1
|
Weigel RK, Alabi CA. Duplex-forming oligocarbamates with tunable nonbonding sites. Chem Sci 2024; 15:9138-9146. [PMID: 38903212 PMCID: PMC11186313 DOI: 10.1039/d4sc00242c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/11/2024] [Indexed: 06/22/2024] Open
Abstract
In biopolymers such as proteins and nucleic acids, monomer sequence encodes for highly specific intra- and intermolecular interactions that direct self-assembly into complex architectures with high fidelity. This remarkable structural control translates into precise control over the properties of the biopolymer. Polymer scientists have sought to achieve similarly precise control over the structure and function of synthetic assemblies. A common strategy for achieving this goal has been to exploit existing biopolymers, known to associate with specific geometries and stoichiometries, for the assembly of synthetic building blocks. However, such systems are neither scalable nor amenable to the relatively harsh conditions required by various materials science applications, particularly those involving non-aqueous environments. To overcome these limitations, we have synthesized sequence-defined oligocarbamates (SeDOCs) that assemble into duplexes through complementary hydrogen bonds between thymine (T) and diaminotriazine (D) pendant groups. The SeDOC platform makes it simple to incorporate non-hydrogen-bonding sites into an oligomer's array of recognition motifs, thereby enabling an investigation into this unexplored handle for controlling the hybridization of complementary ligands. We successfully synthesized monovalent, divalent, and trivalent SeDOCs and characterized their self-assembly via diffusion ordered spectroscopy, 1H-NMR titration, and isothermal titration calorimetry. Our findings reveal that the binding strength of monovalent oligomers with complementary pendant groups is entropically driven and independent of monomer sequence. The results further show that the hybridization of multivalent oligomers is cooperative, that their binding enthalpy (ΔH) and entropy (TΔS) depend on monomer sequence, and that sequence-dependent changes in ΔH and TΔS occur in tandem to minimize the overall change in binding free energy.
Collapse
Affiliation(s)
- R Kenton Weigel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York USA
| | - Christopher A Alabi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York USA
| |
Collapse
|
2
|
Mamardashvili GM, Yu. Kaigorodova E, Lebedev IS, Khodov IA, Mamardashvili NZ. Supramolecular assembly of hydrophilic Co(III)-porphyrin with bidentate ligands in aqueous buffer media. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
3
|
Kaigorodova EY, Mamardashvili GM, Mamardashvili NZ. Co(III)-tetra(4-sulfonatophenyl)porphyrin complexes with bidentate ligands in aqueous buffer media. J PORPHYR PHTHALOCYA 2022. [DOI: 10.1142/s1088424622500262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The processes of hydrophilic Co(III)-tetra(4-sulfonatophenyl)porphyrin supramolecular assembly with 4,4-bipyridyl in aqueous buffer media have been studied by UV-vis, 1D and 2D 1H NMR-spectroscopy. In the case of 1,4-diazabicyclo[2.2.2]octane, pyrazine and piperazine in aqueous solutions, no assembly was observed. Interactions of the hydrophilic Co(III)-tetraarylporphyrin with ionic micelles (cationic surfactants with different alkyl tail lengths) in buffer media were investigated. These studies were performed by the UV-vis, 1D NOESY-spectroscopy and dynamic lightscattering (DLS) methods. The metalloporphyrins were incorporated into the hydrophobic part of micelles, which led to Co(III) reduction to Co(II) in the Co-porphyrinate composition. The rate of Co(III) reduction accompanied by detachment of additional ligands coordinated on Co(III)-porphyrins or disruption of supramolecular dimers and depends on the surfactant concentration and nature. The results obtained indicate the possibility of creating supramolecular porphyrin-based assemblies with the preprogrammed lifetime (from several hours to several days) and could be used in the creation of host-guest systems for recognition, selective binding and the prolonged release of bioactive substrates as the means in the designing of biomimetic systems with effective binding affinities to heterocycles, DNA base pairs and RNA.
Collapse
Affiliation(s)
- Elena Yu. Kaigorodova
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st.1, 153045 Ivanovo, Russian Federation
| | - Galina M. Mamardashvili
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st.1, 153045 Ivanovo, Russian Federation
| | - Nugzar Z. Mamardashvili
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st.1, 153045 Ivanovo, Russian Federation
| |
Collapse
|
4
|
Chen M, Cao JN, Li S, Liu D, Wang J, Zhao H, Wang G, Wu T, Jiang Z, Wang P. Customized self-assembled molecules: rim adjustable coronal polygons with multiple-folds symmetry. Org Chem Front 2021. [DOI: 10.1039/d1qo01316e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three desired discrete metallomacrocyclic wreaths with four-, five- and six-fold symmetry were successfully realized in a controlled fashion.
Collapse
Affiliation(s)
- Mingzhao Chen
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Jia-nan Cao
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Suqing Li
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Die Liu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Jun Wang
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - He Zhao
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Guotao Wang
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| | - Tun Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Zhilong Jiang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Pingshan Wang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education; Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
- Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, China
| |
Collapse
|
5
|
Singh S, Aggarwal A, Mercier PH, Bhupathiraju NVSDK, Landress M, Hanna K. An alternate and efficient method for preparation of 2,6-diacetamido-4-formylpyridine for formation of porphyrin appended with hydrogen bonding motifs. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1799012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Sunaina Singh
- Department of Natural Sciences, LaGuardia Community College of the City University of New York, Long Island City, NY, USA
| | - Amit Aggarwal
- Department of Natural Sciences, LaGuardia Community College of the City University of New York, Long Island City, NY, USA
| | - Phillippe H. Mercier
- Department of Natural Sciences, LaGuardia Community College of the City University of New York, Long Island City, NY, USA
| | | | - Michael Landress
- Department of Natural Sciences, LaGuardia Community College of the City University of New York, Long Island City, NY, USA
| | - Keroles Hanna
- Department of Natural Sciences, LaGuardia Community College of the City University of New York, Long Island City, NY, USA
| |
Collapse
|
6
|
Heard A, Goldup SM. Simplicity in the Design, Operation, and Applications of Mechanically Interlocked Molecular Machines. ACS CENTRAL SCIENCE 2020; 6:117-128. [PMID: 32123730 PMCID: PMC7047278 DOI: 10.1021/acscentsci.9b01185] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 05/17/2023]
Abstract
Mechanically interlocked molecules are perhaps best known as components of molecular machines, a view further reinforced by the Nobel Prize in 2016 to Stoddart and Sauvage. Despite amazing progress since these pioneers of the field reported the first examples of molecular shuttles, genuine applications of interlocked molecular machines remain elusive, and many barriers remain to be overcome before such molecular devices make the transition from impressive prototypes on the laboratory bench to useful products. Here, we discuss simplicity as a design principle that could be applied in the development of the next generation of molecular machines with a view to moving toward real-world applications of these intriguing systems in the longer term.
Collapse
|
7
|
Sujata Kundan, Bajju GD, Gupta D, Roy TK. Novel Axially Ligated Complexes of Zn(II)Porphyrin: Spectroscopic, Computational, and Antibiological Characterization. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s003602361911010x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Syamala PPN, Soberats B, Görl D, Gekle S, Würthner F. Thermodynamic insights into the entropically driven self-assembly of amphiphilic dyes in water. Chem Sci 2019; 10:9358-9366. [PMID: 32110300 PMCID: PMC7017873 DOI: 10.1039/c9sc03103k] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/19/2019] [Indexed: 01/04/2023] Open
Abstract
Self-assembly of amphiphilic dyes and π-systems are more difficult to understand and to control in water compared to organic solvents due to the hydrophobic effect. Herein, we elucidate in detail the self-assembly of a series of archetype bolaamphiphiles bearing a naphthalene bisimide (NBI) π-core with appended oligoethylene glycol (OEG) dendrons of different size. By utilizing temperature-dependent UV-vis spectroscopy and isothermal titration calorimetry (ITC), we have dissected the enthalpic and entropic parameters pertaining to the molecules' self-assembly. All investigated compounds show an enthalpically disfavored aggregation process leading to aggregate growth and eventually precipitation at elevated temperature, which is attributed to the dehydration of oligoethylene glycol units and their concomitant conformational changes. Back-folded conformation of the side chains plays a major role, as revealed by molecular dynamics (MD) and two dimensional NMR (2D NMR) studies, in directing the association. The sterical effect imparted by the jacketing of monomers and dimers also changes the aggregation mechanism from isodesmic to weakly anti-cooperative.
Collapse
Affiliation(s)
- Pradeep P N Syamala
- Universität Würzburg , Institut für Organische Chemie , Am Hubland , 97074 Würzburg , Germany .
- Center for Nanosystems Chemistry & Bavarian Polymer Institute (BPI) , Universität Würzburg , Theodor-Boveri-Weg , 97074 Würzburg , Germany
| | - Bartolome Soberats
- Center for Nanosystems Chemistry & Bavarian Polymer Institute (BPI) , Universität Würzburg , Theodor-Boveri-Weg , 97074 Würzburg , Germany
| | - Daniel Görl
- Center for Nanosystems Chemistry & Bavarian Polymer Institute (BPI) , Universität Würzburg , Theodor-Boveri-Weg , 97074 Würzburg , Germany
| | - Stephan Gekle
- Universität Bayreuth , Biofluid Simulation and Modeling, Theoretische Physik VI & Bavarian Polymer Institute (BPI) , 95440 Bayreuth , Germany .
| | - Frank Würthner
- Universität Würzburg , Institut für Organische Chemie , Am Hubland , 97074 Würzburg , Germany .
- Center for Nanosystems Chemistry & Bavarian Polymer Institute (BPI) , Universität Würzburg , Theodor-Boveri-Weg , 97074 Würzburg , Germany
| |
Collapse
|
9
|
Caprice K, Pupier M, Bauzá A, Frontera A, Cougnon FBL. Synchronized On/Off Switching of Four Binding Sites for Water in a Molecular Solomon Link. Angew Chem Int Ed Engl 2019; 58:8053-8057. [DOI: 10.1002/anie.201902278] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Kenji Caprice
- Department of Organic Chemistry University of Geneva 30 Quai Ernest Ansermet Geneva Switzerland
| | - Marion Pupier
- Department of Organic Chemistry University of Geneva 30 Quai Ernest Ansermet Geneva Switzerland
| | - Antonio Bauzá
- Department de Química Universitat de les Illes Balears Carretera de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Antonio Frontera
- Department de Química Universitat de les Illes Balears Carretera de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Fabien B. L. Cougnon
- Department of Organic Chemistry University of Geneva 30 Quai Ernest Ansermet Geneva Switzerland
| |
Collapse
|
10
|
Caprice K, Pupier M, Bauzá A, Frontera A, Cougnon FBL. Synchronized On/Off Switching of Four Binding Sites for Water in a Molecular Solomon Link. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kenji Caprice
- Department of Organic Chemistry University of Geneva 30 Quai Ernest Ansermet Geneva Switzerland
| | - Marion Pupier
- Department of Organic Chemistry University of Geneva 30 Quai Ernest Ansermet Geneva Switzerland
| | - Antonio Bauzá
- Department de Química Universitat de les Illes Balears Carretera de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Antonio Frontera
- Department de Química Universitat de les Illes Balears Carretera de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Fabien B. L. Cougnon
- Department of Organic Chemistry University of Geneva 30 Quai Ernest Ansermet Geneva Switzerland
| |
Collapse
|
11
|
Đorđević L, Marangoni T, Liu M, De Zorzi R, Geremia S, Minoia A, Lazzaroni R, Ishida Y, Bonifazi D. Templating Porphyrin Anisotropy via Magnetically Aligned Carbon Nanotubes. Chempluschem 2019; 84:1270-1278. [DOI: 10.1002/cplu.201800623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Luka Đorđević
- Department of Chemical and Pharmaceutical SciencesUniversity of Trieste Via L. Giorgieri 1 34127 Trieste Italy
| | - Tomas Marangoni
- Department of Chemical and Pharmaceutical SciencesUniversity of Trieste Via L. Giorgieri 1 34127 Trieste Italy
| | - Mingjie Liu
- RIKEN Center for Emergent Matter Science 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical SciencesUniversity of Trieste Via L. Giorgieri 1 34127 Trieste Italy
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical SciencesUniversity of Trieste Via L. Giorgieri 1 34127 Trieste Italy
| | - Andrea Minoia
- Laboratory for Chemistry of Novel Materials, CIRMAPUniversité de Mons-UMONS Place du Parc 20 B-7000 Mons Belgium
| | - Roberto Lazzaroni
- Laboratory for Chemistry of Novel Materials, CIRMAPUniversité de Mons-UMONS Place du Parc 20 B-7000 Mons Belgium
| | - Yasuhiro Ishida
- RIKEN Center for Emergent Matter Science 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Davide Bonifazi
- School of ChemistryCardiff University Park Place Main Building CF10 3AT United Kingdom
| |
Collapse
|
12
|
Lensen MC, Nolte RJM, Rowan AE, Pyckhout-Hintzen W, Feiters MC, Elemans JAAW. Self-assembly of porphyrin hexamers via bidentate metal-ligand coordination. Dalton Trans 2018; 47:14277-14287. [PMID: 29881835 DOI: 10.1039/c8dt01572d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The supramolecular assembly of metal-porphyrin hexamers with bidentate ligands in chloroform solutions is demonstrated by UV/Vis and 1H NMR-titrations, and Small Angle Neutron Scattering (SANS) experiments. Titrations of zinc porphyrin hexamer Zn1 with 1,4-diazabicyclo[2,2,2]octane (DABCO) revealed that at a DABCO/Zn1 molar ratio of 3, intermolecular sandwich complexes are formed, which can be considered as "circular-shaped porphyrin ladders". These supramolecular complexes further aggregate into larger polymeric stacks, as a result of a combination of cooperativity effects, π-π stacking interactions, and chelate effects. The presence of rodlike assemblies in solution, formed by assembly of Zn1 and DABCO, is confirmed by SANS-experiments. Using a model for cylindrical assemblies, curve fitting calculations reveal that rods with an average length of 26 nm and a radius of 30-35 Å were formed, corresponding to columnar stacks of approximately 30 hexamer molecules. In contrast, the metal-free hexamer H21 did not form extended assemblies due to the absence of coordinative intermolecular interactions.
Collapse
Affiliation(s)
- Marga C Lensen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | | | | | | | | | | |
Collapse
|
13
|
Murphy RB, Pham DT, White JM, Lincoln SF, Johnston MR. Molecular tweezers with a rotationally restricted linker and freely rotating porphyrin moieties. Org Biomol Chem 2018; 16:6206-6223. [PMID: 30106402 DOI: 10.1039/c8ob00944a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The effect of the degree of conformational rigidity and/or flexibility on preorganisation in artificial molecular receptors continues to be actively explored by supramolecular chemists. This work describes a bis-porphyrin architecture, linked via a rigid polycyclic backbone, in which a sterically bulky 2,3,5,6-tetramethylphenyl diimide core restricts rotation to afford two non-interconvertible tweezer conformations; syn- and anti-. After separation, the host-guest chemistry of each conformation was studied independently. The difference in host geometry allows only the syn-conformation to form a strong 1 : 1 bis-porphyrin complex with the diamino ligand 1,4-diazabicyclo[2.2.2]octane (DABCO) (K11 = 1.25 × 108 M-1), with the anti-conformation adopting a 2 : 2 sandwich complex with DABCO (K22 = 5.57 × 1017 M-3).
Collapse
Affiliation(s)
- Rhys B Murphy
- Flinders Centre for NanoScale Science and Technology, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, Australia.
| | | | | | | | | |
Collapse
|
14
|
Luo Q, Hou C, Bai Y, Wang R, Liu J. Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures. Chem Rev 2016; 116:13571-13632. [PMID: 27587089 DOI: 10.1021/acs.chemrev.6b00228] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.
Collapse
Affiliation(s)
- Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yushi Bai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Taipa, Macau SAR 999078, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| |
Collapse
|
15
|
Lopez-Fontal E, Milanesi L, Tomas S. Multivalence cooperativity leading to "all-or-nothing" assembly: the case of nucleation-growth in supramolecular polymers. Chem Sci 2016; 7:4468-4475. [PMID: 30009001 PMCID: PMC6014373 DOI: 10.1039/c6sc00520a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/18/2016] [Indexed: 12/24/2022] Open
Abstract
All-or-nothing molecular assembly events, essential for the efficient regulation of living systems at the molecular level, are emerging properties of complex chemical systems that are largely attributed to the cooperativity of weak interactions. The link between the self-assembly and the interactions responsible for the assembly is however often poorly defined. In this work we demonstrate how the chelate effect (multivalence cooperativity) can play a central role in the regulation of the all-or-nothing assembly of structures (supramolecular polymers here), even if the building blocks are not multivalent. We have studied the formation of double-stranded supramolecular polymers formed from Co-metalloporphyrin and bi-pyridine building blocks. Their cooperative nucleation-elongation assembly can be summarized as a thermodynamic cycle, where the monomer weakly oligomerizes linearly or weakly dimerizes laterally. But thanks to the chelate effect, the lateral dimer readily oligomerizes linearly and the oligomer readily dimerizes laterally, leading to long double stranded polymers. A model based on this simple thermodynamic cycle can be applied to the assembly of polymers with any number of strands, and allows for the determination of the length of the polymer and the all-or-nothing switching concentration from the pairwise binding constants. The model, which is consistent with the behaviour of supramolecular polymers such as microtubules and gelators, clearly shows that all-or-nothing assembly is triggered by a change in the mode of assembly, from non-multivalent to multivalent, when a critical concentration is reached. We believe this model is applicable to many molecular assembly processes, ranging from the formation of cell-cell focal adhesion points to crystallization.
Collapse
Affiliation(s)
- Elkin Lopez-Fontal
- Institute of Structural and Molecular Biology and Department of Biological Sciences , School of Science , Birkbeck University of London , Malet Street , London WC1E 7HX , UK .
| | - Lilia Milanesi
- School of Biological and Chemical Sciences , Queen Mary University of London , Mile End Road , London E1 4NS , UK
| | - Salvador Tomas
- Institute of Structural and Molecular Biology and Department of Biological Sciences , School of Science , Birkbeck University of London , Malet Street , London WC1E 7HX , UK .
| |
Collapse
|
16
|
Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| |
Collapse
|
17
|
Kose K, Motoyanagi J, Kusukawa T, Osuka A, Tsuda A. Formation of Discrete Ladders and a Macroporous Xerogel Film by the Zipperlike Dimerization of Meso-Meso-Linked Zinc(II) Porphyrin Arrays with Di(pyrid-3-yl)acetylene. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
18
|
Kose K, Motoyanagi J, Kusukawa T, Osuka A, Tsuda A. Formation of Discrete Ladders and a Macroporous Xerogel Film by the Zipperlike Dimerization of Meso-Meso-Linked Zinc(II) Porphyrin Arrays with Di(pyrid-3-yl)acetylene. Angew Chem Int Ed Engl 2015; 54:8673-8. [DOI: 10.1002/anie.201502663] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 11/11/2022]
|
19
|
Sun H, Hunter CA, Navarro C, Turega S. Relationship between chemical structure and supramolecular effective molarity for formation of intramolecular H-bonds. J Am Chem Soc 2013; 135:13129-41. [PMID: 23964567 DOI: 10.1021/ja406235d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Effective molarity (EM) is a key parameter that determines the efficiency of a range of supramolecular phenomena from the folding of macromolecules to multivalent ligand binding. Coordination complexes formed between zinc porphyrins equipped H-bond donor sites and pyridine ligands equipped with H-bond acceptor sites have allowed systematic quantification of EM values for the formation of intramolecular H-bonds in 240 different systems. The results provide insights into the relationship of EM to supramolecular architecture, H-bond strength, and solvent. Previous studies on ligands equipped with phosphonate diester and ether H-bond acceptors were inconclusive, but the experiments described here on ligands equipped with phosphine oxide, amide, and ester H-bond acceptors resolve these ambiguities. Chemical double-mutant cycles were used to dissect the thermodynamic contributions of individual H-bond interactions to the overall stabilities of the complexes and hence determine the values of EM, which fall in the range 1-1000 mM. Solvent has little effect on EM, and the values measured in toluene and 1,1,2,2-tetrachloroethane are similar. For H-bond acceptors that have similar geometries but different H-bond strengths (amide and ester), the values of EM are very similar. For H-bond acceptors that have different geometries but similar H-bond strengths (amide and phosphonate diester), there is little correlation between the values of EM. These results imply that supramolecular EMs are independent of solvent and intrinsic H-bond strength but depend on supramolecular architecture and geometric complementarity.
Collapse
Affiliation(s)
- Hongmei Sun
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | | | | | | |
Collapse
|
20
|
Norrehed S, Polavarapu P, Yang W, Gogoll A, Grennberg H. Conformational restriction of flexible molecules in solution by a semirigid bis-porphyrin molecular tweezer. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
21
|
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]
|
22
|
Roche C, Sour A, Sauvage J. A Flexible Copper(I)‐Complexed [4]Rotaxane Containing Two Face‐to‐Face Porphyrinic Plates that Behaves as a Distensible Receptor. Chemistry 2012; 18:8366-76. [DOI: 10.1002/chem.201200389] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Cécile Roche
- Laboratoire de Chimie Organo‐Minérale, Institut de Chimie, Université de Strasbourg‐CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex (France), Fax: (+33) 368851637
| | - Angélique Sour
- Laboratoire de Chimie Organo‐Minérale, Institut de Chimie, Université de Strasbourg‐CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex (France), Fax: (+33) 368851637
| | - Jean‐Pierre Sauvage
- Laboratoire de Chimie Organo‐Minérale, Institut de Chimie, Université de Strasbourg‐CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex (France), Fax: (+33) 368851637
| |
Collapse
|
23
|
Sobral AJFN, Justino LLG, Santos ACC, Silva JA, Arranja CT, Silva MR, Beja AM. Synthesis and structural characterization of a new self-assembled disulfide linked meso-tetrakis-porphyrin macromolecular array. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424608000236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The synthesis of a new self-assembled porphyrin macrostructure based on disulfide bonds, is presented. This constitutes a new way to directly connect porphyrins in macromolecular arrays, to complement the usual methods of intermolecular hydrogen bonds and metal coordination bonding.
Collapse
Affiliation(s)
- Abilio J. F. N. Sobral
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, P-3004-535 Coimbra, Portugal
| | - Licinia L. G. Justino
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, P-3004-535 Coimbra, Portugal
| | - Ana C. C. Santos
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, P-3004-535 Coimbra, Portugal
| | - Joana A. Silva
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, P-3004-535 Coimbra, Portugal
| | - Cláudia T. Arranja
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, P-3004-535 Coimbra, Portugal
| | - Manuela Ramos Silva
- CEMDRX, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, P-3004-516 Coimbra, Portugal
| | - Ana Matos Beja
- CEMDRX, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, P-3004-516 Coimbra, Portugal
| |
Collapse
|
24
|
Chekmeneva E, Hunter CA, Misuraca MC, Turega SM. Steric desolvation enhances the effective molarities of intramolecular H-bonding interactions. Org Biomol Chem 2012; 10:6022-31. [DOI: 10.1039/c2ob25372k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
25
|
|
26
|
Hunter CA, Misuraca MC, Turega SM. Influence of H-Bond Strength on Chelate Cooperativity. J Am Chem Soc 2011; 133:20416-25. [DOI: 10.1021/ja208330y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | | | - Simon M. Turega
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| |
Collapse
|
27
|
Bhosale SV, Kalyankar MB, Nalage SV, Bhosale SV, Lalander CH, Langford SJ. Supramolecular self-assembled nanowires by the aggregation of a protoporphyrin derivative in low-polarity solvents. Supramol Chem 2011. [DOI: 10.1080/10610278.2011.575467] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
28
|
Sprafke JK, Odell B, Claridge TDW, Anderson HL. “Alles-oder-Nichts”-Kooperativität bei der Selbstorganisation eines Annulen-Sandwichs. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008087] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
29
|
Sprafke JK, Odell B, Claridge TDW, Anderson HL. All-or-Nothing Cooperative Self-Assembly of an Annulene Sandwich. Angew Chem Int Ed Engl 2011; 50:5572-5. [DOI: 10.1002/anie.201008087] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Indexed: 11/05/2022]
|
30
|
Misuraca MC, Grecu T, Freixa Z, Garavini V, Hunter CA, van Leeuwen PWNM, Segarra-Maset MD, Turega SM. Relationship between conformational flexibility and chelate cooperativity. J Org Chem 2011; 76:2723-32. [PMID: 21417288 DOI: 10.1021/jo2000397] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A family of four biscarbamates (AA) and four bisphenols (DD) were synthesized, and H-bonding interactions between all AA•DD combinations were characterized using (1)H NMR titrations in carbon tetrachloride. A chemical double mutant cycle analysis shows that there are no secondary electrostatic interactions or allosteric cooperativity in these systems, and the system therefore provides an ideal platform for investigating the relationship between chemical structure and chelate cooperativity. Effective molarities (EMs) were measured for 12 different systems, where the number of rotors in the chains connecting the two H-bond sites was varied from 5 to 20. The association constants vary by less than an order of magnitude for all 12 complexes, and the variation in EM is remarkably small (0.1-0.9 M). The results provide a relationship between EM and the number of rotors in the connecting chains (r): EM ≈ 10r(-3/2). The value of 10 M is the upper limit for the value of EM for a noncovalent intramolecular interaction. Introduction of rotors reduces the value of EM from this maximum in accord with a random walk analysis of the encounter probability of the chain ends (r(-3/2)). Noncovalent EMs never reach the very high values observed for covalent processes, which places limitations on the magnitudes of the effects that one is likely to achieve through the use of chelate cooperativity in supramolecular assembly and catalysis. On the other hand, the decrease in EM due to the introduction of conformational flexibility is less dramatic than one might expect based on the behavior of covalent systems, which limits the losses in binding affinity caused by poor preorganization of the interaction sites.
Collapse
Affiliation(s)
- M Cristina Misuraca
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Hunter CA, Misuraca MC, Turega SM. Dissection of Complex Molecular Recognition Interfaces. J Am Chem Soc 2010; 133:582-94. [DOI: 10.1021/ja1084783] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | - Simon M. Turega
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| |
Collapse
|
32
|
Guo JB, Xiang JF, Chen CF. Synthesis of A Bis-Macrotricyclic Host and Its Complexation with Secondary Ammonium Salts: An Acid-Base Switchable Molecular Handcuff. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000675] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
33
|
Chiral eighteen-component three-dimensional supramolecular entities stabilized by the hydrogen bonding and coordination interactions. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
34
|
Camara-Campos A, Musumeci D, Hunter CA, Turega S. Chemical double mutant cycles for the quantification of cooperativity in H-bonded complexes. J Am Chem Soc 2010; 131:18518-24. [PMID: 19947634 DOI: 10.1021/ja9083495] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical double mutant cycles have been used in conjunction with new H-bonding motifs for the quantification of chelate cooperativity in multiply H-bonded complexes. The double mutant cycle approach specifically deals with the effects of substituents, secondary interactions, and allosteric cooperativity on the free energy contributions from individual H-bond sites and allows dissection of the free energy contribution due to chelate cooperativity associated with the formation of intramolecular noncovalent interactions. Two different doubly H-bonded motifs were investigated in carbon tetrachloride, chloroform, 1,1,2,2-tetrachloroethane, and cyclohexane, and the results were similar in all cases, with effective molarities of 3-33 M for formation of intramolecular H-bonds. This corresponds to a free energy penalty of 3-9 kJ mol(-1) for formation of a bimolecular complex in solution, which is consistent with previous estimates of 6 kJ mol(-1). This result can be used in conjunction with the H-bond parameters, alpha and beta, to make a reasonable estimate of the stability constant for formation of a multiply H-bonded complex between two perfectly complementary partners, or to place an upper limit on the stability constant expected for a less complementary system.
Collapse
Affiliation(s)
- Amaya Camara-Campos
- Krebs Institute, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | | | | | | |
Collapse
|
35
|
|
36
|
|
37
|
Analysis of cooperativity by isothermal titration calorimetry. Int J Mol Sci 2009; 10:3457-77. [PMID: 20111687 PMCID: PMC2812830 DOI: 10.3390/ijms10083457] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 07/28/2009] [Accepted: 07/31/2009] [Indexed: 11/25/2022] Open
Abstract
Cooperative binding pervades Nature. This review discusses the use of isothermal titration calorimetry (ITC) in the identification and characterisation of cooperativity in biological interactions. ITC has broad scope in the analysis of cooperativity as it determines binding stiochiometries, affinities and thermodynamic parameters, including enthalpy and entropy in a single experiment. Examples from the literature are used to demonstrate the applicability of ITC in the characterisation of cooperative systems.
Collapse
|
38
|
Guo DS, Chen K, Zhang HQ, Liu Y. Nano-supramolecular assemblies constructed from water-soluble bis(calix[5]arenes) with porphyrins and their photoinduced electron transfer properties. Chem Asian J 2009; 4:436-45. [PMID: 19130446 DOI: 10.1002/asia.200800410] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Possessing 2D netlike and 1D linear morphologies, two nano-supramolecular architectures A1 and A2 are constructed by tetracationic porphyrin (G1) and dicationic porphyrin (G2), respectively, upon complexation with the novel water-soluble bis(p-sulfonatocalix[5]arenes) bridged at the lower rim (H2). Corresponding to the molecular design, the aggregation morphologies are well manipulated by the inherent binding sites of the building blocks through host-guest interactions as well as charge interactions. In comparison to the simple p-sulfonatocalix[5]arene H1 which can only form particle-type complexes C1 and C2 with porphyrin guests, H2 provides excellent pre-organized structure to construct highly complex nano-supramolecular assemblies. The exhibited electron-transfer process of the supramolecular systems is further investigated by steady-state and time-resolved fluorescence spectroscopy, electrochemical measurements, and transient absorption spectroscopy. The results obtained show that calixarenes are also effective electron donors in PET besides acting as significant building blocks, which gives them many advantages in constructing well-ordered nanomaterials with the capability of electron and energy transport.
Collapse
Affiliation(s)
- Dong-Sheng Guo
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, PR China
| | | | | | | |
Collapse
|
39
|
Tomas S, Milanesi L. Hydrophobically Self-Assembled Nanoparticles as Molecular Receptors in Water. J Am Chem Soc 2009; 131:6618-23. [DOI: 10.1021/ja900561j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Salvador Tomas
- School of Biological and Chemical Sciences and School of Crystallography, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Lilia Milanesi
- School of Biological and Chemical Sciences and School of Crystallography, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| |
Collapse
|
40
|
Molecular recognition and self-assembly special feature: Supramolecular polymer formed by reversible self-assembly of tetrakisporphyrin. Proc Natl Acad Sci U S A 2009; 106:10477-81. [PMID: 19289843 DOI: 10.1073/pnas.0809602106] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
S-shaped tetrakisporphyrin 2 forms supramolecular polymeric assemblies via a complementary affinity of its bisporphyrin units in solution. The self-association constant determined by applying the isodesmic model is >10(6) L mol(-1), which suggests that a sizable polymer forms at millimolar concentrations at room temperature. The electron deficient aromatic guest (TNF) binds within the molecular clefts provided by the bisporphyrin units via a charge-transfer interaction. This guest complexation completely disrupts supramolecular polymeric assembly. The long, fibrous fragments of the polymeric assemblies were characterized by atomic-force microscopy imaging of a film cast on a mica surface. The polymeric assemblies have lengths of >1mum and show a coiled structure with a higher level of organization. The approach discussed in this report concerning the quick preparation of supramolecular polymeric assemblies driven by noncovalent forces sets the stage for the preparation of a previously undescribed class of macromolecular porphyrin architectures.
Collapse
|
41
|
Tsai CJ, del Sol A, Nussinov R. Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. MOLECULAR BIOSYSTEMS 2009; 5:207-16. [PMID: 19225609 PMCID: PMC2898650 DOI: 10.1039/b819720b] [Citation(s) in RCA: 268] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Allostery has come of age; the number, breadth and functional roles of documented protein allostery cases are rising quickly. Since all dynamic proteins are potentially allosteric and allostery plays crucial roles in all cellular pathways, sorting and classifying allosteric mechanisms in proteins should be extremely useful in understanding and predicting how the signals are regulated and transmitted through the dynamic multi-molecular cellular organizations. Classification organizes the complex information thereby unraveling relationships and patterns in molecular activation and repression. In signaling, current classification schemes consider classes of molecules according to their functions; for example, epinephrine and norepinephrine secreted by the central nervous system are classified as neurotransmitters. Other schemes would account for epinephrine when secreted by the adrenal medulla to be hormone-like. Yet, such classifications account for the global function of the molecule; not for the molecular mechanism of how the signal transmission initiates and how it is transmitted. Here we provide a unified view of allostery and the first classification framework. We expect that a classification scheme would assist in comprehension of allosteric mechanisms, in prediction of signaling on the molecular level, in better comprehension of pathways and regulation of the complex signals, in translating them to the cascading events, and in allosteric drug design. We further provide a range of examples illustrating mechanisms in protein allostery and their classification from the cellular functional standpoint.
Collapse
Affiliation(s)
- Chung-Jung Tsai
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA.
| | - Antonio del Sol
- Bioinformatics Research Unit, Research and Development Division, Fujirebio Inc., 51 Komiya-cho, Hachioji-shi, 192-0031, Tokyo, Japan
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA.
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| |
Collapse
|
42
|
Mele G, Li J, Margapoti E, Martina F, Vasapollo G. Synthesis of novel porphyrins cardanol based via cross metathesis. Catal Today 2009. [DOI: 10.1016/j.cattod.2008.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
43
|
Kojima T, Nakanishi T, Honda T, Harada R, Shiro M, Fukuzumi S. Impact of Distortion of Porphyrins on Axial Coordination in (Porphyrinato)zinc(II) Complexes with Aminopyridines as Axial Ligands. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200801040] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
44
|
Hunter CA, Ihekwaba N, Misuraca MC, Segarra-Maset MD, Turega SM. Cooperativity in multiply H-bonded complexes. Chem Commun (Camb) 2009:3964-6. [DOI: 10.1039/b908010d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
45
|
Fukuzumi S, Honda T, Ohkubo K, Kojima T. Charge separation in metallomacrocycle complexes linked with electron acceptors by axial coordination. Dalton Trans 2009:3880-9. [DOI: 10.1039/b901191a] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
46
|
Oliva AI, Ventura B, Würthner F, Camara-Campos A, Hunter CA, Ballester P, Flamigni L. Self-assembly of double-decker cages induced by coordination of perylene bisimide with a trimeric Zn porphyrin: study of the electron transfer dynamics between the two photoactive components. Dalton Trans 2009:4023-37. [DOI: 10.1039/b819496c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
47
|
Barranco-Medina S, Kakorin S, Lázaro JJ, Dietz KJ. Thermodynamics of the dimer-decamer transition of reduced human and plant 2-cys peroxiredoxin. Biochemistry 2008; 47:7196-204. [PMID: 18553980 DOI: 10.1021/bi8002956] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isothermal titration calorimetry (ITC) is a powerful technique for investigating self-association processes of protein complexes and was expected to reveal quantitative data on peroxiredoxin oligomerization by directly measuring the thermodynamic parameters of dimer-dimer interaction. Recombinant classical 2-cysteine peroxoredoxins from Homo sapiens, Arabidopsis thaliana, and Pisum sativum as well as a carboxy-terminally truncated variant were subjected to ITC analysis by stepwise injection into the reaction vessel under various redox conditions. The direct measurement of the decamer-dimer equilibrium of reduced peroxiredoxin revealed a critical concentration in the very low micromolar range. The data suggest a cooperative assembly above this critical transition concentration where a nucleus facilitates assembly. The rather abrupt transition indicates that assembly processes do not occur below the critical transition concentration while oligomerization is efficiently triggered above it. The magnitude of the measured enthalpy confirmed the endothermic nature of the peroxiredoxin oligomerization. Heterocomplexes between peroxiredoxin polypeptides from different species were not formed. We conclude that a functional constraint conserved the dimer-decamer transition with highly similar critical transition concentrations despite emerging sequence variation during evolution.
Collapse
Affiliation(s)
- Sergio Barranco-Medina
- Biochemistry and Physiology of Plants, Faculty of Biology-W5, Bielefeld University, 33501 Bielefeld, Germany
| | | | | | | |
Collapse
|
48
|
Tsai CJ, Sol AD, Nussinov R. Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol 2008; 378:1-11. [PMID: 18353365 PMCID: PMC2684958 DOI: 10.1016/j.jmb.2008.02.034] [Citation(s) in RCA: 361] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 02/15/2008] [Accepted: 02/15/2008] [Indexed: 11/17/2022]
Abstract
Allostery is essential for controlled catalysis, signal transmission, receptor trafficking, turning genes on and off, and apoptosis. It governs the organism's response to environmental and metabolic cues, dictating transient partner interactions in the cellular network. Textbooks taught us that allostery is a change of shape at one site on the protein surface brought about by ligand binding to another. For several years, it has been broadly accepted that the change of shape is not induced; rather, it is observed simply because a larger protein population presents it. Current data indicate that while side chains can reorient and rewire, allostery may not even involve a change of (backbone) shape. Assuming that the enthalpy change does not reverse the free-energy change due to the change in entropy, entropy is mainly responsible for binding.
Collapse
Affiliation(s)
- Chung-Jung Tsai
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
| | - Antonio del Sol
- Bioinformatics Research Unit, Research and Development Division, Fujirebio Inc., 51 Komiya-cho, Hachioji-shi, Tokyo 192-0031, Japan
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
49
|
Kelley RF, Lee SJ, Wilson TM, Nakamura Y, Tiede DM, Osuka A, Hupp JT, Wasielewski MR. Intramolecular energy transfer within butadiyne-linked chlorophyll and porphyrin dimer-faced, self-assembled prisms. J Am Chem Soc 2008; 130:4277-84. [PMID: 18327918 DOI: 10.1021/ja075494f] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis and photophysical properties of butadiyne-linked chlorophyll and porphyrin dimers in toluene solution and in several self-assembled prismatic structures are described. The butadiyne linkage between the 20-positions of the macrocycles results in new electronic transitions polarized along the long axes of the dimers. These transitions greatly increase the ability of these dimers to absorb the solar spectrum over a broad wavelength range. Femtosecond transient absorption spectroscopy reveals the relative rate of rotation of the macrocycles around the butadiyne bond joining them. Following addition of 3-fold symmetric, metal-coordinating ligands, both macrocyclic dimers self-assemble into prismatic structures in which the dimers comprise the faces of the prisms. These structures were confirmed by small-angle X-ray scattering experiments in solution using a synchrotron source. Photoexcitation of the prismatic assemblies reveals that efficient, through-space energy transfer occurs between the macrocyclic dimers within the prisms. The distance dependence of energy transfer between the faces of the prisms was observed by varying the size of the prismatic assemblies through the use of 3-fold symmetric ligands having arms with different lengths. These results show that self-assembly of discrete macrocyclic prisms provides a useful new strategy for controlling singlet exciton flow in antenna systems for artificial photosynthesis and solar cell applications.
Collapse
Affiliation(s)
- Richard F Kelley
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, USA
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|