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Kuchinka J, Willems C, Telyshev DV, Groth T. Control of Blood Coagulation by Hemocompatible Material Surfaces-A Review. Bioengineering (Basel) 2021; 8:bioengineering8120215. [PMID: 34940368 PMCID: PMC8698751 DOI: 10.3390/bioengineering8120215] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022] Open
Abstract
Hemocompatibility of biomaterials in contact with the blood of patients is a prerequisite for the short- and long-term applications of medical devices such as cardiovascular stents, artificial heart valves, ventricular assist devices, catheters, blood linings and extracorporeal devices such as artificial kidneys (hemodialysis), extracorporeal membrane oxygenation (ECMO) and cardiopulmonary bypass. Although lower blood compatibility of materials and devices can be handled with systemic anticoagulation, its side effects, such as an increased bleeding risk, make materials that have a better hemocompatibility highly desirable, particularly in long-term applications. This review provides a short overview on the basic mechanisms of blood coagulation including plasmatic coagulation and blood platelets, as well as the activation of the complement system. Furthermore, a survey on concepts for tailoring the blood response of biomaterials to improve the hemocompatibility of medical devices is given which covers different approaches that either inhibit interaction of material surfaces with blood components completely or control the response of the coagulation system, blood platelets and leukocytes.
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Affiliation(s)
- Janna Kuchinka
- Department Biomedical Materials, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (J.K.); (C.W.)
| | - Christian Willems
- Department Biomedical Materials, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (J.K.); (C.W.)
| | - Dmitry V. Telyshev
- Institute of Biomedical Systems, National Research University of Electronic Technology, Zelenograd, 124498 Moscow, Russia;
- Laboratory of Biomedical Nanotechnologies, Institute of Bionic Technologies and Engineering, I.M. Sechenov First Moscow State University, 119991 Moscow, Russia
| | - Thomas Groth
- Department Biomedical Materials, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (J.K.); (C.W.)
- Laboratory of Biomedical Nanotechnologies, Institute of Bionic Technologies and Engineering, I.M. Sechenov First Moscow State University, 119991 Moscow, Russia
- Interdisciplinary Center of Materials Science, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Correspondence: ; Tel.: +49-3455528460
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Chirumbolo S, Vella A. Molecules, Information and the Origin of Life: What Is Next? Molecules 2021; 26:molecules26041003. [PMID: 33672848 PMCID: PMC7917628 DOI: 10.3390/molecules26041003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
How life did originate and what is life, in its deepest foundation? The texture of life is known to be held by molecules and their chemical-physical laws, yet a thorough elucidation of the aforementioned questions still stands as a puzzling challenge for science. Focusing solely on molecules and their laws has indirectly consolidated, in the scientific knowledge, a mechanistic (reductionist) perspective of biology and medicine. This occurred throughout the long historical path of experimental science, affecting subsequently the onset of the many theses and speculations about the origin of life and its maintenance. Actually, defining what is life, asks for a novel epistemology, a ground on which living systems’ organization, whose origin is still questioned via chemistry, physics and even philosophy, may provide a new key to focus onto the complex nature of the human being. In this scenario, many issues, such as the role of information and water structure, have been long time neglected from the theoretical basis on the origin of life and marginalized as a kind of scenic backstage. On the contrary, applied science and technology went ahead on considering molecules as the sole leading components in the scenery. Water physics and information dynamics may have a role in living systems much more fundamental than ever expected. Can an organism be simply explained by a mechanistic view of its nature or we need “something else”? Probably, we can earn sound foundations about life by simply changing our prejudicial view about living systems simply as complex, highly ordered machines. In this manuscript we would like to reappraise many fundamental aspects of molecular and chemical biology and reading them through a new paradigm, which includes Prigogine’s dissipative structures and informational dissipation (Shannon dissipation). This would provide readers with insightful clues about how biology and chemistry may be thoroughly revised, referring to new models, such as informational dissipation. We trust they are enabled to address a straightforward contribution in elucidating what life is for science. This overview is not simply a philosophical speculation, but it would like to affect deeply our way to conceive and describe the foundations of organisms’ life, providing intriguing suggestions for readers in the field.
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Affiliation(s)
- Salvatore Chirumbolo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
- Correspondence: ; Tel.: +39-0458027645
| | - Antonio Vella
- Verona-Unit of Immunology, Azienda Ospedaliera Universitaria Integrata, 37134 Verona, Italy;
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Sakti AW, Nishimura Y, Nakai H. Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aditya W. Sakti
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
| | - Hiromi Nakai
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering Waseda University Tokyo Japan
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Irwin BWJ, Vukovic S, Payne MC, Huggins DJ. Large-Scale Study of Hydration Environments through Hydration Sites. J Phys Chem B 2019; 123:4220-4229. [PMID: 31025866 DOI: 10.1021/acs.jpcb.9b02490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hydration sites are locations of interest to water and they can be used to classify the behavior of water around chemical motifs commonly found on the surface of proteins. Inhomogeneous fluid solvation theory (IFST) is a method for calculating hydration free-energy changes from molecular dynamics (MD) trajectories. In this paper, hydration sites are identified from MD simulations of 380 diverse protein structures. The hydration free energies of the hydration sites are calculated using IFST and distributions of these free-energy changes are analyzed. The results show that for some hydration sites near features conventionally regarded as attractive to water, such as hydrogen bond donors, the water molecules are actually relatively weakly bound and are easily displaced. We also construct plots of the spatial density of hydration sites with high, medium, and low hydration free-energy changes which represent weakly and strongly bound hydration sites. It is found that these plots show consistent features around common polar amino acids for all of the proteins studied.
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Affiliation(s)
- Benedict W J Irwin
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Sinisa Vukovic
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Michael C Payne
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K
| | - David J Huggins
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K.,Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Department of Physiology and Biophysics , Weill Cornell Medical College , 1300 York Avenue , New York , New York 10065 , United States
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Gerogiokas G, Southey MWY, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Henchman RH, Michel J. Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory. J Phys Chem B 2016; 120:10442-10452. [PMID: 27645529 DOI: 10.1021/acs.jpcb.6b07993] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular dynamics simulations have been analyzed with the Grid Cell Theory (GCT) method to spatially resolve the binding enthalpies and entropies of water molecules at the interface of 17 structurally diverse proteins. Correlations between computed energetics and structural descriptors have been sought to facilitate the development of simple models of protein hydration. Little correlation was found between GCT-computed binding enthalpies and continuum electrostatics calculations. A simple count of contacts with functional groups in charged amino acids correlates well with enhanced water stabilization, but the stability of water near hydrophobic and polar residues depends markedly on its coordination environment. The positions of X-ray-resolved water molecules correlate with computed high-density hydration sites, but many unresolved waters are significantly stabilized at the protein surfaces. A defining characteristic of ligand-binding pockets compared to nonbinding pockets was a greater solvent-accessible volume, but average water thermodynamic properties were not distinctive from other interfacial regions. Interfacial water molecules are frequently stabilized by enthalpy and destabilized entropy with respect to bulk, but counter-examples occasionally occur. Overall detailed inspection of the local coordinating environment appears necessary to gauge the thermodynamic stability of water in protein structures.
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Affiliation(s)
- Georgios Gerogiokas
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
| | - Michelle W Y Southey
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael P Mazanetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Alexander Heifetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael Bodkin
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard J Law
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.,School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - J Michel
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
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Peter EK, Agarwal M, Kim B, Pivkin IV, Shea JE. How water layers on graphene affect folding and adsorption of TrpZip2. J Chem Phys 2014; 141:22D511. [DOI: 10.1063/1.4896984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Mrigya Agarwal
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
| | - BongKeun Kim
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Igor V. Pivkin
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
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Zykwinska A, Pihet M, Radji S, Bouchara JP, Cuenot S. Self-assembly of proteins into a three-dimensional multilayer system: investigation of the surface of the human fungal pathogen Aspergillus fumigatus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1137-44. [PMID: 24631542 DOI: 10.1016/j.bbapap.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
Abstract
Hydrophobins are small surface active proteins that fulfil a wide spectrum of functions in fungal growth and development. The human fungal pathogen Aspergillus fumigatus expresses RodA hydrophobins that self-assemble on the outer conidial surface into tightly organized nanorods known as rodlets. AFM investigation of the conidial surface allows us to evidence that RodA hydrophobins self-assemble into rodlets through bilayers. Within bilayers, hydrophilic domains of hydrophobins point inward, thus making a hydrophilic core, while hydrophobic domains point outward. AFM measurements reveal that several rodlet bilayers are present on the conidial surface thus showing that proteins self-assemble into a complex three-dimensional multilayer system. The self-assembly of RodA hydrophobins into rodlets results from attractive interactions between stacked β-sheets, which conduct to a final linear cross-β spine structure. A Monte Carlo simulation shows that anisotropic interactions are the main driving forces leading the hydrophobins to self-assemble into parallel rodlets, which are further structured in nanodomains. Taken together, these findings allow us to propose a mechanism, which conducts RodA hydrophobins to a highly ordered rodlet structure. The mechanism of hydrophobin assembly into rodlets offers new prospects for the development of more efficient strategies leading to disruption of rodlet formation allowing a rapid detection of the fungus by the immune system.
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Affiliation(s)
- Agata Zykwinska
- Institut des Matériaux Jean Rouxel, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France
| | - Marc Pihet
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire d'Angers, France; UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES-EA 3142 Angers, France
| | - Sadia Radji
- IPREM Equipe de Physique et Chimie des Polymères, UMR 5254 CNRS, Université de Pau et des Pays de l'Adour, Hélioparc, 2 Avenue du Président Angot, 64053 Pau Cedex, France
| | - Jean-Philippe Bouchara
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire d'Angers, France; UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES-EA 3142 Angers, France
| | - Stéphane Cuenot
- Institut des Matériaux Jean Rouxel, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France.
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Weber JK, Pande VS. Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions. J Chem Phys 2013; 138:085103. [PMID: 23464179 PMCID: PMC3598771 DOI: 10.1063/1.4792638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/04/2013] [Indexed: 11/14/2022] Open
Abstract
The structure and properties of water at biological interfaces differ drastically from bulk due to effects including confinement and the presence of complicated charge distributions. This non-bulk-like behavior generally arises from water frustration, wherein all favorable interactions among water molecules cannot be simultaneously satisfied. While the frustration of interfacial water is ubiquitous in the cell, the role this frustration plays in mediating biophysical processes like protein folding is not well understood. To investigate the impact of frustration at interfaces, we here derive a general field theoretic model for the interaction of bulk and disordered vector fields at an embedded surface. We calculate thermodynamic and correlation functions for the model in two and three dimensions, and we compare our results to Monte Carlo simulations of lattice system analogs. In our analysis, we see that field-field cross correlations near the interface in the model give rise to a loss in entropy like that seen in glassy systems. We conclude by assessing our theory's utility as a coarse-grained model for water at polar biological interfaces.
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Affiliation(s)
- Jeffrey K Weber
- Department of Chemistry, Stanford University, Stanford, California 94305-4401, USA
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Daub CD, Bratko D, Luzar A. Nanoscale Wetting Under Electric Field from Molecular Simulations. MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY 2011; 307:155-79. [DOI: 10.1007/128_2011_188] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Wang J, Kudesia S, Bratko D, Luzar A. Computational probe of cavitation events in protein systems. Phys Chem Chem Phys 2011; 13:19902-10. [PMID: 21922115 DOI: 10.1039/c1cp22082a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Jihang Wang
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
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