1
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Fontecilla-Camps JC. The Complex Roles of Adenosine Triphosphate in Bioenergetics. Chembiochem 2022; 23:e202200064. [PMID: 35353443 DOI: 10.1002/cbic.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/16/2022] [Indexed: 11/09/2022]
Abstract
ATP is generally defined as the "energy currency" of the cell. Its phosphoanhydride P-O bonds are often considered to be "high energy" linkages that release free energy when broken, and its hydrolysis is described as "strongly exergonic". However, breaking bonds cannot release energy and ATP hydrolysis in motor and active transport proteins is not "strongly exergonic". So, the relevance of ATP resides elsewhere. As important as the nucleotide are the proteins that undergo functionally relevant conformational changes upon both ATP binding and release of ADP and inorganic phosphate. ATP phosphorylates proteins for signaling, active transport, and substrates in condensation reactions. The ensuing dephosphorylation has different consequences in each case. In signaling and active transport the phosphate group is hydrolyzed whereas in condensation reactions the phosphoryl fragment acts as a dehydrating agent. As it will be discussed in this article, ATP does much more than simply contribute free energy to biological processes.
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2
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Wang C, Chu Y, Hu M, Cai W, Wang Q, Qi G, Li S, Xu J, Deng F. Insight into Carbocation‐Induced Noncovalent Interactions in the Methanol‐to‐Olefins Reaction over ZSM‐5 Zeolite by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Chao Wang
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yueying Chu
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Min Hu
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Wenjin Cai
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qiang Wang
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Guodong Qi
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Shenhui Li
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Jun Xu
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Feng Deng
- National Center for Magnetic Resonance in Wuhan State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan 430071 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
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3
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Wang C, Chu Y, Hu M, Cai W, Wang Q, Qi G, Li S, Xu J, Deng F. Insight into Carbocation-Induced Noncovalent Interactions in the Methanol-to-Olefins Reaction over ZSM-5 Zeolite by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2021; 60:26847-26854. [PMID: 34636120 DOI: 10.1002/anie.202112948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 11/06/2022]
Abstract
Carbocations such as cyclic carbenium ions are important intermediates in the zeolite-catalyzed methanol-to-olefins (MTO) reaction. The MTO reaction propagates through a complex hydrocarbon pool process. Understanding the carbocation-involved hydrocarbon pool reaction on a molecular level still remains challenging. Here we show that electron-deficient cyclopentenyl cations stabilized in ZSM-5 zeolite are able to capture the alkanes, methanol, and olefins produced during MTO reaction via noncovalent interactions. Intermolecular spatial proximities/interactions are identified by using two-dimensional 13 C-13 C correlation solid-state NMR spectroscopy. Combined NMR experiments and theoretical analysis suggests that in addition to the dispersion and CH/π interactions, the multiple functional groups in the cyclopentenyl cations produce strong attractive force via cation-induced dipole, cation-dipole and cation-π interactions. These carbocation-induced noncovalent interactions modulate the product selectivity of hydrocarbon pool reaction.
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Affiliation(s)
- Chao Wang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yueying Chu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Min Hu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wenjin Cai
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qiang Wang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Guodong Qi
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shenhui Li
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jun Xu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Feng Deng
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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4
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Seo SB, Lee S, Jeon HG, Jeong KS. Dramatic Enhancement of Binding Affinities Between Foldamer-Based Receptors and Anions by Intra-Receptor π-Stacking. Angew Chem Int Ed Engl 2020; 59:10441-10445. [PMID: 32157775 DOI: 10.1002/anie.202002657] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Indexed: 01/01/2023]
Abstract
As a synthetic model for intra-protein interactions that reinforce binding affinities between proteins and ligands, the energetic interplay of binding and folding was investigated using foldamer-based receptors capable of adopting helical structures. The receptors were designed to have identical hydrogen-bonding sites for anion binding but different aryl appendages that simply provide additional π-stacking within the helical backbones without direct interactions with the bound anions. In particular, the presence of electron-deficient aryl appendages led to dramatic enhancements in the association constant between the receptor and chloride or nitrate ions, by up to three orders of magnitude. Extended stacking within the receptor contributes to the stabilization of the entire folding structure of complexes, thereby enhancing binding affinities.
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Affiliation(s)
- Sung Beom Seo
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Seungwon Lee
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hae-Geun Jeon
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kyu-Sung Jeong
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
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5
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Seo SB, Lee S, Jeon H, Jeong K. Dramatic Enhancement of Binding Affinities Between Foldamer‐Based Receptors and Anions by Intra‐Receptor π‐Stacking. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sung Beom Seo
- Department of Chemistry Yonsei University Seoul 03722 Republic of Korea
| | - Seungwon Lee
- Department of Chemistry Yonsei University Seoul 03722 Republic of Korea
| | - Hae‐Geun Jeon
- Department of Chemistry Yonsei University Seoul 03722 Republic of Korea
| | - Kyu‐Sung Jeong
- Department of Chemistry Yonsei University Seoul 03722 Republic of Korea
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6
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Shimoyama D, Haino T. Entropy‐Driven Cooperativity in the Guest Binding of an Octaphosphonate Bis‐cavitand. Chemistry 2020; 26:3074-3079. [DOI: 10.1002/chem.201905036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Daisuke Shimoyama
- Department of ChemistryGraduate School of ScienceHiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
| | - Takeharu Haino
- Department of ChemistryGraduate School of ScienceHiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
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7
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Gimeno MC, Herrera RP. Hydrogen Bonding and Internal or External Lewis or Brønsted Acid Assisted (Thio)urea Catalysts. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901344] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- M. Concepción Gimeno
- Departamento de Química Inorgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC-Universidad de Zaragoza; C/ Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Raquel P. Herrera
- Departamento de Química Orgánica. Laboratorio de Organocatálisis Asimétrica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC-Universidad de Zaragoza; C/ Pedro Cerbuna 12 50009 Zaragoza Spain
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8
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Santarsia S, Grosso AS, Trovão F, Jiménez-Barbero J, Carvalho AL, Nativi C, Marcelo F. Molecular Recognition of a Thomsen-Friedenreich Antigen Mimetic Targeting Human Galectin-3. ChemMedChem 2018; 13:2030-2036. [PMID: 30094951 DOI: 10.1002/cmdc.201800525] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 11/11/2022]
Abstract
Overexpression of the Thomsen-Friedenreich (TF) antigen in cell membrane proteins occurs in 90 % of adenocarcinomas. Additionally, the binding of the TF antigen to human galectin-3 (Gal-3), also frequently overexpressed in malignancy, promotes cancer progression and metastasis. In this context, structures that interfere with this specific interaction have the potential to prevent cancer metastasis. A multidisciplinary approach combining the optimized synthesis of a TF antigen mimetic with NMR, X-ray crystallography methods, and isothermal titration calorimetry assays was used to unravel the molecular structural details that govern the Gal-3/TF mimetic interaction. The TF mimetic has a binding affinity for Gal-3 similar to that of the TF natural antigen and retains the binding epitope and bioactive conformation observed for the native antigen. Furthermore, from a thermodynamic perspective, a decrease in the enthalpic contribution was observed for the Gal-3/TF mimetic complex; however, this behavior is compensated by a favorable gain in entropy. From a structural perspective, these results establish our TF mimetic as a scaffold to design multivalent solutions to potentially interfere with Gal-3 aberrant interactions and for likely use in hampering Gal-3-mediated cancer cell adhesion and metastasis.
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Affiliation(s)
- Sabrina Santarsia
- Department of Chemistry Ugo Schiff, University of Florence, Via della Lastruccia, 13-50019, Sesto Fiorentino, Italy
| | - Ana Sofia Grosso
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Filipa Trovão
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC-bioGUNE Bizkaia, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48005, Bilbao, Spain.,Department of Organic Chemistry II, EHU-UPV, 48040, Leioa, Spain
| | - Ana Luísa Carvalho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Cristina Nativi
- Department of Chemistry Ugo Schiff, University of Florence, Via della Lastruccia, 13-50019, Sesto Fiorentino, Italy
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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9
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Mandal S, Selvam S, Cui Y, Hoque ME, Mao H. Mechanical Cooperativity in DNA Cruciform Structures. Chemphyschem 2018; 19:2627-2634. [PMID: 29992736 DOI: 10.1002/cphc.201800480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Indexed: 01/20/2023]
Abstract
Unlike short-range chemical bonds that maintain chemical properties of a biological molecule, long-range mechanical interactions determine mechanochemical properties of molecules. Limited by experimental approaches, however, direct quantification of such mechanical interactions is challenging. Using magneto-optical tweezers, herein we found torque can change the topology and mechanochemical property of DNA cruciform, a naturally occurring structure consisting of two opposing hairpin arms. Both mechanical and thermodynamic stabilities of DNA cruciforms increase with positive torque, which have been attributed to the topological coupling between DNA template and the cruciform. The coupling exists simultaneously in both arms of a cruciform, which coordinates the folding and unfolding of the cruciform, leading to a mechanical cooperativity not observed previously. As DNA torque readily varies during transcriptions, our finding suggests that DNA cruciforms can modulate transcriptions by adjusting their properties according to the torque.
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Affiliation(s)
- Shankar Mandal
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Sangeetha Selvam
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Yunxi Cui
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Mohammed Enamul Hoque
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
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10
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Baudet K, Guerra S, Piguet C. Chemical Potential of the Solvent: A Crucial Player for Rationalizing Host-Guest Affinities. Chemistry 2017; 23:16787-16798. [DOI: 10.1002/chem.201703184] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Karine Baudet
- Department of Inorganic, Analytical and Applied Chemistry; University of Geneva; 30 quai E. Ansermet 1211 Geneva 4 Switzerland
| | - Sebastiano Guerra
- Department of Inorganic, Analytical and Applied Chemistry; University of Geneva; 30 quai E. Ansermet 1211 Geneva 4 Switzerland
| | - Claude Piguet
- Department of Inorganic, Analytical and Applied Chemistry; University of Geneva; 30 quai E. Ansermet 1211 Geneva 4 Switzerland
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11
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Xu JF, Chen L, Zhang X. How to Make Weak Noncovalent Interactions Stronger. Chemistry 2015; 21:11938-46. [DOI: 10.1002/chem.201500568] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 12/20/2022]
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12
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Zhao Y. Cooperatively enhanced receptors for biomimetic molecular recognition. Chemphyschem 2013; 14:3878-85. [PMID: 24151236 DOI: 10.1002/cphc.201300744] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 08/22/2013] [Indexed: 11/06/2022]
Abstract
The concept of preorganization suggests that organizing a receptor around its guest during binding is detrimental, because the cost of conformational change is assumed to be paid out of the binding energy. Although this concept has historically guided the synthesis of a great many synthetic hosts, in recent years, chemists have begun to synthesize receptors that resemble proteins in their cooperative conformational changes. Such changes could enhance the host-guest interactions, in particular if the binding of the guest triggers previously unengaged noncovalent interactions within the host. These hosts, referred to as cooperatively enhanced receptors, corroborate with their biological counterparts to support the approach of creating high-affinity receptors through the combined strategies of cooperativity and preorganization. Solvents, often the invisible participants of any solution-based supramolecular process, should be properly considered in the design of synthetic receptors, whether preorganized or cooperatively enhanced.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111 (USA), Fax: (+1) 515-294-5845.
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13
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Dutronc T, Terazzi E, Guénée L, Buchwalder KL, Spoerri A, Emery D, Mareda J, Floquet S, Piguet C. Enthalpy-Entropy Compensation Combined with Cohesive Free-Energy Densities for Tuning the Melting Temperatures of Cyanobiphenyl Derivatives. Chemistry 2013; 19:8447-56. [DOI: 10.1002/chem.201300587] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Indexed: 11/08/2022]
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14
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Carrillo R, Morales EQ, Martín VS, Martín T. A Novel Approach for the Evaluation of Positive Cooperative Guest Binding: Kinetic Consequences of Structural Tightening. Chemistry 2013; 19:7042-8. [DOI: 10.1002/chem.201300583] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Indexed: 11/10/2022]
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15
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Mikata Y, Fujimoto T, Imai N, Kondo S. Differentiation of Oxygen Atom Chirality in Copper(II) Complexes with Dipicolylamine‐Derived Ligands. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yuji Mikata
- KYOUSEI Science Center, Nara Women's University, Nara 630‐8506, Japan, Fax: +81‐742‐20‐3095, http://koto10.nara‐wu.ac.jp/Profiles/4/0000384/prof_e.html
| | - Tomomi Fujimoto
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara 630‐8506, Japan
| | - Noko Imai
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara 630‐8506, Japan
| | - Shin‐ichi Kondo
- Department of Materials and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990‐8560, Japan
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16
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Biela A, Betz M, Heine A, Klebe G. Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding. ChemMedChem 2012; 7:1423-34. [PMID: 22733601 DOI: 10.1002/cmdc.201200206] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 05/21/2012] [Indexed: 12/18/2022]
Abstract
The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected.
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Affiliation(s)
- Adam Biela
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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17
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Xing B, Jiang T, Wu X, Liew R, Zhou J, Zhang D, Yeow EKL. Molecular Interactions between Glycopeptide Vancomycin and Bacterial Cell Wall Peptide Analogues. Chemistry 2011; 17:14170-7. [DOI: 10.1002/chem.201102195] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Indexed: 11/11/2022]
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18
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Rostami A, Taylor MS. Polymers for Anion Recognition and Sensing. Macromol Rapid Commun 2011; 33:21-34. [DOI: 10.1002/marc.201100528] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/12/2011] [Indexed: 01/25/2023]
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19
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Carrillo R, Feher-Voelger A, Martín T. Enantioselective Cooperativity Between Intra-Receptor Interactions and Guest Binding: Quantification of Reinforced Chiral Recognition. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103970] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Carrillo R, Feher-Voelger A, Martín T. Enantioselective Cooperativity Between Intra-Receptor Interactions and Guest Binding: Quantification of Reinforced Chiral Recognition. Angew Chem Int Ed Engl 2011; 50:10616-20. [DOI: 10.1002/anie.201103970] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/25/2011] [Indexed: 11/08/2022]
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21
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Frontera A, Gamez P, Mascal M, Mooibroek TJ, Reedijk J. Anion-π-Wechselwirkungen ins rechte Licht gerückt. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100208] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Frontera A, Gamez P, Mascal M, Mooibroek TJ, Reedijk J. Putting anion-π interactions into perspective. Angew Chem Int Ed Engl 2011; 50:9564-83. [PMID: 21928463 DOI: 10.1002/anie.201100208] [Citation(s) in RCA: 520] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/16/2011] [Indexed: 01/20/2023]
Abstract
Supramolecular chemistry is a field of scientific exploration that probes the relationship between molecular structure and function. It is the chemistry of the noncovalent bond, which forms the basis of highly specific recognition, transport, and regulation events that actuate biological processes. The classic design principles of supramolecular chemistry include strong, directional interactions like hydrogen bonding, halogen bonding, and cation-π complexation, as well as less directional forces like ion pairing, π-π, solvophobic, and van der Waals potentials. In recent years, the anion-π interaction (an attractive force between an electron-deficient aromatic π system and an anion) has been recognized as a hitherto unexplored noncovalent bond, the nature of which has been interpreted through both experimental and theoretical investigations. The design of selective anion receptors and channels based on this interaction represent important advances in the field of supramolecular chemistry. The objectives of this Review are 1) to discuss current thinking on the nature of this interaction, 2) to survey key experimental work in which anion-π bonding is demonstrated, and 3) to provide insights into the directional nature of anion-π contact in X-ray crystal structures.
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Affiliation(s)
- Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.
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Tulyakova E, Delbaere S, Fedorov Y, Jonusauskas G, Moiseeva A, Fedorova O. Multimodal Metal Cation Sensing with Bis(macrocyclic) Dye. Chemistry 2011; 17:10752-62. [DOI: 10.1002/chem.201100998] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elena Tulyakova
- CNRS UMR 8516, Université Lille Nord de France, 3 rue du Professeur Laguesse BP83, 59006 Lille (France)
| | - Stephanie Delbaere
- CNRS UMR 8516, Université Lille Nord de France, 3 rue du Professeur Laguesse BP83, 59006 Lille (France)
| | - Yuri Fedorov
- A. N. Nesmeyanov Institute of Organoelement Compounds, 28 Vavilova street, 119991 Moscow (Russian Federation)
| | - Gedaminas Jonusauskas
- Laboratoire Ondes et Matière d'Aquitaine, Bordeaux University I, UMR CNRS 5798, 351 Cours de la Libiration, 33405 Talence (France)
| | - Anna Moiseeva
- Chemistry Department, M. V. Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow (Russian Federation)
| | - Olga Fedorova
- A. N. Nesmeyanov Institute of Organoelement Compounds, 28 Vavilova street, 119991 Moscow (Russian Federation)
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Sohtome Y, Shin B, Horitsugi N, Noguchi K, Nagasawa K. Linking Conformational Flexibility and Kinetics: Catalytic 1,4-Type Friedel-Crafts Reactions of Phenols Utilizing 1,3-Diamine-Tethered Guanidine/Bisthiourea Organocatalysts. Chem Asian J 2011; 6:2463-70. [DOI: 10.1002/asia.201100363] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Indexed: 11/09/2022]
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Liskamp RMJ, Rijkers DTS, Kruijtzer JAW, Kemmink J. Peptides and proteins as a continuing exciting source of inspiration for peptidomimetics. Chembiochem 2011; 12:1626-53. [PMID: 21751324 DOI: 10.1002/cbic.201000717] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 12/17/2022]
Abstract
Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the "stem" of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide-peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.
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Affiliation(s)
- Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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Urbach AR, Ramalingam V. Molecular Recognition of Amino Acids, Peptides, and Proteins by Cucurbit[n]uril Receptors. Isr J Chem 2011. [DOI: 10.1002/ijch.201100035] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Palomino GT, Cabello CP, Areán CO. Enthalpy-Entropy Correlation for Hydrogen Adsorption on MOFs: Variable-Temperature FTIR Study of Hydrogen Adsorption on MIL-100(Cr) and MIL-101(Cr). Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001116] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ko YH, Kim Y, Kim H, Kim K. U-Shaped Conformation of Alkyl Chains Bound to a Synthetic Receptor Cucurbit[8]uril. Chem Asian J 2010; 6:652-7. [DOI: 10.1002/asia.201000665] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Indexed: 11/08/2022]
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Bonelli B, Armandi M, Areán CO, Garrone E. Ammonia-Solvated Ammonium Species in the NH4-ZSM-5 Zeolite. Chemphyschem 2010; 11:3255-61. [DOI: 10.1002/cphc.201000477] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sohtome Y, Shin B, Horitsugi N, Takagi R, Noguchi K, Nagasawa K. Entropy-Controlled Catalytic Asymmetric 1,4-Type Friedel-Crafts Reaction of Phenols Using Conformationally Flexible Guanidine/Bisthiourea Organocatalyst. Angew Chem Int Ed Engl 2010; 49:7299-303. [DOI: 10.1002/anie.201003172] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sohtome Y, Shin B, Horitsugi N, Takagi R, Noguchi K, Nagasawa K. Entropy-Controlled Catalytic Asymmetric 1,4-Type Friedel-Crafts Reaction of Phenols Using Conformationally Flexible Guanidine/Bisthiourea Organocatalyst. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003172] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Areán CO, Chavan S, Cabello CP, Garrone E, Palomino GT. Thermodynamics of Hydrogen Adsorption on Metal-Organic Frameworks. Chemphyschem 2010; 11:3237-42. [DOI: 10.1002/cphc.201000523] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Matsumoto S, Iwamoto H, Mizutani T. Water Accessibility to the Binding Cleft as a Major Switching Factor from Entropy-Driven to Enthalpy-Driven Binding of an Alkyl Group by Synthetic Receptors. Chem Asian J 2010; 5:1163-70. [DOI: 10.1002/asia.200900679] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Schober K, Hartmann E, Zhang H, Gschwind R. 1H-DOSY-Spektren von Liganden für hochenantioselektive Reaktionen - eine schnelle und einfache Methode zur Optimierung katalytischer Reaktionsbedingungen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907247] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Schober K, Hartmann E, Zhang H, Gschwind R. 1H DOSY Spectra of Ligands for Highly Enantioselective Reactions-A Fast and Simple NMR Method to Optimize Catalytic Reaction Conditions. Angew Chem Int Ed Engl 2010; 49:2794-7. [DOI: 10.1002/anie.200907247] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bach A, Chi CN, Pang GF, Olsen L, Kristensen AS, Jemth P, Strømgaard K. Design and synthesis of highly potent and plasma-stable dimeric inhibitors of the PSD-95-NMDA receptor interaction. Angew Chem Int Ed Engl 2010; 48:9685-9. [PMID: 19937879 DOI: 10.1002/anie.200904741] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Anders Bach
- Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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Bach A, Chi C, Pang G, Olsen L, Kristensen A, Jemth P, Strømgaard K. Design and Synthesis of Highly Potent and Plasma-Stable Dimeric Inhibitors of the PSD-95-NMDA Receptor Interaction. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904741] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jones C, Dan Pantoş G, Morrison A, Smith M. Plagiarizing Proteins: Enhancing Efficiency in Asymmetric Hydrogen-Bonding Catalysis through Positive Cooperativity. Angew Chem Int Ed Engl 2009; 48:7391-4. [DOI: 10.1002/anie.200903063] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Jones C, Dan Pantoş G, Morrison A, Smith M. Plagiarizing Proteins: Enhancing Efficiency in Asymmetric Hydrogen-Bonding Catalysis through Positive Cooperativity. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903063] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.
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Affiliation(s)
- Hans-Jörg Schneider
- Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken, Deutschland.
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Yang Z, Vorpagel ER, Laskin J. Influence of the charge state on the structures and interactions of vancomycin antibiotics with cell-wall analogue peptides: experimental and theoretical studies. Chemistry 2009; 15:2081-90. [PMID: 19156658 DOI: 10.1002/chem.200802010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Charge matters! The charge state significantly influences the conformation and the binding energy between vancomycin antibiotic and bacterial cell-wall analogue peptides (see figure). Surface-induced dissociation (SID) studies provide a quantitative comparison between the stabilities of different charge states of the complex.In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the noncovalent complex between the vancomycin and the cell-wall peptide analogue N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala (V-Ac(2)LKdAdA). The binding energies between the vancomycin and the peptide were obtained from the RRKM (Rice, Ramsperger, Kassel, Marcus) modeling of the time- and energy-resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex towards fragmentation increases in the order: doubly protonated<singly protonated<deprotonated. Dissociation of the singly protonated and singly deprotonated complex is characterized by very large entropy effects, which indicate a substantial increase in the conformational flexibility of the resulting products. The experimental threshold energies of (1.75+/-0.08) eV ((40.3+/-1.8) kcal mol(-1)) and (1.34+/-0.08) eV ((30.9+/-1.8) kcal mol(-1)) obtained for the deprotonated and singly protonated complexes, respectively, are in excellent agreement with the results of density functional theory calculations. The increased stability of the deprotonated complex observed experimentally is attributed to the presence of three charged sites in the deprotonated complex, as compared with only one charged site in the singly protonated complex. The low binding energy of (0.93+/-0.04) eV ((21.4+/-0.9) kcal mol(-1)) obtained for the doubly protonated complex suggests that this ion is destabilized by Coulomb repulsion between the singly protonated vancomycin and the singly protonated peptide comprising the complex.
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Affiliation(s)
- Zhibo Yang
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 (K8-88), Richland, WA 99352, USA
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Affiliation(s)
- Stefan Kubik
- Fachbereich Chemie-Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Strasse, D-67663, Kaiserslautern, Germany.
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Bolz I, Spange S. An Enolisable Barbiturate with Adjustable Hydrogen-Bonding Structure for UV/Vis Detection of Nucleic Acid Bases and Related Compounds. Chemistry 2008; 14:9338-46. [DOI: 10.1002/chem.200800626] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Bonelli B, Areán CO, Armandi M, Delgado MR, Garrone E. Variable-Temperature Infrared Spectroscopy Studies on the Thermodynamics of CO Adsorption on the Zeolite Ca-Y. Chemphyschem 2008; 9:1747-51. [DOI: 10.1002/cphc.200800238] [Citation(s) in RCA: 11] [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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Määttä JAE, Airenne TT, Nordlund HR, Jänis J, Paldanius TA, Vainiotalo P, Johnson MS, Kulomaa MS, Hytönen VP. Rational Modification of Ligand-Binding Preference of Avidin by Circular Permutation and Mutagenesis. Chembiochem 2008; 9:1124-35. [DOI: 10.1002/cbic.200700671] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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You CC, Agasti S, Rotello V. Isomeric Control of Protein Recognition with Amino Acid- and Dipeptide-Functionalized Gold Nanoparticles. Chemistry 2007; 14:143-50. [DOI: 10.1002/chem.200701234] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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