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Zhang HN, Huang X, Jin GX. Efficient and Selective Construction of 4 1 2 Metalla-links Using Weak C-H⋅⋅⋅Halogen Interactions. Angew Chem Int Ed Engl 2024; 63:e202405399. [PMID: 38570193 DOI: 10.1002/anie.202405399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/05/2024]
Abstract
Through a coordination-driven self-assembly method, four4 1 2 ${4_1^2 }$ metalla-links and one tetranuclear monocycle were constructed with high selectivity and yield by adjusting the substituent species of the building blocks, as evidenced using X-ray crystallographic analysis, electrospray ionization-time-of-flight/mass spectrometry (ESI-TOF/MS), elemental analysis and detailed solution-state nuclear magnetic resonance (NMR) spectroscopy. Based on X-ray crystallographic analysis and independent gradient model analysis, a significant factor leading to the formation of4 1 2 ${4_1^2 }$ metalla-links was the introduction of F, Cl, Br and I atoms, which generated additional weak C-H⋅⋅⋅X (X=F, Cl, Br and I) interactions. Furthermore, the dynamic conversion of4 1 2 ${4_1^2 }$ metalla-links to monocyclic rings in methanol solution was systematically investigated using quantitative 1H NMR techniques.
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Affiliation(s)
- Hai-Ning Zhang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Department of Chemistry, Fudan University, 2005 Songhu Rd, 200438, Shanghai, P. R. China
| | - Xi Huang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Department of Chemistry, Fudan University, 2005 Songhu Rd, 200438, Shanghai, P. R. China
| | - Guo-Xin Jin
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Department of Chemistry, Fudan University, 2005 Songhu Rd, 200438, Shanghai, P. R. China
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2
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Triethylenetetramine-impregnated ZIF-8 nanoparticles for CO2 adsorption. J CO2 UTIL 2023. [DOI: 10.1016/j.jcou.2023.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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3
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Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Proteins are the workhorse of life. They are the building infrastructure of living systems; they are the most efficient molecular machines known, and their enzymatic activity is still unmatched in versatility by any artificial system. Perhaps proteins' most remarkable feature is their modularity. The large amount of information required to specify each protein's function is analogically encoded with an alphabet of just ∼20 letters. The protein folding problem is how to encode all such information in a sequence of 20 letters. In this review, we go through the last 30 years of research to summarize the state of the art and highlight some applications related to fundamental problems of protein evolution.
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Affiliation(s)
- Giulia Magi Meconi
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | - Ivan R Sasselli
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Jose N Onuchic
- Center for Theoretical Biological Physics, Department of Physics & Astronomy, Department of Chemistry, Department of Biosciences, Rice University, Houston, TX 77251, United States of America
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Bld. Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, 48940 Leioa, Spain
- Basque Foundation for Science, Ikerbasque, 48009, Bilbao, Spain
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4
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Rashad MM, El-Kemary NM, Amer S, El-Kemary M. Bovine serum albumin/chitosan-nanoparticle bio-complex; spectroscopic study and in vivo toxicological - Hypersensitivity evaluation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119582. [PMID: 33636493 DOI: 10.1016/j.saa.2021.119582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
This study, investigates the interaction of bovine serum albumin (BSA) with synthesized chitosan nanoparticles (CSNPs) using steady-state fluorescence and UV-vis absorbance spectroscopy as well as picosecond time-resolved fluorescence technique. The fluorescence quenching mechanism of BSA by CSNPs indicates the presence of both static and dynamic mechanism. The loading efficiency of BSA-CSNPs exhibited a decrease by about 6% in neutral pH under physiological temperature. Transmission electron microcopy (TEM) images revealed the Synthesized CSNPs were irregular in shape with size of ~42 nm. The safety and biocompatibility of BSA-CSNPs inside the body was investigated after intraperitoneal (IP) injection of male mice for nine days, analysis of in vivo results, revealed no toxicity with a hypocholesterolemic effect and a predicted mild activation of WBCs due to CSNPs adjuvant and immunogenic peptides in BSA. Accordingly, no signs of hypersensitivity were observed due to the administration of such formulations. The results can be used for a better understanding the interaction of CSNPs within biological protein environment.
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Affiliation(s)
- Moataz M Rashad
- Institute of Nanoscience & Nanotechnology, Kafrelsheikh University, 33516 Kafr Elsheikh, Egypt
| | - Nesma M El-Kemary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Kafrelsheikh University, 33516 Kafr Elsheikh, Egypt
| | - Said Amer
- Department of Zoology, Faculty of Science, KafrelSheikh University, 33516 Kafr ElSheikh, Egypt
| | - Maged El-Kemary
- Institute of Nanoscience & Nanotechnology, Kafrelsheikh University, 33516 Kafr Elsheikh, Egypt; Pharos University, Alexandria, Egypt.
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5
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Nerattini F, Tubiana L, Cardelli C, Bianco V, Dellago C, Coluzza I. Protein design under competing conditions for the availability of amino acids. Sci Rep 2020; 10:2684. [PMID: 32060385 PMCID: PMC7021711 DOI: 10.1038/s41598-020-59401-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/08/2019] [Indexed: 11/09/2022] Open
Abstract
Isolating the properties of proteins that allow them to convert sequence into the structure is a long-lasting biophysical problem. In particular, studies focused extensively on the effect of a reduced alphabet size on the folding properties. However, the natural alphabet is a compromise between versatility and optimisation of the available resources. Here, for the first time, we include the impact of the relative availability of the amino acids to extract from the 20 letters the core necessary for protein stability. We present a computational protein design scheme that involves the competition for resources between a protein and a potential interaction partner that, additionally, gives us the chance to investigate the effect of the reduced alphabet on protein-protein interactions. We devise a scheme that automatically identifies the optimal reduced set of letters for the design of the protein, and we observe that even alphabets reduced down to 4 letters allow for single protein folding. However, it is only with 6 letters that we achieve optimal folding, thus recovering experimental observations. Additionally, we notice that the binding between the protein and a potential interaction partner could not be avoided with the investigated reduced alphabets. Therefore, we suggest that aggregation could have been a driving force in the evolution of the large protein alphabet.
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Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Ivan Coluzza
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 182, 20014, San Sebastian, Spain. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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6
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Nerattini F, Tubiana L, Cardelli C, Bianco V, Dellago C, Coluzza I. Design of Protein–Protein Binding Sites Suggests a Rationale for Naturally Occurring Contact Areas. J Chem Theory Comput 2018; 15:1383-1392. [DOI: 10.1021/acs.jctc.8b00667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Ivan Coluzza
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Spain
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7
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Lim CW. π-Box Molecule: Complexation Study for Flexible Fatty Acid Alkyl Chains in Water. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Choon Woo Lim
- Department of Chemistry, College of Life Science and Nano-technology; Hannam University; Daejeon 305-811 Republic of Korea
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Karimiahmadabadi M, Erfan S, Földesi A, Chattopadhyaya J. Distal Two-Bond versus Three-Bond Electronegative Oxo-Substituent Effect Controls the Kinetics and Thermodynamics of the Conversion of a C-Nitroso Function to the Corresponding Oxime in the Conformationally Locked Pentofuranose (Bicyclo[2.2.1]heptane) System. J Org Chem 2014; 79:7266-76. [DOI: 10.1021/jo500266k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mansoureh Karimiahmadabadi
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sayeh Erfan
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Andras Földesi
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jyoti Chattopadhyaya
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
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Lim CW, Le HT, Jung GS, Kim TW. A Pd II-Containing Self-Assembled Macrocyclic Host Induces Helical Coiling of Fatty Acids. Chemistry 2013; 19:1209-12. [DOI: 10.1002/chem.201202947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/21/2012] [Indexed: 11/05/2022]
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