This thesis is concerned with the investigation of structure and dynamics of biological macromolecular assemblies by atomic force microscopy (AFM).  ...

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Reviakine, Ilya,

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Atomic force microscopy of biological macromolecules and their assemblies

Reviakine, Ilya

Dissertations of the University of Groningen

   University of GroningenAtomic force microscopy of biological macromolecules and their assembliesReviakine, IlyaIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2000Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Reviakine, I. (2000). Atomic force microscopy of biological macromolecules and their assemblies. s.n.CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 31-10-2023XSUMMARYThe Thesis is concerned with the investigation of stmctureand dynamics of biological macromolecular assemblies by atomicforce microscopy (AFM). The technique of AFM enables theinvestigator to visualize the surface topography of an object with upto atomic resolution. It also offers an exciting possibility to study abiological system in a near-native nvironrnent: i.e., in fluid, and tovisualize processes in real time at sub-molecular resolution. These,and other characteristics ofthe technique, are discussed in detail inSection 1 of the Thesis. SecÍion 1 also contains a review of therelevant literature.In Sec'tion 11, Chapter I the formation of supportedphospholipid bilayers (SPBs) on mica surface is investigated. WhileSPBs have been used by the scientific community since theirintroduction in mid-80's. the mechanism of their formation hasremained obscure. It was possible to visualize, in buffer, intactindividual liposornes adsorbed to the mica surface and follow theirbehavior. This allowed the experimental data to be compared withthe theoretical predictions available in the literature, resulting in aconsistent picture of the process, which was found to be consistentwith the results obtained by spectroscopic means in other groups.The results of this Chapter provide the foundation for the threesubsequent Sec:lions. Chapter 2 is concerned with the topographystructure and with the dynaniics of SPBs composed of phospholipidmlxtures.Section 111 is concerned with the surface structure ofmembrane-binding proteins. Annexin A5, described in the firstClrapter of this Section, was used as a model to demonstrate, for thefirst time, the ability of SPBs to support the growth of protein 2Dcrystals. This was achieved by extending the well-establishedprocedure for growing protein 2D crystals on phospholipidmonolayers at the air-water interface to SPBs. The equivalence of'SPBs and lipid rnonolayers insofar as the crystallization of annexinA5 is concerned was demonstrated through the comparison of high-resolution structural data on the two crystal forms annexin A5crystallizes in (both on SPBs and monolayers) obtained by electroncrystallography and AFM. The crystal fonns observed by AFM andelectron microscopy (EM) were shown to be identical and fomredunder equivalent conditions. This allowed, firstly, a detailedinvestigation of the surface structure of annexin A5, including thecomparison of AFM topography with tliat expected from the X-rayXistructure of the protein, and secondly, a study of the relationshipbetween the two crystals forms in Section IV.Inthe second Chapter,the topography structure of another protein crystallized on an SpB -streptavidin - is discussed.The two 2D crystal forms which annexin A5 crystallizes inhave been known through the EM studies of this protein for sometime. Evidence that they are related by a direct phase transition isprovided, and the mechanism of the transformation is proposed inthis Section (Section lV)basedon AFM and EM observations.Section Zdiscusses in some detail the issue of contrastmechanism in AFM. This question has been voiced since the veryconception of AFM, and, in spite of significant advances, had notbeen resolved satisfactory. The data accumulated throughout hework discussed in the preceding sections is compared critically withthe literature, and possible contributions to the contrast arediscussed.

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   University of GroningenAtomic force microscopy of biological macromolecules and their assembliesReviakine, IlyaIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2000Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Reviakine, I. (2000). Atomic force microscopy of biological macromolecules and their assemblies. s.n.CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 07-06-2022XSUMMARYThe Thesis is concerned with the investigation of stmctureand dynamics of biological macromolecular assemblies by atomicforce microscopy (AFM). The technique of AFM enables theinvestigator to visualize the surface topography of an object with upto atomic resolution. It also offers an exciting possibility to study abiological system in a near-native nvironrnent: i.e., in fluid, and tovisualize processes in real time at sub-molecular resolution. These,and other characteristics ofthe technique, are discussed in detail inSection 1 of the Thesis. SecÍion 1 also contains a review of therelevant literature.In Sec'tion 11, Chapter I the formation of supportedphospholipid bilayers (SPBs) on mica surface is investigated. WhileSPBs have been used by the scientific community since theirintroduction in mid-80's. the mechanism of their formation hasremained obscure. It was possible to visualize, in buffer, intactindividual liposornes adsorbed to the mica surface and follow theirbehavior. This allowed the experimental data to be compared withthe theoretical predictions available in the literature, resulting in aconsistent picture of the process, which was found to be consistentwith the results obtained by spectroscopic means in other groups.The results of this Chapter provide the foundation for the threesubsequent Sec:lions. Chapter 2 is concerned with the topographystructure and with the dynaniics of SPBs composed of phospholipidmlxtures.Section 111 is concerned with the surface structure ofmembrane-binding proteins. Annexin A5, described in the firstClrapter of this Section, was used as a model to demonstrate, for thefirst time, the ability of SPBs to support the growth of protein 2Dcrystals. This was achieved by extending the well-establishedprocedure for growing protein 2D crystals on phospholipidmonolayers at the air-water interface to SPBs. The equivalence of'SPBs and lipid rnonolayers insofar as the crystallization of annexinA5 is concerned was demonstrated through the comparison of high-resolution structural data on the two crystal forms annexin A5crystallizes in (both on SPBs and monolayers) obtained by electroncrystallography and AFM. The crystal fonns observed by AFM andelectron microscopy (EM) were shown to be identical and fomredunder equivalent conditions. This allowed, firstly, a detailedinvestigation of the surface structure of annexin A5, including thecomparison of AFM topography with tliat expected from the X-rayXistructure of the protein, and secondly, a study of the relationshipbetween the two crystals forms in Section IV.Inthe second Chapter,the topography structure of another protein crystallized on an SpB -streptavidin - is discussed.The two 2D crystal forms which annexin A5 crystallizes inhave been known through the EM studies of this protein for sometime. Evidence that they are related by a direct phase transition isprovided, and the mechanism of the transformation is proposed inthis Section (Section lV)basedon AFM and EM observations.Section Zdiscusses in some detail the issue of contrastmechanism in AFM. This question has been voiced since the veryconception of AFM, and, in spite of significant advances, had notbeen resolved satisfactory. The data accumulated throughout hework discussed in the preceding sections is compared critically withthe literature, and possible contributions to the contrast arediscussed.

   University of GroningenAtomic force microscopy of biological macromolecules and their assembliesReviakine, IlyaIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2000Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Reviakine, I. (2000). Atomic force microscopy of biological macromolecules and their assemblies. s.n.CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 12-10-2022XSUMMARYThe Thesis is concerned with the investigation of stmctureand dynamics of biological macromolecular assemblies by atomicforce microscopy (AFM). The technique of AFM enables theinvestigator to visualize the surface topography of an object with upto atomic resolution. It also offers an exciting possibility to study abiological system in a near-native nvironrnent: i.e., in fluid, and tovisualize processes in real time at sub-molecular resolution. These,and other characteristics ofthe technique, are discussed in detail inSection 1 of the Thesis. SecÍion 1 also contains a review of therelevant literature.In Sec'tion 11, Chapter I the formation of supportedphospholipid bilayers (SPBs) on mica surface is investigated. WhileSPBs have been used by the scientific community since theirintroduction in mid-80's. the mechanism of their formation hasremained obscure. It was possible to visualize, in buffer, intactindividual liposornes adsorbed to the mica surface and follow theirbehavior. This allowed the experimental data to be compared withthe theoretical predictions available in the literature, resulting in aconsistent picture of the process, which was found to be consistentwith the results obtained by spectroscopic means in other groups.The results of this Chapter provide the foundation for the threesubsequent Sec:lions. Chapter 2 is concerned with the topographystructure and with the dynaniics of SPBs composed of phospholipidmlxtures.Section 111 is concerned with the surface structure ofmembrane-binding proteins. Annexin A5, described in the firstClrapter of this Section, was used as a model to demonstrate, for thefirst time, the ability of SPBs to support the growth of protein 2Dcrystals. This was achieved by extending the well-establishedprocedure for growing protein 2D crystals on phospholipidmonolayers at the air-water interface to SPBs. The equivalence of'SPBs and lipid rnonolayers insofar as the crystallization of annexinA5 is concerned was demonstrated through the comparison of high-resolution structural data on the two crystal forms annexin A5crystallizes in (both on SPBs and monolayers) obtained by electroncrystallography and AFM. The crystal fonns observed by AFM andelectron microscopy (EM) were shown to be identical and fomredunder equivalent conditions. This allowed, firstly, a detailedinvestigation of the surface structure of annexin A5, including thecomparison of AFM topography with tliat expected from the X-rayXistructure of the protein, and secondly, a study of the relationshipbetween the two crystals forms in Section IV.Inthe second Chapter,the topography structure of another protein crystallized on an SpB -streptavidin - is discussed.The two 2D crystal forms which annexin A5 crystallizes inhave been known through the EM studies of this protein for sometime. Evidence that they are related by a direct phase transition isprovided, and the mechanism of the transformation is proposed inthis Section (Section lV)basedon AFM and EM observations.Section Zdiscusses in some detail the issue of contrastmechanism in AFM. This question has been voiced since the veryconception of AFM, and, in spite of significant advances, had notbeen resolved satisfactory. The data accumulated throughout hework discussed in the preceding sections is compared critically withthe literature, and possible contributions to the contrast arediscussed.

   University of GroningenAtomic force microscopy of biological macromolecules and their assembliesReviakine, IlyaIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2000Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Reviakine, I. (2000). Atomic force microscopy of biological macromolecules and their assemblies. s.n.CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 09-09-2023XSUMMARYThe Thesis is concerned with the investigation of stmctureand dynamics of biological macromolecular assemblies by atomicforce microscopy (AFM). The technique of AFM enables theinvestigator to visualize the surface topography of an object with upto atomic resolution. It also offers an exciting possibility to study abiological system in a near-native nvironrnent: i.e., in fluid, and tovisualize processes in real time at sub-molecular resolution. These,and other characteristics ofthe technique, are discussed in detail inSection 1 of the Thesis. SecÍion 1 also contains a review of therelevant literature.In Sec'tion 11, Chapter I the formation of supportedphospholipid bilayers (SPBs) on mica surface is investigated. WhileSPBs have been used by the scientific community since theirintroduction in mid-80's. the mechanism of their formation hasremained obscure. It was possible to visualize, in buffer, intactindividual liposornes adsorbed to the mica surface and follow theirbehavior. This allowed the experimental data to be compared withthe theoretical predictions available in the literature, resulting in aconsistent picture of the process, which was found to be consistentwith the results obtained by spectroscopic means in other groups.The results of this Chapter provide the foundation for the threesubsequent Sec:lions. Chapter 2 is concerned with the topographystructure and with the dynaniics of SPBs composed of phospholipidmlxtures.Section 111 is concerned with the surface structure ofmembrane-binding proteins. Annexin A5, described in the firstClrapter of this Section, was used as a model to demonstrate, for thefirst time, the ability of SPBs to support the growth of protein 2Dcrystals. This was achieved by extending the well-establishedprocedure for growing protein 2D crystals on phospholipidmonolayers at the air-water interface to SPBs. The equivalence of'SPBs and lipid rnonolayers insofar as the crystallization of annexinA5 is concerned was demonstrated through the comparison of high-resolution structural data on the two crystal forms annexin A5crystallizes in (both on SPBs and monolayers) obtained by electroncrystallography and AFM. The crystal fonns observed by AFM andelectron microscopy (EM) were shown to be identical and fomredunder equivalent conditions. This allowed, firstly, a detailedinvestigation of the surface structure of annexin A5, including thecomparison of AFM topography with tliat expected from the X-rayXistructure of the protein, and secondly, a study of the relationshipbetween the two crystals forms in Section IV.Inthe second Chapter,the topography structure of another protein crystallized on an SpB -streptavidin - is discussed.The two 2D crystal forms which annexin A5 crystallizes inhave been known through the EM studies of this protein for sometime. Evidence that they are related by a direct phase transition isprovided, and the mechanism of the transformation is proposed inthis Section (Section lV)basedon AFM and EM observations.Section Zdiscusses in some detail the issue of contrastmechanism in AFM. This question has been voiced since the veryconception of AFM, and, in spite of significant advances, had notbeen resolved satisfactory. The data accumulated throughout hework discussed in the preceding sections is compared critically withthe literature, and possible contributions to the contrast arediscussed.

University of Groningen

   University of GroningenAtomic force microscopy of biological macromolecules and their assembliesReviakine, IlyaIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2000Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Reviakine, I. (2000). Atomic force microscopy of biological macromolecules and their assemblies.Groningen: s.n.CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 12-11-2019XSUMMARYThe Thesis is concerned with the investigation of stmctureand dynamics of biological macromolecular assemblies by atomicforce microscopy (AFM). The technique of AFM enables theinvestigator to visualize the surface topography of an object with upto atomic resolution. It also offers an exciting possibility to study abiological system in a near-native nvironrnent: i.e., in fluid, and tovisualize processes in real time at sub-molecular resolution. These,and other characteristics ofthe technique, are discussed in detail inSection 1 of the Thesis. SecÍion 1 also contains a review of therelevant literature.In Sec'tion 11, Chapter I the formation of supportedphospholipid bilayers (SPBs) on mica surface is investigated. WhileSPBs have been used by the scientific community since theirintroduction in mid-80's. the mechanism of their formation hasremained obscure. It was possible to visualize, in buffer, intactindividual liposornes adsorbed to the mica surface and follow theirbehavior. This allowed the experimental data to be compared withthe theoretical predictions available in the literature, resulting in aconsistent picture of the process, which was found to be consistentwith the results obtained by spectroscopic means in other groups.The results of this Chapter provide the foundation for the threesubsequent Sec:lions. Chapter 2 is concerned with the topographystructure and with the dynaniics of SPBs composed of phospholipidmlxtures.Section 111 is concerned with the surface structure ofmembrane-binding proteins. Annexin A5, described in the firstClrapter of this Section, was used as a model to demonstrate, for thefirst time, the ability of SPBs to support the growth of protein 2Dcrystals. This was achieved by extending the well-establishedprocedure for growing protein 2D crystals on phospholipidmonolayers at the air-water interface to SPBs. The equivalence of'SPBs and lipid rnonolayers insofar as the crystallization of annexinA5 is concerned was demonstrated through the comparison of high-resolution structural data on the two crystal forms annexin A5crystallizes in (both on SPBs and monolayers) obtained by electroncrystallography and AFM. The crystal fonns observed by AFM andelectron microscopy (EM) were shown to be identical and fomredunder equivalent conditions. This allowed, firstly, a detailedinvestigation of the surface structure of annexin A5, including thecomparison of AFM topography with tliat expected from the X-rayXistructure of the protein, and secondly, a study of the relationshipbetween the two crystals forms in Section IV.Inthe second Chapter,the topography structure of another protein crystallized on an SpB -streptavidin - is discussed.The two 2D crystal forms which annexin A5 crystallizes inhave been known through the EM studies of this protein for sometime. Evidence that they are related by a direct phase transition isprovided, and the mechanism of the transformation is proposed inthis Section (Section lV)basedon AFM and EM observations.Section Zdiscusses in some detail the issue of contrastmechanism in AFM. This question has been voiced since the veryconception of AFM, and, in spite of significant advances, had notbeen resolved satisfactory. The data accumulated throughout hework discussed in the preceding sections is compared critically withthe literature, and possible contributions to the contrast arediscussed.

Atomic force microscopy of biological macromolecules and their assemblies

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