1
|
Roterman I, Stapor K, Fabian P, Konieczny L. Connexins and Pannexins—Similarities and Differences According to the FOD-M Model. Biomedicines 2022; 10:biomedicines10071504. [PMID: 35884807 PMCID: PMC9313468 DOI: 10.3390/biomedicines10071504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
Connexins and pannexins are the transmembrane proteins of highly distinguished biological activity in the form of transport of molecules and electrical signals. Their common role is to connect the external environment with the cytoplasm of the cell, while connexin is also able to link two cells together allowing the transport from one to another. The analysis presented here aims to identify the similarities and differences between connexin and pannexin. As a comparative criterion, the hydrophobicity distribution in the structure of the discussed proteins was used. The comparative analysis is carried out with the use of a mathematical model, the FOD-M model (fuzzy oil drop model in its Modified version) expressing the specificity of the membrane’s external field, which in the case of the discussed proteins is significantly different from the external field for globular proteins in the polar environment of water. The characteristics of the external force field influence the structure of protein allowing the activity in a different environment.
Collapse
Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland
- Correspondence:
| | - Katarzyna Stapor
- Department of Applied Informatics, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Piotr Fabian
- Department of Algorithmics and Software, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Leszek Konieczny
- Chair of Medical Biochemistry—Jagiellonian University—Medical College, Kopernika 7, 31-034 Kraków, Poland;
| |
Collapse
|
2
|
McCabe JW, Mallis CS, Kocurek KI, Poltash ML, Shirzadeh M, Hebert MJ, Fan L, Walker TE, Zheng X, Jiang T, Dong S, Lin CW, Laganowsky A, Russell DH. First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. Anal Chem 2020; 92:11155-11163. [PMID: 32662991 PMCID: PMC7967297 DOI: 10.1021/acs.analchem.0c01285] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rotationally averaged collision cross section (CCS) values for a series of proteins and protein complexes ranging in size from 8.6 to 810 kDa are reported. The CCSs were obtained using a native electrospray ionization drift tube ion mobility-Orbitrap mass spectrometer specifically designed to enhance sensitivity while having high-resolution ion mobility and mass capabilities. Periodic focusing (PF)-drift tube (DT)-ion mobility (IM) provides first-principles determination of the CCS of large biomolecules that can then be used as CCS calibrants. The experimental, first-principles CCS values are compared to previously reported experimentally determined and computationally calculated CCS using projected superposition approximation (PSA), the Ion Mobility Projection Approximation Calculation Tool (IMPACT), and Collidoscope. Experimental CCS values are generally in agreement with previously reported CCSs, with values falling within ∼5.5%. In addition, an ion mobility resolution (CCS centroid divided by CCS fwhm) of ∼60 is obtained for pyruvate kinase (MW ∼ 233 kDa); however, ion mobility resolution for bovine serum albumin (MW ∼ 68 kDa) is less than ∼20, which arises from sample impurities and underscores the importance of sample quality. The high resolution afforded by the ion mobility-Orbitrap mass analyzer provides new opportunities to understand the intricate details of protein complexes such as the impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced by ligand binding.
Collapse
Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Klaudia I Kocurek
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Ting Jiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shiyu Dong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
3
|
Bing T, Shen L, Wang J, Wang L, Liu X, Zhang N, Xiao X, Shangguan D. Aptameric Probe Specifically Binding Protein Heterodimer Rather Than Monomers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900143. [PMID: 31179220 PMCID: PMC6548965 DOI: 10.1002/advs.201900143] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/03/2019] [Indexed: 05/19/2023]
Abstract
Dimerization of proteins occurs frequently and plays integral roles in biological processes. However, no single molecular probe is available for in situ detection of protein dimers on cells and tissues because of the difficulty of isolating complete protein dimers for probe preparation and screening, which has greatly hampered the biomedical study of protein dimers. Herein, a G-rich DNA aptamer (termed BG2) that only binds alkaline phosphatase (AP) heterodimers rather than monomers is reported. This aptamer is generated by the cell-SELEX (systematic evolution of ligands by exponential enrichment) technique and proves to fold into a duplex stabilized antiparallel G-quadruplex structure. Using BG2 as molecular probe, AP heterodimers are found to be expressed on several kinds of cancer cells. As an affinity ligand, BG2 could isolate AP heterodimers from cell lysate. BG2 is also demonstrated to be applicable for tumor imaging in mice xenografted with cells highly expressing AP heterodimers. AP isozymes are found in several tissues and blood throughout the body, but the function and tissue distribution of AP heterodimers are totally unknown; therefore, BG2 could serve as a molecular probe to uncover the mystery of AP heterodimers. The generation of aptameric probes by cell-SELEX will open up a new situation for the study of protein dimers.
Collapse
Affiliation(s)
- Tao Bing
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Luyao Shen
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Junyan Wang
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Linlin Wang
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Nan Zhang
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xiao Xiao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing100190China
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| |
Collapse
|
4
|
Zhang YJ, Zhu C, Ding Y, Yan ZW, Li GH, Lan Y, Wen JF, Chen B. Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton. BMC Genomics 2018; 19:469. [PMID: 29914356 PMCID: PMC6006717 DOI: 10.1186/s12864-018-4845-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/31/2018] [Indexed: 01/24/2023] Open
Abstract
Background Eukaryotic cells contain a huge variety of internally specialized subcellular compartments. Stoichiogenomics aims to reveal patterns of elements usage in biological macromolecules. However, the stoichiogenomic characteristics and how they adapt to various subcellular microenvironments are still unknown. Results Here we first updated the definition of stoichiogenomics. Then we applied it to subcellular research, and detected distinctive nitrogen content of nuclear and hydrogen, sulfur content of extracellular proteomes. Specially, we found that acidic amino acids (AAs) content of cytoskeletal proteins is the highest. The increased charged AAs are mainly caused by the eukaryotic originated cytoskeletal proteins. Functional subdivision of the cytoskeleton showed that activation, binding/association, and complexes are the three largest functional categories. Electrostatic interaction analysis showed an increased electrostatic interaction between both primary sequences and PPI interfaces of 3D structures, in the cytoskeleton. Conclusions This study creates a blueprint of subcellular stoichiogenomic characteristics, and explains that charged AAs of the cytoskeleton increased greatly in evolution, which offer material basis for the eukaryotic cytoskeletal proteins to act in two ways of electrostatic interactions, and further perform their activation, binding/association and complex formation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4845-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yu-Juan Zhang
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China
| | - Chengxu Zhu
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Yiran Ding
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Zheng-Wen Yan
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China
| | - Yang Lan
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China.
| | - Bin Chen
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China.
| |
Collapse
|
5
|
Michurin OM, Tolmachova K, Afonin S, Babii O, Grage SL, Ulrich AS, Komarov IV, Radchenko DS. Conformationally Constrained Mono-Fluorinated Arginine as a Cationic Label for Solid-State 19
F NMR Analysis of Membrane-Bound Peptides. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kateryna Tolmachova
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; vul. Murmanska 1 02660 Kyiv Ukraine
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
| |
Collapse
|