demonstrates the power of tandem experiment and simulation for understanding flow-induced changes in biomechanical state and global conformation of macromolecules.
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Affiliation(s)
- Yi Wang
- Department of Materials Science and Engineering, Bethlehem, Pennsylvania
| | - Michael Morabito
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania
| | - X Frank Zhang
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania; Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania.
| | - Edmund Webb
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Bethlehem, Pennsylvania
| | - Xuanhong Cheng
- Department of Materials Science and Engineering, Bethlehem, Pennsylvania; Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania.
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Languin-Cattoën O, Melchionna S, Derreumaux P, Stirnemann G, Sterpone F. Three Weaknesses for Three Perturbations: Comparing Protein Unfolding Under Shear, Force, and Thermal Stresses. J Phys Chem B 2018; 122:11922-11930. [PMID: 30444631 DOI: 10.1021/acs.jpcb.8b08711] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The perturbation of a protein conformation by a physiological fluid flow is crucial in various biological processes including blood clotting and bacterial adhesion to human tissues. Investigating such mechanisms by computer simulations is thus of great interest, but it requires development of ad hoc strategies to mimic the complex hydrodynamic interactions acting on the protein from the surrounding flow. In this study, we apply the Lattice Boltzmann Molecular Dynamics (LBMD) technique built on the implicit solvent coarse-grained model for protein Optimized Potential for Efficient peptide structure Prediction (OPEP) and a mesoscopic representation of the fluid solvent, to simulate the unfolding of a small globular cold-shock protein in shear flow and to compare it to the unfolding mechanisms caused either by mechanical or thermal perturbations. We show that each perturbation probes a specific weakness of the protein and causes the disruption of the native fold along different unfolding pathways. Notably, the shear flow and the thermal unfolding exhibit very similar pathways, while because of the directionality of the perturbation, the unfolding under force is quite different. For force and thermal disruption of the native state, the coarse-grained simulations are compared to all-atom simulations in explicit solvent, showing an excellent agreement in the explored unfolding mechanisms. These findings encourage the use of LBMD based on the OPEP model to investigate how a flow can affect the function of larger proteins, for example, in catch-bond systems.
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Affiliation(s)
- Olivier Languin-Cattoën
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | | | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Guillaume Stirnemann
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
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