Origin of Mechanical Strength of Bovine Carbonic Anhydrase Studied by Molecular Dynamics Simulation

Ohta, Satoko; Alam, Mohammad Taufiq; Arakawa, Hideo; Ikai, Atsushi

doi:10.1529/biophysj.104.045138

Cited by 42 publications

(35 citation statements)

References 39 publications

(61 reference statements)

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“…The difference in the two velocities will stretch the hypothetical spring whose extension will be interpreted as the tensile force on the protein. We applied this method to the unfolding process of carbonic anhydrase and obtained results consistent with experimental observations (Ohta et al 2004). …”

Section: Nanobiomechanics Of Proteins and Biomembrane A Ikai 2165supporting

confidence: 75%

Nanobiomechanics of proteins and biomembrane

Ikai

2008

Phil. Trans. R. Soc. B

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A review of the work done in the Laboratory of Biodynamics of Tokyo Institute of Technology in the last decade has been summarized in this article in relation to the results reported from other laboratories. The emphasis here is the application of nanomechanics based on the force mode of atomic force microscopy (AFM) to proteins and protein-based biological structures. Globular proteins were stretched in various ways to detect the localized rigidity inside of the molecule. When studied by this method, bovine carbonic anhydrase II (BCA II), calmodulin and OspA protein all showed the presence of localized rigid structures inside the molecules. Protein compression experiments were done on BCA II to obtain an estimate of the Young modulus and its change in the process of denaturation. Then, the AFM probe method was turned on to cell membranes and cytoplasmic components. Force curves accompanying the extraction process of membrane proteins from intact cells were analysed in relation to their interaction with the cytoskeletal components. By pushing the AFM probe further into the cytoplasm, mRNAs were recovered from a live cell with minimal damage, and multiplied using PCR technology for their identification. Altogether, the work introduced here forms the basis of nanomechanics of protein and protein-based biostructures and application of the nanomechanical technology to cell biology.

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Section: Nanobiomechanics Of Proteins and Biomembrane A Ikai 2165supporting

confidence: 75%

Nanobiomechanics of proteins and biomembrane

Ikai

2008

Phil. Trans. R. Soc. B

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“…In particular, for single protein molecules, by measuring force extension (F-E) curves showing saw-tooth patterns, typical strengths of their internal interactions such as hydrogen bonds have been clarified step by step [1][2][3][4][5]. In addition, the atomic details of their mechanical unfolding process have been studied well by theoretical simulations including the steered molecular dynamics (SMD) simulations [6][7][8][9][10][11][12][13][14][15]. Owing to these works, the relationships between the saw-tooth patterns in the F-E curves and the structural changes such as hydrogen bond breaking have been clarified for single protein molecules.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Study of Forced Dissociation Process of Wheat Germ Agglutinin Dimer

Tagami

Sekiguchi

Ikai

2009

e-J. Surf. Sci. Nanotechnol.

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Molecular dynamics simulations are performed to study the mechanical dissociation pathways of a wheat germ agglutinin (WGA) dimer under the tensile force exerted by the atomic force microscopy (AFM). We found a dissociation pathway in which both monomer units are elongated and their tertial structures are destroyed before the rupture. The force extension (F-E) curves are found to show successive saw-tooth peaks indicating the stepwise destruction of interactions inside monomer structures. In addition, the interactions at their interfaces are found to be destroyed at the largest force peak. At the rupture where the dimer dissociates completely, a small jump is observed in the F-E curve, which amounts to 70 pN.

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“…In these proteins, the disadvantage of less efficient folding may be balanced by a functional advantage connected with the presence of these knots. Numerous experimental (13)(14)(15)(16) and theoretical (17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) studies have been devoted to understanding the precise nature of the structural and functional advantages created by the presence of these knots in protein backbones. It has been proposed that in some cases the protein knots and slipknots provide a stabilizing function that can act by holding together certain protein domains (4).…”

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Conservation of complex knotting and slipknotting patterns in proteins

Sułkowska

Rawdon

Millett

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

227

229

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While analyzing all available protein structures for the presence of knots and slipknots, we detected a strict conservation of complex knotting patterns within and between several protein families despite their large sequence divergence. Because protein folding pathways leading to knotted native protein structures are slower and less efficient than those leading to unknotted proteins with similar size and sequence, the strict conservation of the knotting patterns indicates an important physiological role of knots and slipknots in these proteins. Although little is known about the functional role of knots, recent studies have demonstrated a proteinstabilizing ability of knots and slipknots. Some of the conserved knotting patterns occur in proteins forming transmembrane channels where the slipknot loop seems to strap together the transmembrane helices forming the channel.protein knots | knot theory | topology T here are increasing numbers of known proteins that form linear open knots in their native folded structure (1, 2). In general, knots in proteins are orders of magnitude less frequent than would be expected for random polymers with similar length, compactness, and flexibility (3). In principle, the polypeptide chains folding into knotted native protein structures encounter more kinetic difficulties than unknotted proteins (4-12). Therefore, it is believed that knotted protein structures were, in part, eliminated during evolution because proteins that fold slowly and/or nonreproducibly should be evolutionarily disadvantageous for the hosting organisms. Nevertheless, there are several families of proteins that reproducibly form simple knots, complex knots, and slipknots (1, 2). In these proteins, the disadvantage of less efficient folding may be balanced by a functional advantage connected with the presence of these knots. Numerous experimental (13-16) and theoretical (17-27) studies have been devoted to understanding the precise nature of the structural and functional advantages created by the presence of these knots in protein backbones. It has been proposed that in some cases the protein knots and slipknots provide a stabilizing function that can act by holding together certain protein domains (4). In the majority of cases, however, one is unable to determine the precise structural and functional advantages provided by the presence of knots.To shed light on the function and formation of protein knots, we performed a thorough characterization of knotting within protein structures deposited in the Protein Data Bank (PDB) (28) by creating a precise mapping of the position and size of the knotted and slipknotted domains and knot tails (1, 2). We identified the types of knots that are formed by the backbone of the entire polypeptide chain and also by all continuous backbone portions of a given protein (1, 2). To characterize the knotting of proteins with linear backbones, one needs to set aside the orthodox rule of knot theory that states that all linear chains are unknotted because, by a continuous deformation,...

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Origin of Mechanical Strength of Bovine Carbonic Anhydrase Studied by Molecular Dynamics Simulation

Cited by 42 publications

References 39 publications

Nanobiomechanics of proteins and biomembrane

Nanobiomechanics of proteins and biomembrane

Molecular Dynamics Study of Forced Dissociation Process of Wheat Germ Agglutinin Dimer

Conservation of complex knotting and slipknotting patterns in proteins

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