1
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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2
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Linke H, Höcker B, Furuta K, Forde NR, Curmi PMG. Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers. Biophys Rev 2020; 12:1041-1054. [PMID: 32651904 PMCID: PMC7429643 DOI: 10.1007/s12551-020-00717-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have provided many structural and biophysical insights and enabled the development of models for motor function. However, from the study of highly evolved, biological motors, it remains difficult to discern detailed mechanisms, for example, about the relative role of different force generation mechanisms, or how information is communicated across a protein to achieve the necessary coordination. A promising, complementary approach to answering these questions is to build synthetic protein motors from the bottom up. Indeed, much effort has been invested in functional protein design, but so far, the "holy grail" of designing and building a functional synthetic protein motor has not been realized. Here, we review the progress made to date, and we put forward a roadmap for achieving the aim of constructing the first artificial, autonomously running protein motor. Specifically, we propose to break down the task into (i) enzymatic control of track binding, (ii) the engineering of asymmetry and (iii) the engineering of allosteric control for internal communication. We also propose specific approaches for solving each of these challenges.
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Affiliation(s)
- Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE 22100, Lund, Sweden
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia.
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3
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Qu H, Ma Q, Wang L, Mao Y, Eisenstein M, Soh HT, Zheng L. Measuring Aptamer Folding Energy Using a Molecular Clamp. J Am Chem Soc 2020; 142:11743-11749. [PMID: 32491843 DOI: 10.1021/jacs.0c01570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Folding energy (ΔGfold) offers a useful metric for characterizing the stability and function of aptamers. However, experimentally measuring the folding energy is challenging, and there is currently no general technique to measure this parameter directly. In this work, we present a simple approach for measuring aptamer folding energy. First, the aptamer is stretched under equilibrium conditions with a double-stranded DNA "molecular clamp" that is coupled to the aptamer ends. We then measure the total internal energy of stressed DNA molecules using time-lapse gel electrophoresis and compare the folding and unfolding behavior of molecular clamp-stressed molecules that incorporate either the aptamer or unstructured random single-stranded DNA in order to derive the aptamer folding energy. Using this approach, we measured a folding energy of 10.40 kJ/mol for the HD22 thrombin aptamer, which is consistent with other predictions and estimates. We also analyzed a simple hairpin structure, generating a folding energy result of 9.05 kJ/mol, consistent with the value predicted by computational models (9.24 kJ/mol). We believe our strategy offers an accessible and generalizable approach for obtaining such measurements with virtually any aptamer.
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Affiliation(s)
- Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Qihui Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yu Mao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States.,Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Hyongsok Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States.,Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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4
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Wang J, Song Q, Guo X, Cui X, Tan L, Dong L. Precise Cross-Dimensional Regulation of the Structure of a Photoreversible DNA Nanoswitch. Anal Chem 2019; 91:14530-14537. [PMID: 31617350 DOI: 10.1021/acs.analchem.9b03547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, an accurately and digitally regulated allosteric nanoswitch based on the conformational control of two DNA hairpins was developed. By switching between UV irradiation and blue light conditions, the second molecular beacon (H#2) would bind/separate with a repression sequence (RES) via the introduced PTG molecules (a photosensitive azobenzene derivative), resulting in the target aptamer sequence in the first molecular beacon (H#1) not being able/being able to hold the stem-loop configuration, hence losing/regaining the ability to bind with the target. Importantly, we successfully monitor conformation changes of the nanoswitch by an elegant mathematical model for connecting Ki (the dissociation constant between RES and H#2) with Kd (the overall equilibrium constant of the nanoswitch binding the target), hence realizing "observing" DNA structure across dimensions from "structural visualization" to digitization and, accurately, digitally regulating DNA structure from digitization to "structural visualization".
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Affiliation(s)
- Jing Wang
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China.,School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
| | - Qitao Song
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China.,Peking-Tsinghua Center for Life Sciences , Peking University , 100871 Beijing , China
| | - Xiaogang Guo
- College of Chemistry and Chemical Engineering , Yangtze Normal. University , Chongqing 408100 , China
| | - Xun Cui
- School of Materials Science and Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Luxi Tan
- School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
| | - Lichun Dong
- School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
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5
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Barnes CA, Shen Y, Ying J, Takagi Y, Torchia DA, Sellers JR, Bax A. Remarkable Rigidity of the Single α-Helical Domain of Myosin-VI As Revealed by NMR Spectroscopy. J Am Chem Soc 2019; 141:9004-9017. [PMID: 31117653 PMCID: PMC6556874 DOI: 10.1021/jacs.9b03116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 11/29/2022]
Abstract
Although the α-helix has long been recognized as an all-important element of secondary structure, it generally requires stabilization by tertiary interactions with other parts of a protein's structure. Highly charged single α-helical (SAH) domains, consisting of a high percentage (>75%) of Arg, Lys, and Glu residues, are exceptions to this rule but have been difficult to characterize structurally. Our study focuses on the 68-residue medial tail domain of myosin-VI, which is found to contain a highly ordered α-helical structure extending from Glu-6 to Lys-63. High hydrogen exchange protection factors (15-150), small (ca. 4 Hz) 3 JHNHα couplings, and a near-perfect fit to an ideal model α-helix for its residual dipolar couplings (RDCs), measured in a filamentous phage medium, support the high regularity of this helix. Remarkably, the hydrogen exchange rates are far more homogeneous than the protection factors derived from them, suggesting that for these transiently broken helices the intrinsic exchange rates derived from the amino acid sequence are not appropriate reference values. 15N relaxation data indicate a very high degree of rotational diffusion anisotropy ( D∥/ D⊥ ≈ 7.6), consistent with the hydrodynamic behavior predicted for such a long, nearly straight α-helix. Alignment of the helix by a paramagnetic lanthanide ion attached to its N-terminal region shows a decrease in alignment as the distance from the tagging site increases. This decrease yields a precise measure for the persistence length of 224 ± 10 Å at 20 °C, supporting the idea that the role of the SAH helix is to act as an extension of the myosin-VI lever arm.
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6
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Mizutani Y. Time-Resolved Resonance Raman Spectroscopy and Application to Studies on Ultrafast Protein Dynamics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170218] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043
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7
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Lin W, Ma J, Nong D, Xu C, Zhang B, Li J, Jia Q, Dou S, Ye F, Xi X, Lu Y, Li M. Helicase Stepping Investigated with One-Nucleotide Resolution Fluorescence Resonance Energy Transfer. PHYSICAL REVIEW LETTERS 2017; 119:138102. [PMID: 29341672 DOI: 10.1103/physrevlett.119.138102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 06/07/2023]
Abstract
Single-molecule Förster resonance energy transfer is widely applied to study helicases by detecting distance changes between a pair of dyes anchored to overhangs of a forked DNA. However, it has been lacking single-base pair (1-bp) resolution required for revealing stepping kinetics of helicases. We designed a nanotensioner in which a short DNA is bent to exert force on the overhangs, just as in optical or magnetic tweezers. The strategy improved the resolution of Förster resonance energy transfer to 0.5 bp, high enough to uncover differences in DNA unwinding by yeast Pif1 and E. coli RecQ whose unwinding behaviors cannot be differentiated by currently practiced methods. We found that Pif1 exhibits 1-bp-stepping kinetics, while RecQ breaks 1 bp at a time but sequesters the nascent nucleotides and releases them randomly. The high-resolution data allowed us to propose a three-parameter model to quantitatively interpret the apparently different unwinding behaviors of the two helicases which belong to two superfamilies.
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Affiliation(s)
- Wenxia Lin
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daguan Nong
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghua Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuoxing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuguang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Abstract
Allostery is indispensable for a protein to work, where a locally applied stimulus is transmitted to a distant part of the molecule. While the allostery due to chemical stimuli such as ligand binding has long been studied, the growing interest in mechanobiology prompts the study of the mechanically stimulated allostery, the physical mechanism of which has not been established. By molecular dynamics simulation of a motor protein myosin, we found that a locally applied mechanical stimulus induces electrostatic potential change at distant regions, just like the piezoelectricity. This novel allosteric mechanism, "piezoelectric allostery", should be of particularly high value for mechanosensor/transducer proteins.
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Affiliation(s)
- Jun Ohnuki
- Department of Pure and Applied Physics, Waseda University, Tokyo 169-8555, Japan
| | - Takato Sato
- Department of Pure and Applied Physics, Waseda University, Tokyo 169-8555, Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics, Waseda University, Tokyo 169-8555, Japan
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9
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Arslan S, Khafizov R, Thomas CD, Chemla YR, Ha T. Protein structure. Engineering of a superhelicase through conformational control. Science 2015; 348:344-7. [PMID: 25883358 DOI: 10.1126/science.aaa0445] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Conformational control of biomolecular activities can reveal functional insights and enable the engineering of novel activities. Here we show that conformational control through intramolecular cross-linking of a helicase monomer with undetectable unwinding activity converts it into a superhelicase that can unwind thousands of base pairs processively, even against a large opposing force. A natural partner that enhances the helicase activity is shown to achieve its stimulating role also by selectively stabilizing the active conformation. Our work provides insight into the regulation of nucleic acid unwinding activity and introduces a monomeric superhelicase without nuclease activities, which may be useful for biotechnological applications.
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Affiliation(s)
- Sinan Arslan
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rustem Khafizov
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher D Thomas
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Yann R Chemla
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taekjip Ha
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801, USA.
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10
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Joseph C, Tseng CY, Zocchi G, Tlusty T. Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme. PLoS One 2014; 9:e101442. [PMID: 25000118 PMCID: PMC4085160 DOI: 10.1371/journal.pone.0101442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/06/2014] [Indexed: 01/22/2023] Open
Abstract
The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae). The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory.
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Affiliation(s)
- Collin Joseph
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California, United States of America
| | - Chiao-Yu Tseng
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California, United States of America
| | - Giovanni Zocchi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - Tsvi Tlusty
- Institute for Advanced Study, Princeton, New Jersey, United States of America
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11
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Brantley JN, Bailey CB, Cannon JR, Clark KA, Vanden Bout DA, Brodbelt JS, Keatinge‐Clay AT, Bielawski CW. Mechanically Modulating the Photophysical Properties of Fluorescent Protein Biocomposites for Ratio‐ and Intensiometric Sensors. Angew Chem Int Ed Engl 2014; 53:5088-92. [DOI: 10.1002/anie.201306988] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 01/26/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Johnathan N. Brantley
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Constance B. Bailey
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Joe R. Cannon
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Katie A. Clark
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - David A. Vanden Bout
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
| | - Adrian T. Keatinge‐Clay
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA)
| | - Christopher W. Bielawski
- Department of Chemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712 (USA) http://keatinge‐clay.cm.utexas.edu http://bielawski.cm.utexas.edu
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12
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Brantley JN, Bailey CB, Cannon JR, Clark KA, Vanden Bout DA, Brodbelt JS, Keatinge-Clay AT, Bielawski CW. Mechanically Modulating the Photophysical Properties of Fluorescent Protein Biocomposites for Ratio- and Intensiometric Sensors. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Sacquin-Mora S. Motions and mechanics: investigating conformational transitions in multi-domain proteins with coarse-grain simulations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.843176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
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14
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Führing J, Cramer JT, Routier FH, Lamerz AC, Baruch P, Gerardy-Schahn R, Fedorov R. Catalytic Mechanism and Allosteric Regulation of UDP-Glucose Pyrophosphorylase from Leishmania major. ACS Catal 2013. [DOI: 10.1021/cs4007777] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jana Führing
- Institute
for Cellular Chemistry, OE4330, Hannover Medical School, Carl-Neuberg-Strasse
1, 30625 Hannover, Germany
| | - Johannes T. Cramer
- Institute
for Cellular Chemistry, OE4330, Hannover Medical School, Carl-Neuberg-Strasse
1, 30625 Hannover, Germany
| | - Françoise H. Routier
- Institute
for Cellular Chemistry, OE4330, Hannover Medical School, Carl-Neuberg-Strasse
1, 30625 Hannover, Germany
| | - Anne-Christin Lamerz
- Institute
for Cellular Chemistry, OE4330, Hannover Medical School, Carl-Neuberg-Strasse
1, 30625 Hannover, Germany
| | - Petra Baruch
- Research
Division for Structural Analysis, OE8830, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Rita Gerardy-Schahn
- Institute
for Cellular Chemistry, OE4330, Hannover Medical School, Carl-Neuberg-Strasse
1, 30625 Hannover, Germany
| | - Roman Fedorov
- Research
Division for Structural Analysis, OE8830, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
- Institute
for Biophysical Chemistry, OE4350, Hannover Medical School, Carl-Neuberg-Strasse
1, 30625 Hannover, Germany
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15
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Mechanistic and functional diversity in the mechanosensory kinases of the titin-like family. Biochem Soc Trans 2013; 41:1066-71. [DOI: 10.1042/bst20130085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The giant cytoskeletal kinases of the titin-like family are emerging as key mediators of stretch-sensing in muscle. It is thought that their elastic conformational deformation during muscle function regulates both their catalysis and the recruitment of regulatory proteins to signalosomes that assemble in their vicinity. In the present article, we discuss the speciation of mechanosensory mechanisms in titin-like kinases, their scaffolding properties and the kinase/pseudokinase domain variations that define a rich functional diversity across the family.
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16
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Brantley JN, Bailey CB, Wiggins KM, Keatinge-Clay AT, Bielawski CW. Mechanobiochemistry: harnessing biomacromolecules for force-responsive materials. Polym Chem 2013. [DOI: 10.1039/c3py00001j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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17
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Abstract
A protein at equilibrium is commonly thought of as a fully relaxed structure, with the intra-molecular interactions showing fluctuations around their energy minimum. In contrast, here we find direct evidence for a protein as a molecular tensegrity structure, comprising a balance of tensed and compressed interactions, a concept that has been put forward for macroscopic structures. We quantified the distribution of inter-residue prestress in ubiquitin and immunoglobulin from all-atom molecular dynamics simulations. The network of highly fluctuating yet significant inter-residue forces in proteins is a consequence of the intrinsic frustration of a protein when sampling its rugged energy landscape. In beta sheets, this balance of forces is found to compress the intra-strand hydrogen bonds. We estimate that the observed magnitude of this pre-compression is enough to induce significant changes in the hydrogen bond lifetimes; thus, prestress, which can be as high as a few 100 pN, can be considered a key factor in determining the unfolding kinetics and pathway of proteins under force. Strong pre-tension in certain salt bridges on the other hand is connected to the thermodynamic stability of ubiquitin. Effective force profiles between some side-chains reveal the signature of multiple, distinct conformational states, and such static disorder could be one factor explaining the growing body of experiments revealing non-exponential unfolding kinetics of proteins. The design of prestress distributions in engineering proteins promises to be a new tool for tailoring the mechanical properties of made-to-order nanomaterials. A tensegrity structure is one composed of members that are permanently under either tension or compression, and the balance of these tensile and compressive forces provides the structure with its mechanical stability. Macroscale tensegrity structures, which include Buckminster Fuller's geodesic domes, achieve exceptional structural integrity with a minimal use of resources. The question we address in this work is whether nature makes use of molecular-scale tensegrity in the design of proteins. Using Molecular Dynamics simulations of the protein ubiquitin, we measure the network of pairwise forces connecting the amino acid residues and show that this network does indeed have the character of a tensegrity structure. Furthermore, we find that the arrangement of tensile and compressive forces is such that hydrogen bonds in the protein's beta sheet, which are crucial for bearing mechanical loads, are compressed. This pre-compression is enough to significantly lengthen the lifetime of a bond under a given force, and thus should be an important factor in determining the protein's mechanical strength. The rational design of molecular prestress networks promises to be a new avenue for the engineering of proteins with made-to-order mechanical properties, for applications in medicine, materials and nanotechnology.
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18
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Pereverzev YV, Prezhdo E, Sokurenko EV. The two-pathway model of the biological catch-bond as a limit of the allosteric model. Biophys J 2012; 101:2026-36. [PMID: 22004757 DOI: 10.1016/j.bpj.2011.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/11/2011] [Indexed: 01/25/2023] Open
Abstract
Catch-binding is a counterintuitive phenomenon in which the lifetime of a receptor/ligand bond increases when a force is applied to break the bond. Several mechanisms have been proposed to rationalize catch-binding. In the two-pathway model, the force drives the system away from its native dissociation pathway into an alternative pathway involving a higher energy barrier. Here, we analyze an allosteric model suggesting that a force applied to the complex alters the distribution of receptor conformations, and as a result, induces changes in the ligand-binding site. The model assumes explicitly that the allosteric transitions govern the properties of the ligand site. We demonstrate that the dynamics of the ligand is described by two relaxation times, one of which arises from the allosteric site. Therefore, we argue that one can characterize the allosteric transitions by studying the receptor/ligand binding. We show that the allosteric description reduces to the two-pathway model in the limit when the allosteric transitions are faster than the bond dissociation. The formal results are illustrated with two systems, P-selectin/PSGL-1 and FimH/mannose, subjected to both constant and time-dependent forces. The report advances our understanding of catch-binding by combining alternative physical models into a unified description and makes the problem more tractable for the bond mechanics community.
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Affiliation(s)
- Yuriy V Pereverzev
- Department of Chemistry, University of Rochester, Rochester, New York, USA
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19
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Wang A, Zocchi G. Artificial modulation of the gating behavior of a K+ channel in a KvAP-DNA chimera. PLoS One 2011; 6:e18598. [PMID: 21526187 PMCID: PMC3079724 DOI: 10.1371/journal.pone.0018598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 03/06/2011] [Indexed: 11/19/2022] Open
Abstract
We present experiments where the gating behavior of a voltage-gated ion channel is modulated by artificial ligand binding. We construct a channel-DNA chimera with the KvAP potassium channel reconstituted in an artificial membrane. The channel is functional and the single channel ion conductivity unperturbed by the presence of the DNA. However, the channel opening probability vs. bias voltage, i.e., the gating, can be shifted considerably by the electrostatic force between the charges on the DNA and the voltage sensing domain of the protein. Different hybridization states of the chimera DNA thus lead to different response curves of the channel.
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Affiliation(s)
- Andrew Wang
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California, United States of America
| | - Giovanni Zocchi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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20
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21
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22
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Sacquin-Mora S, Delalande O, Baaden M. Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress. Biophys J 2011; 99:3412-9. [PMID: 21081090 DOI: 10.1016/j.bpj.2010.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/11/2010] [Accepted: 09/15/2010] [Indexed: 01/27/2023] Open
Abstract
The coupling between the mechanical properties of enzymes and their biological activity is a well-established feature that has been the object of numerous experimental and theoretical works. In particular, recent experiments show that enzymatic function can be modulated anisotropically by mechanical stress. We study such phenomena using a method for investigating local flexibility on the residue scale that combines a reduced protein representation with Brownian dynamics simulations. We performed calculations on the enzyme guanylate kinase to study its mechanical response when submitted to anisotropic deformations. The resulting modifications of the protein's rigidity profile can be related to the changes in substrate binding affinity observed experimentally. Further analysis of the principal components of motion of the trajectories shows how the application of a mechanical constraint on the protein can disrupt its dynamics, thus leading to a decrease of the enzyme's catalytic rate. Eventually, a systematic probe of the protein surface led to the prediction of potential hotspots where the application of an external constraint would produce a large functional response both from the mechanical and dynamical points of view. Such enzyme-engineering approaches open the possibility to tune catalytic function by varying selected external forces.
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Affiliation(s)
- Sophie Sacquin-Mora
- Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, CNRS UPR9080, Paris, France.
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23
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Saccà B, Niemeyer CM. Functionalization of DNA nanostructures with proteins. Chem Soc Rev 2011; 40:5910-21. [DOI: 10.1039/c1cs15212b] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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24
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Abstract
An allosteric model is used to describe changes in lifetimes of biological receptor-ligand bonds subjected to an external force. Force-induced transitions between the two states of the allosteric site lead to changes in the receptor conformation. The ligand bound to the receptor fluctuates between two different potentials formed by the two receptor conformations. The effect of the force on the receptor-ligand interaction potential is described by the Bell mechanism. The probability of detecting the ligand in the bound state is found to depend on the relaxation times of both ligand and allosteric sites. An analytic expression for the bond lifetime is derived as a function of force. The formal theoretical results are used to explain the anomalous force and time dependences of the integrin-fibronectin bond lifetimes measured by atomic force microscopy (Kong, F.; et al J. Cell Biol. 2009, 185, 1275-1284). The analytic expression and model parameters describe very well all anomalous dependences identified in the experiments.
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Affiliation(s)
| | - Oleg V. Prezhdo
- Department of Chemistry, University of Washington, Seattle, WA 98195
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25
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Diezmann F, Eberhard H, Seitz O. Native chemical ligation in the synthesis of internally modified oligonucleotide-peptide conjugates. Biopolymers 2010; 94:397-404. [PMID: 20593471 DOI: 10.1002/bip.21440] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Peptide-oligonucleotide conjugates have frequently been synthesized to improve cellular delivery of antisense or antigene compounds, to allow the immobilization of peptide and protein conjugates on DNA arrays, or to decorate nucleic acid architectures with peptide functions. In such applications, the site of conjugation is of little importance, and peptides have predominantly been appended to one of the terminal ends of the oligonucleotide by using an oxime-, thioether-, or disulfide-linkage or native chemical ligation. We, herein, demonstrate the first coupling of peptides to sequence internal sites. This attachment mode provides better control of the spatial arrangement of peptides presented by self-assembled nucleic acid scaffolds. Internal modification requires special phosphoramidite building blocks that can be used in automated DNA synthesis. For this purpose, Fmoc/StBu-protected cysteine was attached via an aminopropargyl linker to the C5-position of uridine. The rigid triple bond conferred a high reactivity in native chemical ligation reactions of 5-6mer peptide thioesters with up to 15 nucleotides long oligonucleotides. The desired peptide-oligonucleotide conjugates were obtained in high yields after purification. UV melt experiments revealed that the peptide modification does not hamper nucleic acid hybridization. This finding marked an important step in our research program devoted to studies of multivalent presentation of peptides via modular assembly of nucleic acid complexes.
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Affiliation(s)
- Franziska Diezmann
- Institute of Chemistry, Humboldt-University of Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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26
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Tseng CY, Wang A, Zocchi G, Rolih B, Levine AJ. Elastic energy of protein-DNA chimeras. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:061912. [PMID: 20365195 DOI: 10.1103/physreve.80.061912] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 09/22/2009] [Indexed: 05/29/2023]
Abstract
We present experimental measurements of the equilibrium elastic energy of protein-DNA chimeras, for two different sets of attachment points of the DNA "molecular spring" on the surface of the protein. Combining these with measurements of the enzyme's activity under stress and a mechanical model of the system, we determine how the elastic energy is partitioned between the DNA and the protein. The analysis shows that the protein is mechanically stiffer than the DNA spring.
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Affiliation(s)
- Chiao-Yu Tseng
- Department of Physics and Astronomy, UCLA, Los Angeles, California 90095-1596, USA
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27
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Wang Y, Wang A, Qu H, Zocchi G. Protein-DNA chimeras: synthesis of two-arm chimeras and non-mechanical effects of the DNA spring. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:335103. [PMID: 21828597 DOI: 10.1088/0953-8984/21/33/335103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA molecular springs have recently been used to control the activity of enzymes and ribozymes. In this approach, the mechanical stress exerted by the molecular spring alters the enzyme's conformation and thus the enzymatic activity. Here we describe a method alternative to our previous one to attach DNA molecular springs to proteins, where two separate DNA 'arms' are coupled to the protein and subsequently ligated. We report certain non-mechanical effects associated with the DNA spring observed in some chimeras with specific DNA sequences and the nucleotide binding enzyme guanylate kinase. If a ssDNA 'arm' is attached to the protein by one end only, we find that in some cases (depending on the DNA sequence and attachment point on the protein's surface) the unhybridized DNA arm inhibits the enzyme, while hybridization of the DNA arm leads to an apparent activation of the enzyme. One interpretation is that, in these cases, hybridization of the DNA arm removes it from the vicinity of the active site of the enzyme. We show how mechanical and non-mechanical effects of the DNA spring can be distinguished. This is important if one wants to use the protein-DNA chimeras to quantitatively study the response of the enzyme to mechanical perturbations.
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Affiliation(s)
- Yong Wang
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095-1547, USA
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28
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Abstract
We argue that the mechanical control of proteins-the notion of controlling chemical reactions and processes by mechanics-is conceptually interesting. We give a brief review of the main accomplishments so far, leading to our present approach of using DNA molecular springs to exert controlled stresses on proteins. Our focus is on the physical principles that underlie both artificial mechanochemical devices and natural mechanisms of allostery.
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Affiliation(s)
- Giovanni Zocchi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095-1547, USA.
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29
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Wang A, Zocchi G. Elastic energy driven polymerization. Biophys J 2009; 96:2344-52. [PMID: 19289060 DOI: 10.1016/j.bpj.2008.11.065] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 09/11/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022] Open
Abstract
We present a molecular system where polymerization is controlled externally by tuning the elastic energy of the monomers. The elastic energy, provided by a DNA molecular spring, destabilizes the monomer state through a process analogous to domain swapping. This energy can be large (of approximately 10 kT) and thus drive polymerization at relatively low monomer concentrations. The monomer-dimer equilibrium provides a measurement of the elastic energy of the monomer, which in this construction appears limited by kink formation in the DNA molecular spring, in accord with previous theoretical and experimental investigations of the elasticity of sharply bent DNA.
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Affiliation(s)
- Andrew Wang
- Department of Physics & Astronomy, University of California, Los Angeles, California, USA
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30
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Pereverzev YV, Prezhdo OV, Sokurenko EV. Allosteric role of the large-scale domain opening in biological catch-binding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:051913. [PMID: 19518486 DOI: 10.1103/physreve.79.051913] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Indexed: 05/27/2023]
Abstract
The proposed model demonstrates the allosteric role of the two-domain region of the receptor protein in the increased lifetimes of biological receptor/ligand bonds subjected to an external force. The interaction between the domains is represented by a bounded potential, containing two minima corresponding to the attached and separated conformations of the two protein domains. The dissociative potential with a single minimum describing receptor/ligand binding fluctuates between deep and shallow states, depending on whether the domains are attached or separated. A number of valuable analytic expressions are derived and are used to interpret experimental data for two catch bonds. The P-selectin/P-selectin-glycoprotein-ligand-1 (PSGL-1) bond is controlled by the interface between the epidermal growth factor (EGF) and lectin domains of P-selectin, and the type 1 fimbrial adhesive protein (FimH)/mannose bond is governed by the interface between the lectin and pilin domains of FimH. Catch-binding occurs in these systems when the external force stretches the receptor proteins and increases the interdomain distance. The allosteric effect is supported by independent measurements, in which the domains are kept separated by attachment of another ligand. The proposed model accurately describes the experimentally observed anomalous behavior of the lifetimes of the P-selectin/PSGL-1 and FimH/mannose complexes as a function of applied force and provides valuable insights into the mechanism of catch-binding.
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Affiliation(s)
- Yuriy V Pereverzev
- Departments of Chemistry and Microbiology, University of Washington, Seattle, Washington 98195, USA
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31
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Sacquin-Mora S, Lavery R. Modeling the mechanical response of proteins to anisotropic deformation. Chemphyschem 2009; 10:115-8. [PMID: 19006155 DOI: 10.1002/cphc.200800480] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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32
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Zelin E, Silverman SK. Efficient control of group I intron ribozyme catalysis by DNA constraints. Chem Commun (Camb) 2009:767-9. [PMID: 19322435 DOI: 10.1039/b820676g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double-stranded DNA constraints enable efficient control of catalysis by a large multi-domain group I intron ribozyme.
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Affiliation(s)
- Elena Zelin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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33
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Röglin L, Seitz O. Controlling the activity of peptides and proteins with smart nucleic acid–protein hybrids. Org Biomol Chem 2008; 6:3881-7. [DOI: 10.1039/b807838f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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34
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Affiliation(s)
- Elena Zelin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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35
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Gianneschi N, Ghadiri M. Design of Molecular Logic Devices Based on a Programmable DNA-Regulated Semisynthetic Enzyme. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Röglin L, Ahmadian MR, Seitz O. DNA-Controlled Reversible Switching of Peptide Conformation and Bioactivity. Angew Chem Int Ed Engl 2007; 46:2704-7. [PMID: 17330908 DOI: 10.1002/anie.200603889] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lars Röglin
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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37
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Röglin L, Ahmadian M, Seitz O. DNA-gesteuerte reversible Schaltung der Konformation und der Bioaktivität eines Peptids. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603889] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Silverman SK. Control of macromolecular structure and function using covalently attached double-stranded DNA constraints. ACTA ACUST UNITED AC 2007; 3:24-9. [PMID: 17216052 DOI: 10.1039/b614116a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biophysical properties of DNA suggest its use for applications beyond serving as the genetic material. Several recent reports describe the use of covalently attached double-stranded DNA for controlling the structures of other macromolecules such as protein and RNA. These exploitations of DNA rigidity are conceptually distinct from many other studies in the area of "DNA nanotechnology". Double-stranded DNA constraints provide a means of introducing selective tension onto other molecules. This should facilitate fundamental investigations of macromolecular folding landscapes and tertiary interactions, as well as allow study of the mechanotransduction of biochemical signals. Use of a DNA constraint as the key element of a sensor has already been demonstrated, and such applications will be enhanced by improvements in the signal readout methods. If practical challenges such as delivery and stability can be addressed, these new efforts may also enable development of selective sensors for in vivo applications.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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39
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Gianneschi NC, Ghadiri MR. Design of molecular logic devices based on a programmable DNA-regulated semisynthetic enzyme. Angew Chem Int Ed Engl 2007; 46:3955-8. [PMID: 17427900 PMCID: PMC2790070 DOI: 10.1002/anie.200700047] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nathan C. Gianneschi
- Dr. N. C. Gianneschi, Prof. Dr. M. R. Ghadiri, Departments of Chemistry and Molecular Biology and the, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037 (USA), Fax: (+1) 858-784-2798
| | - M. Reza Ghadiri
- Dr. N. C. Gianneschi, Prof. Dr. M. R. Ghadiri, Departments of Chemistry and Molecular Biology and the, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037 (USA), Fax: (+1) 858-784-2798, E-mail:
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40
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Abstract
Since the introduction of the induced-fit theory by D. E. Koshland Jr., it has been established that conformational motion invariably accompanies the execution of protein function. The catalytic activity of kinases, specifically, is associated with large conformational changes ( approximately 1 nm amplitude). In the case of guanylate kinase, upon substrate binding, the LID and nucleotide-monophosphate-binding domains are brought together and toward the CORE with large concerted movements about the alpha3 (helix 3) axis. However, whether the change in conformation mostly affects the catalytic rate or mostly increases binding affinities for one or the other substrate is unclear. We investigate this question using a nanotechnology approach based on mechanical stress. Using an "allosteric spring probe", we bias conformational states in favor of the "open" (substrate-free) conformation of the enzyme; the result is that the binding constant for the substrate guanosine monophosphate (GMP) is reduced by up to a factor of 10, whereas the binding constant for adenosine triphosphate (ATP) and the catalytic rate are essentially unaffected. The results show that the GMP-induced conformational change, which promotes catalysis, does not promote ATP binding, consistent with previous mutagenesis studies. Furthermore, they show that this conformational change is of the induced-fit type with respect to GMP binding (but not ATP binding). We elaborate on this point by proposing a quantitative criterion for the classification of conformational changes with respect to the induced-fit theory. More generally, these results show that the allosteric spring probe can be used to affect enzymatic activity in a continuously controlled manner, and also to affect specific steps of the reaction mechanism while leaving others unaffected. It is presumed that this will enable informative comparisons with the results of future molecular dynamics or statistical mechanics computations.
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Affiliation(s)
- Brian Choi
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
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41
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Hible G, Daalova P, Gilles AM, Cherfils J. Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G. Biochimie 2006; 88:1157-64. [PMID: 16690197 DOI: 10.1016/j.biochi.2006.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 04/04/2006] [Indexed: 11/24/2022]
Abstract
Guanosine monophosphate kinases (GMPK), by catalyzing the phosphorylation of GMP or dGMP, are of dual potential in assisting the activation of anti-viral prodrugs or as candidates for antibiotic strategies. Human GMPK is an obligate step for the activation of acyclic guanosine analogs, such as ganciclovir, which necessitate efficient phosphorylation, while GMPK from bacterial pathogens, in which this enzyme is essential, are potential targets for therapeutic inhibition. Here we analyze these two aspects of GMPK activity with the crystal structures of Escherichia coli GMPK in complex with ganciclovir-monophosphate (GCV-MP) and with a bi-substrate inhibitor, Ap5G. GCV-MP binds as GMP to the GMP-binding domain, which is identical in E. coli and human GMPKs, but unlike the natural substrate fails to stabilize the closed, catalytically-competent conformation of this domain. Comparison with GMP- and GDP-bound GMPK structures identifies the 2'hydroxyl of the ribose moiety as responsible for hooking the GMP-binding domain onto the CORE domain. Absence of this hydroxyl in GCV-MP impairs the stabilization of the active conformation, and explains why GCV-MP is phosphorylated less efficiently than GMP, but as efficiently as dGMP. In contrast, Ap5G is an efficient inhibitor of GMPK. The crystal structure shows that Ap5G locks an incompletely closed conformation of the enzyme, in which the adenine moiety is located outside its expected binding site. Instead, it binds at a subunit interface that is unique to the bacterial enzyme, which is in equilibrium between a dimeric and an hexameric form in solution. This suggests that inhibitors could be designed to bind at this interface such as to prevent nucleotide-induced domain closure. Altogether, these complexes point to domain motions as critical components to be evaluated in therapeutic strategies targeting NMP kinases, with opposite effects depending on whether efficient phosphorylation or inhibition is being sought after.
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Affiliation(s)
- G Hible
- Laboratoire d'Enzymologie et Biochimie Structurales, bâtiment 34, CNRS, avenue de la Terrasse, 91198 Gif sur Yvette cedex, France
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42
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Miduturu CV, Silverman SK. Modulation of DNA Constraints That Control Macromolecular Folding. Angew Chem Int Ed Engl 2006; 45:1918-21. [PMID: 16485308 DOI: 10.1002/anie.200504124] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Miduturu CV, Silverman SK. Modulation of DNA Constraints That Control Macromolecular Folding. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Demidov VV, Dokholyan NV, Witte-Hoffmann C, Chalasani P, Yiu HW, Ding F, Yu Y, Cantor CR, Broude NE. Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc Natl Acad Sci U S A 2006; 103:2052-6. [PMID: 16461889 PMCID: PMC1413755 DOI: 10.1073/pnas.0511078103] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Fluorescent proteins have proven to be excellent reporters and biochemical sensors with a wide range of applications. In a split form, they are not fluorescent, but their fluorescence can be restored by supplementary protein-protein or protein-nucleic acid interactions that reassemble the split polypeptides. However, in prior studies, it took hours to restore the fluorescence of a split fluorescent protein because the formation of the protein chromophore slowly occurred de novo concurrently with reassembly. Here we provide evidence that a fluorogenic chromophore can self-catalytically form within an isolated N-terminal fragment of the enhanced green fluorescent protein (EGFP). We show that restoration of the split protein fluorescence can be driven by nucleic acid complementary interactions. In our assay, fluorescence development is fast (within a few minutes) when complementary oligonucleotide-linked fragments of the split EGFP are combined. The ability of our EGFP system to respond quickly to DNA hybridization should be useful for detecting the kinetics of many other types of pairwise interactions both in vitro and in living cells.
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Affiliation(s)
- Vadim V. Demidov
- *Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215
- To whom correspondence may be addressed. E-mail:
, , or
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599; and
| | - Carlos Witte-Hoffmann
- *Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Poornima Chalasani
- *Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Hung-Wei Yiu
- *Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Feng Ding
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599; and
| | - Yong Yu
- *Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Charles R. Cantor
- *Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215
- Sequenom, Inc., San Diego, CA 92121
- To whom correspondence may be addressed. E-mail:
, , or
| | - Natalia E. Broude
- *Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215
- To whom correspondence may be addressed. E-mail:
, , or
| |
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