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Angelo M, Bhargava Y, Aoki ST. A primer for junior trainees: Recognition of RNA modifications by RNA-binding proteins. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024. [PMID: 39037148 DOI: 10.1002/bmb.21854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 06/19/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
The complexity of RNA cannot be fully expressed with the canonical A, C, G, and U alphabet. To date, over 170 distinct chemical modifications to RNA have been discovered in living systems. RNA modifications can profoundly impact the cellular outcomes of messenger RNAs (mRNAs), transfer and ribosomal RNAs, and noncoding RNAs. Additionally, aberrant RNA modifications are associated with human disease. RNA modifications are a rising topic within the fields of biochemistry and molecular biology. The role of RNA modifications in gene regulation, disease pathogenesis, and therapeutic applications increasingly captures the attention of the scientific community. This review aims to provide undergraduates, junior trainees, and educators with an appreciation for the significance of RNA modifications in eukaryotic organisms, alongside the skills required to identify and analyze fundamental RNA-protein interactions. The pumilio RNA-binding protein and YT521-B homology (YTH) family of modified RNA-binding proteins serve as examples to highlight the fundamental biochemical interactions that underlie the specific recognition of both unmodified and modified ribonucleotides, respectively. By instilling these foundational, textbook concepts through practical examples, this review contributes an analytical toolkit that facilitates engagement with RNA modifications research at large.
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Affiliation(s)
- Murphy Angelo
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Yash Bhargava
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Scott Takeo Aoki
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
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2
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Aboul Hosn S, El Ahmadieh C, Thoumi S, Sinno A, Al Khoury C. Cimicifugoside H-2 as an Inhibitor of IKK1/Alpha: A Molecular Docking and Dynamic Simulation Study. Biomolecules 2024; 14:860. [PMID: 39062574 PMCID: PMC11274867 DOI: 10.3390/biom14070860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
One of the most challenging issues scientists face is finding a suitable non-invasive treatment for cancer, as it is widespread around the world. The efficacy of phytochemicals that target oncogenic pathways appears to be quite promising and has gained attention over the past few years. We investigated the effect of docking phytochemicals isolated from the rhizomes of the Cimicifuga foetida plant on different domains of the IκB kinase alpha (IKK1/alpha) protein. The Cimicifugoside H-2 phytochemical registered a high docking score on the activation loop of IKK1/alpha amongst the other phytochemicals compared to the positive control. The interaction of the protein with Cimicifugoside H-2 was mostly stabilized by hydrogen bonds and hydrophobic interactions. A dynamic simulation was then performed with the Cimicifugoside H-2 phytochemical on the activation loop of IKK1/alpha, revealing that Cimicifugoside H-2 is a possible inhibitor of this protein. The pharmacokinetic properties of the drug were also examined to assess the safety of administering the drug. Therefore, in this in silico study, we discovered that the Cimicifugoside H-2 phytochemical inhibits the actively mutated conformation of IKK1/alpha, potentially suppressing the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway.
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Affiliation(s)
- Shahd Aboul Hosn
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
| | - Christina El Ahmadieh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Aia Sinno
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
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3
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Ullrich SR, Fuchs H, Ashworth-Güth C. Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level. Front Microbiol 2024; 15:1357152. [PMID: 38384274 PMCID: PMC10879576 DOI: 10.3389/fmicb.2024.1357152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
The tendency of the periplasmic redox proteins in acidophiles to have more positive redox potentials (Em) than their homologous counterparts in neutrophiles suggests an adaptation to acidic pH at protein level, since thermodynamics of electron transfer processes are also affected by acidic pH. Since this conclusion is mainly based on the electrochemical characterization of redox proteins from extreme acidophiles of the genus Acidithiobacillus, we aimed to characterize three recombinant redox proteins of the more moderate acidophile Ferrovum sp. PN-J47-F6. We applied protein film voltammetry and linear sweep voltammetry coupled to UV/Vis spectroscopy to characterize the redox behavior of HiPIP-41, CytC-18, and CytC-78, respectively. The Em-values of HiPIP-41 (571 ± 16 mV), CytC-18 (276 ± 8 mV, 416 ± 2 mV), and CytC-78 (308 ± 7 mV, 399 ± 7 mV) were indeed more positive than those of homologous redox proteins in neutrophiles. Moreover, our findings suggest that the adaptation of redox proteins with respect to their Em occurs more gradually in response to the pH, since there are also differences between moderate and more extreme acidophiles. In order to address structure function correlations in these redox proteins with respect to structural features affecting the Em, we conducted a comparative structural analysis of the Ferrovum-derived redox proteins and homologs of Acidithiobacillus spp. and neutrophilic proteobacteria. Hydrophobic contacts in the redox cofactor binding pockets resulting in a low solvent accessibility appear to be the major factor contributing to the more positive Em-values in acidophile-derived redox proteins. While additional cysteines in HiPIPs of acidophiles might increase the effective shielding of the [4Fe-4S]-cofactor, the tight shielding of the heme centers in acidophile-derived cytochromes is achieved by a drastic increase in hydrophobic contacts (A.f. Cyc41), and by a larger fraction of aromatic residues in the binding pockets (CytC-18, CytC-78).
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Affiliation(s)
- Sophie R. Ullrich
- Environmental Microbiology Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
- Biohydrometallurgy Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Helena Fuchs
- Biohydrometallurgy Group, Institute for Biological Sciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Charlotte Ashworth-Güth
- Salt and Mineral Chemistry Group, Institute for Inorganic Chemistry, TU Bergakademie Freiberg, Freiberg, Germany
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4
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Maloney BE, Carpio KL, Bilyeu AN, Saunders DRD, Park SL, Pohl AE, Ball NC, Raetz JL, Huang CY, Higgs S, Barrett ADT, Roman-Sosa G, Kenney JL, Vanlandingham DL, Huang YJS. Identification of the flavivirus conserved residues in the envelope protein hinge region for the rational design of a candidate West Nile live-attenuated vaccine. NPJ Vaccines 2023; 8:172. [PMID: 37932282 PMCID: PMC10628263 DOI: 10.1038/s41541-023-00765-0] [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: 01/30/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
The flavivirus envelope protein is a class II fusion protein that drives flavivirus-cell membrane fusion. The membrane fusion process is triggered by the conformational change of the E protein from dimer in the virion to trimer, which involves the rearrangement of three domains, EDI, EDII, and EDIII. The movement between EDI and EDII initiates the formation of the E protein trimer. The EDI-EDII hinge region utilizes four motifs to exert the hinge effect at the interdomain region and is crucial for the membrane fusion activity of the E protein. Using West Nile virus (WNV) NY99 strain derived from an infectious clone, we investigated the role of eight flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region in the conformational change of E protein from dimer to trimer and viral entry. Single mutations of the E-A54, E-I130, E-I135, E-I196, and E-Y201 residues affected infectivity. Importantly, the E-A54I and E-Y201P mutations fully attenuated the mouse neuroinvasive phenotype of WNV. The results suggest that multiple flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region play a critical role in the structure-function of the E protein and some contribute to the virulence phenotype of flaviviruses as demonstrated by the attenuation of the mouse neuroinvasive phenotype of WNV. Thus, as a proof of concept, residues in the EDI-EDII hinge region are proposed targets to engineer attenuating mutations for inclusion in the rational design of candidate live-attenuated flavivirus vaccines.
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Affiliation(s)
- Bailey E Maloney
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Kassandra L Carpio
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Ashley N Bilyeu
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Danielle R D Saunders
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
- Department of Biology, Dean of Faculty, United States Air Force Academy, Colorado Springs, CO, 80840, USA
| | - So Lee Park
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Adrienne E Pohl
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Natalia Costa Ball
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Janae L Raetz
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Claire Y Huang
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Stephen Higgs
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Alan D T Barrett
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Gleyder Roman-Sosa
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Institute of Virology, University of Veterinary Medicine Hanover, Foundation, Buentewg 17, 30559, Hanover, Germany
| | - Joanie L Kenney
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Dana L Vanlandingham
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Yan-Jang S Huang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA.
- Department of Microbiology and Immunology and SUNY Center for Vector-Borne Diseases, Institute of Global Health and Translation Science, Upstate Medical University, Syracuse, NY, 13210, USA.
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5
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Yang C, Kim Y, Kim SO, Lee SJ, Choi J, Ihee H. Length and Charge of the N-terminus Regulate the Lifetime of the Signaling State of Photoactive Yellow Protein. J Phys Chem B 2023; 127:9001-9013. [PMID: 37819381 DOI: 10.1021/acs.jpcb.3c03841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Photoactive yellow protein (PYP) is one of the most extensively studied photoreceptors. Nevertheless, the role of the N-terminus in the photocycle and structural transitions is still elusive. Here, we attached additional amino acids to the N-terminus of PYP and investigated the effect of the length and charge of additional N-terminal residues using circular dichroism, two-dimensional nuclear magnetic resonance (2D-NMR), transient absorption (TA), and transient grating (TG) spectroscopic techniques. TA experiments showed that, except for negatively charged residues (5D-PYP), additional N-terminal residues of PYP generally enable faster dark recovery from the putative signaling state (pB2) to the ground state (pG). TG data showed that although the degree of structural changes can be controlled by adjusting specific amino acid residues in the extended N-terminus of N-terminal extended PYPs (NE-PYPs), the dark recovery times of wt-PYP and NE-PYPs, except for 5D-PYP, are independent of the structural differences between pG and pB2 states. These results demonstrate that the recovery time and the degree of structural change can be regulated by controlling the length and sequence of N-terminal residues of PYP. The findings in this study emphasize the need for careful attention to the remaining amino acid residues when designing recombinant proteins for genetic engineering purposes.
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Affiliation(s)
- Cheolhee Yang
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Youngmin Kim
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seong Ok Kim
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Jin Lee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Jungkweon Choi
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
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6
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Spanò A, Fanton L, Pizzolato D, Moi J, Vinci F, Pesce A, Dongmo Foumthuim CJ, Giacometti A, Simeoni M. Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins. BMC Bioinformatics 2023; 24:336. [PMID: 37697267 PMCID: PMC10496328 DOI: 10.1186/s12859-023-05466-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Residue Interaction Networks (RINs) map the crystallographic description of a protein into a graph, where amino acids are represented as nodes and non-covalent bonds as edges. Determination and visualization of a protein as a RIN provides insights on the topological properties (and hence their related biological functions) of large proteins without dealing with the full complexity of the three-dimensional description, and hence it represents an invaluable tool of modern bioinformatics. RESULTS We present RINmaker, a fast, flexible, and powerful tool for determining and visualizing RINs that include all standard non-covalent interactions. RINmaker is offered as a cross-platform and open source software that can be used either as a command-line tool or through a web application or a web API service. We benchmark its efficiency against the main alternatives and provide explicit tests to show its performance and its correctness. CONCLUSIONS RINmaker is designed to be fully customizable, from a simple and handy support for experimental research to a sophisticated computational tool that can be embedded into a large computational pipeline. Hence, it paves the way to bridge the gap between data-driven/machine learning approaches and numerical simulations of simple, physically motivated, models.
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Affiliation(s)
- Alvise Spanò
- Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
| | - Lorenzo Fanton
- Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
| | - Davide Pizzolato
- Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
| | - Jacopo Moi
- Department of Molecular Science and Nanosystems, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
| | - Francesco Vinci
- Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
| | - Alberto Pesce
- Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
| | - Cedrix J Dongmo Foumthuim
- Department of Molecular Science and Nanosystems, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
| | - Achille Giacometti
- Department of Molecular Science and Nanosystems, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy
- European Centre for Living Technology (ECLT), Dorsoduro 3246, 30123, Venice, Italy
| | - Marta Simeoni
- Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy.
- European Centre for Living Technology (ECLT), Dorsoduro 3246, 30123, Venice, Italy.
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7
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Nikolsky KS, Kulikova LI, Petrovskiy DV, Rudnev VR, Butkova TV, Malsagova KA, Kopylov AT, Kaysheva AL. Three-helix bundle and SH3-type barrels: autonomously stable structural motifs in small and large proteins. J Biomol Struct Dyn 2023:1-15. [PMID: 37640007 DOI: 10.1080/07391102.2023.2250450] [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: 05/26/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
In this study, we investigated two variants of a three-helix bundle and SH3-type barrel, compact in space, present in small and large proteins of various living organisms. Using a neural graph network, proteins with three-helix bundle (n = 1377) and SH3-type barrels (n = 1914) spatial folds were selected. Molecular experiments were performed for small proteins with these folds, and motifs were studied autonomously outside the protein environment at 300, 340, and 370 K. A comparative analysis of the main parameters of the structures in the course of the experiment was performed, including gyration radius, area accessible to the solvent, number of hydrophobic and hydrogen bonds, and root-mean-square deviation of atomic positions (RMSD). We exhibited an autonomous stability of the studied folds outside the protein environment in an aquatic medium. We aimed to demonstrate the possibility of analyzing three-helix bundle and SH3-type barrels autonomously outside the protein globule, thereby reducing the computational time and increasing performance without significant loss of information.Communicated by Ramaswamy H. Sarma.
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8
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Włodarczyk R, Těšický M, Vinkler M, Novotný M, Remisiewicz M, Janiszewski T, Minias P. Divergent evolution drives high diversity of toll-like receptors (TLRs) in passerine birds: Buntings and finches. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104704. [PMID: 37019350 DOI: 10.1016/j.dci.2023.104704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Toll-like receptors (TLRs) form a key component of animal innate immunity, being responsible for recognition of conserved microbial structures. As such, TLRs may be subject to diversifying and balancing selection, which maintains allelic variation both within and between populations. However, most research on TLRs in non-model avian species is focused on bottlenecked populations with depleted genetic variation. Here, we assessed variation at the extracellular domains of three TLR genes (TLR1LA, TLR3, TLR4) across eleven species from two passerine families of buntings (Emberizidae) and finches (Fringillidae), all having large breeding population sizes (millions of individuals). We found extraordinary TLR polymorphism in our study taxa, with >100 alleles detected at TLR1LA and TLR4 across species and high haplotype diversity (>0.75) in several species. Despite recent species divergence, no nucleotide allelic variants were shared between species, suggesting rapid TLR evolution. Higher variation at TLR1LA and TLR4 than TLR3 was associated with a stronger signal of diversifying selection, as measured with nucleotide substitutions rates and the number of positively selected sites (PSS). Structural protein modelling of TLRs showed that some PSS detected within TLR1LA and TLR4 were previously recognized as functionally important sites or were located in their proximity, possibly affecting ligand recognition. Furthermore, we identified PSS responsible for major surface electrostatic charge clustering, which may indicate their adaptive importance. Our study provides compelling evidence for the divergent evolution of TLR genes in buntings and finches and indicates that high TLR variation may be adaptively maintained via diversifying selection acting on functional ligand binding sites.
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Affiliation(s)
- Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Martin Těšický
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic
| | - Marian Novotný
- Charles University, Faculty of Science, Department of Cell Biology, Viničná 7, 128 43, Prague, Czech Republic
| | - Magdalena Remisiewicz
- Bird Migration Research Station, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Tomasz Janiszewski
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
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9
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Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. Conformational Dynamics of the Activated GLP-1 Receptor-G s Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS CENTRAL SCIENCE 2023; 9:992-1007. [PMID: 37252352 PMCID: PMC10214531 DOI: 10.1021/acscentsci.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 05/31/2023]
Abstract
Despite advances in characterizing the structures and functions of G protein-coupled receptors (GPCRs), our understanding of GPCR activation and signaling is still limited by the lack of information on conformational dynamics. It is particularly challenging to study the dynamics of GPCR complexes with their signaling partners because of their transient nature and low stability. Here, by combining cross-linking mass spectrometry (CLMS) with integrative structure modeling, we map the conformational ensemble of an activated GPCR-G protein complex at near-atomic resolution. The integrative structures describe heterogeneous conformations for a high number of potential alternative active states of the GLP-1 receptor-Gs complex. These structures show marked differences from the previously determined cryo-EM structure, especially at the receptor-Gs interface and in the interior of the Gs heterotrimer. Alanine-scanning mutagenesis coupled with pharmacological assays validates the functional significance of 24 interface residue contacts only observed in the integrative structures, yet absent in the cryo-EM structure. Through the integration of spatial connectivity data from CLMS with structure modeling, our study provides a new approach that is generalizable to characterizing the conformational dynamics of GPCR signaling complexes.
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Affiliation(s)
- Shijia Yuan
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Lisha Xia
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Wang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Wu
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Chen Pan
- National
Facility for Protein Science in Shanghai, Shanghai Advanced Research
Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Zhiran Fan
- Biocreater
(WuHan) Biotechnology Co., Ltd, Wuhan 430075, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Department of
Chemical Biology, College of Chemistry and Molecular Engineering,
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Raymond C. Stevens
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Andrej Sali
- Quantitative
Biosciences Institute, University of California,
San Francisco, San Francisco, California 94143, United States
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94143, United States
| | - Liping Sun
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
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10
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Serdyuk OP, Abdullatypov AV, Smolygina LD, Ashikhmin AA, Bolshakov MA. Simultaneous functioning of different light-harvesting complexes-a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions. PeerJ 2023; 11:e14769. [PMID: 36743963 PMCID: PMC9897067 DOI: 10.7717/peerj.14769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/29/2022] [Indexed: 02/03/2023] Open
Abstract
Novel peripheral light-harvesting (LH) complex designated as LL LH2 was isolated along with LH4 complex from Rhodopseudomonas palustris cells grown under low light intensity (LL). FPLC-MS/MS allowed to reveal PucABd and PucBabc apoproteins in LL LH2 complex, which is different from previously described LH4 complex containing PucABd, PucABa and PucBb. The main carotenoids in LL LH2 complex were rhodopin and 3,4-didehydrorhodopin. Three-dimensional modeling demonstrated which amino acid residues of all the β-subunits could interact with carotenoids (Car) and bacteriochlorophyll a (BChl a). Analysis of amino acid sequences of α-subunits of both LL complexes showed presence of different C-terminal motifs, IESSVNVG in αa subunit and IESSIKAV in αd subunit, in the same positions of C-termini, which could reflect different retention force of LL LH2 and LH4 on hydroxyl apatite, facilitating successful isolation of these complexes. Differences of these LL complexes in protein and carotenoid composition, in efficiency of energy transfer from Car to BChl a, which is two times lower in LL LH2 than in LH4, allow to assign it to a novel type of light-harvesting complex in Rhodopseudomonas palustris.
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Affiliation(s)
- Olga Petrovna Serdyuk
- Institute of Basic Biological Problems of the Russian Academy of Sciences—A Separate Subdivision of PSCBR RAS (IBBP RAS), Pushchino, Moscow Region, Russian Federation
| | - Azat Vadimovich Abdullatypov
- Institute of Basic Biological Problems of the Russian Academy of Sciences—A Separate Subdivision of PSCBR RAS (IBBP RAS), Pushchino, Moscow Region, Russian Federation
| | - Lidiya Dmitrievna Smolygina
- Institute of Basic Biological Problems of the Russian Academy of Sciences—A Separate Subdivision of PSCBR RAS (IBBP RAS), Pushchino, Moscow Region, Russian Federation
| | - Aleksandr Aleksandrovich Ashikhmin
- Institute of Basic Biological Problems of the Russian Academy of Sciences—A Separate Subdivision of PSCBR RAS (IBBP RAS), Pushchino, Moscow Region, Russian Federation
| | - Maxim Alexandrovich Bolshakov
- Institute of Basic Biological Problems of the Russian Academy of Sciences—A Separate Subdivision of PSCBR RAS (IBBP RAS), Pushchino, Moscow Region, Russian Federation
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11
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Krchlíková V, Hron T, Těšický M, Li T, Ungrová L, Hejnar J, Vinkler M, Elleder D. Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET. Viruses 2022; 15:3. [PMID: 36680044 PMCID: PMC9861763 DOI: 10.3390/v15010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are key RNA virus sensors belonging to the RIG-I-like receptor (RLR) family. The activation of the RLR inflammasome leads to the establishment of antiviral state, mainly through interferon-mediated signaling. The evolutionary dynamics of RLRs has been studied mainly in mammals, where rare cases of RLR gene losses were described. By in silico screening of avian genomes, we previously described two independent disruptions of MDA5 in two bird orders. Here, we extend this analysis to approximately 150 avian genomes and report 16 independent evolutionary events of RIG-I inactivation. Interestingly, in almost all cases, these inactivations are coupled with genetic disruptions of RIPLET/RNF135, an ubiquitin ligase RIG-I regulator. Complete absence of any detectable RIG-I sequences is unique to several galliform species, including the domestic chicken (Gallus gallus). We further aimed to determine compensatory evolution of MDA5 in RIG-I-deficient species. While we were unable to show any specific global pattern of adaptive evolution in RIG-I-deficient species, in galliforms, the analyses of positive selection and surface charge distribution support the hypothesis of some compensatory evolution in MDA5 after RIG-I loss. This work highlights the dynamic nature of evolution in bird RNA virus sensors.
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Affiliation(s)
- Veronika Krchlíková
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Lenka Ungrová
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Daniel Elleder
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
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12
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Identification of the Shigella flexneri Wzy Domain Modulating Wzz pHS-2 Interaction and Detection of the Wzy/Wzz/Oag Complex. J Bacteriol 2022; 204:e0022422. [PMID: 35980183 PMCID: PMC9487639 DOI: 10.1128/jb.00224-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shigella flexneri implements the Wzy-dependent pathway to biosynthesize the O antigen (Oag) component of its surface lipopolysaccharide. The inner membrane polymerase WzySF catalyzes the repeat addition of undecaprenol-diphosphate-linked Oag (Und-PP-RUs) to produce a polysaccharide, the length of which is tightly regulated by two competing copolymerase proteins, WzzSF (short-type Oag; 10 to 17 RUs) and WzzpHS-2 (very-long-type Oag; >90 RUs). The nature of the interaction between WzySF and WzzSF/WzzpHS-2 in Oag polymerization remains poorly characterized, with the majority of the literature characterizing the individual protein constituents of the Wzy-dependent pathway. Here, we report instead a major investigation into the specific binding interactions of WzySF with its copolymerase counterparts. For the first time, a region of WzySF that forms a unique binding site for WzzpHS-2 has been identified. Specifically, this work has elucidated key WzySF moieties at the N- and C-terminal domains (NTD and CTD) that form an intramolecular pocket modulating the WzzpHS-2 interaction. Novel copurification data highlight that disruption of residues within this NTD-CTD pocket impairs the interaction with WzzpHS-2 without affecting WzzSF binding, thereby specifically disrupting polymerization of longer polysaccharide chains. This study provides a novel understanding of the molecular interaction of WzySF with WzzSF/WzzpHS-2 in the Wzy-dependent pathway and, furthermore, detects the Wzy/Wzz/Und-PP-Oag complex for the first time. Beyond S. flexneri, this work may be extended to provide insight into the interactions between protein homologues expressed by related species, especially members of Enterobacteriaceae, that produce dual Oag chain length determinants. IMPORTANCE Shigella flexneri is a pathogen causing significant morbidity and mortality, predominantly devastating the pediatric age group in developing countries. A major virulence factor contributing to S. flexneri pathogenesis is its surface lipopolysaccharide, which is comprised of three domains: lipid A, core oligosaccharide, and O antigen (Oag). The Wzy-dependent pathway is the most common biosynthetic mechanism implemented for Oag biosynthesis by Gram-negative bacteria, including S. flexneri. The nature of the interaction between the polymerase, WzySF, and the polysaccharide copolymerases, WzzSF and WzzpHS-2, in Oag polymerization is poorly characterized. This study investigates the molecular interplay between WzySF and its copolymerases, deciphering key interactions in the Wzy-dependent pathway that may be extended beyond S. flexneri, providing insight into Oag biosynthesis in Gram-negative bacteria.
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Giangregorio N, Pierri CL, Tonazzi A, Incampo G, Tragni V, De Grassi A, Indiveri C. Proline/Glycine residues of the PG-levels guide conformational changes along the transport cycle in the mitochondrial carnitine/acylcarnitine carrier (SLC25A20). Int J Biol Macromol 2022; 221:1453-1465. [PMID: 36122779 DOI: 10.1016/j.ijbiomac.2022.09.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
Mitochondrial carnitine/acylcarnitine carrier (CAC) is a member of the mitochondrial carrier (MC) family and imports acylcarnitine into the mitochondrial matrix in exchange for carnitine, playing a pivotal role in carnitine shuttle, crucial for fatty acid oxidation. The crystallized structure of CAC has not been solved yet, however, the availability of several in vitro/in silico studies, also based on the crystallized structures of the ADP/ATP carrier in the cytosolic-conformation and in the matrix-conformation, has made possible to confirm the hypothesis of the single-binding centered-gated pore mechanism for all the members of the MC family. In addition, our recent bioinformatics analyses allowed quantifying in silico the importance of protein residues of MC substrate binding region, of those involved in the formation of the matrix and cytosolic gates, and of those belonging to the Pro/Gly (PG) levels, proposed to be crucial for the tilting/kinking/bending of the six MC transmembrane helices, funneling the substrate translocation pathway. Here we present a combined in silico/in vitro analysis employed for investigating the role played by a group of 6 proline residues and 6 glycine residues, highly conserved in CAC, belonging to MC PG-levels. Residues of the PG-levels surround the similarly located MC common substrate binding region, and were proposed to lead conformational changes and substrate translocation, following substrate binding. For our analysis, we employed 3D molecular modeling approaches, alanine scanning site-directed mutagenesis and in vitro transport assays. Our analysis reveals that P130 (H3), G268 (H6) and G220 (H5), mutated in alanine, affect severely CAC transport activity (mutant catalytic efficiency lower than 5 % compared to the wild type CAC), most likely due to their major role in triggering CAC conformational changes, following carnitine binding. Notably, P30A (H1) and G121A (H3) CAC mutants, increase the carnitine uptake up to 217 % and 112 %, respectively, compared to the wild type CAC.
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Affiliation(s)
- Nicola Giangregorio
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy.
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy.
| | - Annamaria Tonazzi
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy
| | - Giovanna Incampo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Vincenzo Tragni
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Cesare Indiveri
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy; Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via Bucci 4C, 87036 Arcavacata di Rende, Italy
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14
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Tossounian MA, Baczynska M, Dalton W, Newell C, Ma Y, Das S, Semelak JA, Estrin DA, Filonenko V, Trujillo M, Peak-Chew SY, Skehel M, Fraternali F, Orengo C, Gout I. Profiling the Site of Protein CoAlation and Coenzyme A Stabilization Interactions. Antioxidants (Basel) 2022; 11:antiox11071362. [PMID: 35883853 PMCID: PMC9312308 DOI: 10.3390/antiox11071362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/26/2022] [Accepted: 06/26/2022] [Indexed: 11/30/2022] Open
Abstract
Coenzyme A (CoA) is a key cellular metabolite known for its diverse functions in metabolism and regulation of gene expression. CoA was recently shown to play an important antioxidant role under various cellular stress conditions by forming a disulfide bond with proteins, termed CoAlation. Using anti-CoA antibodies and liquid chromatography tandem mass spectrometry (LC-MS/MS) methodologies, CoAlated proteins were identified from various organisms/tissues/cell-lines under stress conditions. In this study, we integrated currently known CoAlated proteins into mammalian and bacterial datasets (CoAlomes), resulting in a total of 2093 CoAlated proteins (2862 CoAlation sites). Functional classification of these proteins showed that CoAlation is widespread among proteins involved in cellular metabolism, stress response and protein synthesis. Using 35 published CoAlated protein structures, we studied the stabilization interactions of each CoA segment (adenosine diphosphate (ADP) moiety and pantetheine tail) within the microenvironment of the modified cysteines. Alternating polar-non-polar residues, positively charged residues and hydrophobic interactions mainly stabilize the pantetheine tail, phosphate groups and the ADP moiety, respectively. A flexible nature of CoA is observed in examined structures, allowing it to adapt its conformation through interactions with residues surrounding the CoAlation site. Based on these findings, we propose three modes of CoA binding to proteins. Overall, this study summarizes currently available knowledge on CoAlated proteins, their functional distribution and CoA-protein stabilization interactions.
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Affiliation(s)
- Maria-Armineh Tossounian
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Maria Baczynska
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - William Dalton
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Charlie Newell
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Yilin Ma
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Sayoni Das
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Jonathan Alexis Semelak
- Departmento de Química Inorgánica Analítica y Química Física, INQUIMAE-CONICET, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; (J.A.S.); (D.A.E.)
| | - Dario Ariel Estrin
- Departmento de Química Inorgánica Analítica y Química Física, INQUIMAE-CONICET, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina; (J.A.S.); (D.A.E.)
| | - Valeriy Filonenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine;
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay;
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Sew Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London WC2R 2LS, UK;
| | - Christine Orengo
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (M.-A.T.); (M.B.); (W.D.); (C.N.); (Y.M.); (S.D.); (C.O.)
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine;
- Correspondence:
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15
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PIF - A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures. Methods 2022; 205:63-72. [PMID: 35724844 DOI: 10.1016/j.ymeth.2022.04.018] [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: 02/06/2022] [Revised: 03/13/2022] [Accepted: 04/16/2022] [Indexed: 11/22/2022] Open
Abstract
Proteins play an essential role in the functioning of living organisms. The enormity of the atomic interactions in proteins is essential in controlling their spatial structures and dynamics. It can also provide scientists with valuable information that help to determine the native structures of proteins. This paper presents the PIF (Protein Interaction Finder) library for the Java language, enabling the identification of selected atomic interactions (hydrogen and disulfide bonds, ionic, hydrophobic, aromatic-aromatic, sulfur-aromatic, and amino-aromatic interactions) based on the three-dimensional structure of proteins. The interaction calculation rules applied in PIF rely on documented theoretical foundations gathered from experimental studies of interactions in native protein structures. The library has a universal purpose, supporting drug discovery and development processes and protein structure modeling. Finding the atomic interactions can also deliver numerical features for various Artificial Intelligence (AI) models built for protein analysis. The conducted research comparing the results obtained with the use of the PIF library and competing tools has shown that our solution can effectively determine the interactions occurring in protein structures for entire collections of proteins. Moreover, as a solution that provides a programming interface, the PIF library can be used in any Java project, making it a universal tool.
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16
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Tragni V, Primiano G, Tummolo A, Cafferati Beltrame L, La Piana G, Sgobba MN, Cavalluzzi MM, Paterno G, Gorgoglione R, Volpicella M, Guerra L, Marzulli D, Servidei S, De Grassi A, Petrosillo G, Lentini G, Pierri CL. Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs. Molecules 2022; 27:3494. [PMID: 35684429 PMCID: PMC9182050 DOI: 10.3390/molecules27113494] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial diseases (MDs) may result from mutations affecting nuclear or mitochondrial genes, encoding mitochondrial proteins, or non-protein-coding mitochondrial RNA. Despite the great variability of affected genes, in the most severe cases, a neuromuscular and neurodegenerative phenotype is observed, and no specific therapy exists for a complete recovery from the disease. The most used treatments are symptomatic and based on the administration of antioxidant cocktails combined with antiepileptic/antipsychotic drugs and supportive therapy for multiorgan involvement. Nevertheless, the real utility of antioxidant cocktail treatments for patients affected by MDs still needs to be scientifically demonstrated. Unfortunately, clinical trials for antioxidant therapies using α-tocopherol, ascorbate, glutathione, riboflavin, niacin, acetyl-carnitine and coenzyme Q have met a limited success. Indeed, it would be expected that the employed antioxidants can only be effective if they are able to target the specific mechanism, i.e., involving the central and peripheral nervous system, responsible for the clinical manifestations of the disease. Noteworthily, very often the phenotypes characterizing MD patients are associated with mutations in proteins whose function does not depend on specific cofactors. Conversely, the administration of the antioxidant cocktails might determine the suppression of endogenous oxidants resulting in deleterious effects on cell viability and/or toxicity for patients. In order to avoid toxicity effects and before administering the antioxidant therapy, it might be useful to ascertain the blood serum levels of antioxidants and cofactors to be administered in MD patients. It would be also worthwhile to check the localization of mutations affecting proteins whose function should depend (less or more directly) on the cofactors to be administered, for estimating the real need and predicting the success of the proposed cofactor/antioxidant-based therapy.
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Affiliation(s)
- Vincenzo Tragni
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Guido Primiano
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Albina Tummolo
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Lucas Cafferati Beltrame
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Gianluigi La Piana
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Noemi Sgobba
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Giulia Paterno
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Ruggiero Gorgoglione
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Lorenzo Guerra
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Domenico Marzulli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Serenella Servidei
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Giuseppe Petrosillo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Giovanni Lentini
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
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17
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Patro LPP, Rathinavelan T. STRIDER: Steric hindrance and metal coordination identifier. Comput Biol Chem 2022; 98:107686. [DOI: 10.1016/j.compbiolchem.2022.107686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 11/03/2022]
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18
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Tragni V, Preziusi F, Laera L, Onofrio A, Mercurio I, Todisco S, Volpicella M, De Grassi A, Pierri CL. Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. EPMA J 2022; 13:149-175. [PMID: 35013687 PMCID: PMC8732965 DOI: 10.1007/s13167-021-00267-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022]
Abstract
Aims The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM. Methods In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein-protein interface. Results Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike "boat-shaped" receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the "stern" or "bow" regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the "hull" region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities. Conclusion In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00267-w.
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Affiliation(s)
- Vincenzo Tragni
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Francesca Preziusi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Luna Laera
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Angelo Onofrio
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Ivan Mercurio
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Simona Todisco
- Department of Sciences, University of Basilicata, Viale dell’Ateneo Lucano, 10-85100 Potenza, Italy
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
- BROWSer S.r.l. at Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
- BROWSer S.r.l. at Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
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Ngai CK, Lam SL, Lee HK, Guo P. A purine and a backbone discontinuous site alter the structure and thermal stability of DNA minidumbbells containing two pentaloops. FEBS Lett 2022; 596:826-840. [DOI: 10.1002/1873-3468.14293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Cheuk Kit Ngai
- Department of Chemistry The Chinese University of Hong Kong Shatin New Territories Hong Kong SAR China
| | - Sik Lok Lam
- Department of Chemistry The Chinese University of Hong Kong Shatin New Territories Hong Kong SAR China
| | - Hung Kay Lee
- Department of Chemistry The Chinese University of Hong Kong Shatin New Territories Hong Kong SAR China
| | - Pei Guo
- School of Biology and Biological Engineering South China University of Technology Guangzhou Guangdong 51006 China
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Scafuri N, Soler MA, Spitaleri A, Rocchia W. Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein-Protein Docking. J Chem Theory Comput 2021; 17:7271-7280. [PMID: 34653335 PMCID: PMC8582249 DOI: 10.1021/acs.jctc.1c00789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Protein–protein
docking typically consists of the generation
of putative binding conformations, which are subsequently ranked by
fast heuristic scoring functions. The simplicity of these functions
allows for computational efficiency but has severe repercussions on
their discrimination capabilities. In this work, we show the effectiveness
of suitable descriptors calculated along short scaled molecular dynamics
runs in recognizing the nearest-native bound conformation among a
set of putative structures generated by the HADDOCK tool for eight
protein–protein systems.
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Affiliation(s)
- Nicola Scafuri
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
| | - Miguel A Soler
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
| | - Andrea Spitaleri
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
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21
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Repeated MDA5 Gene Loss in Birds: An Evolutionary Perspective. Viruses 2021; 13:v13112131. [PMID: 34834938 PMCID: PMC8619217 DOI: 10.3390/v13112131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Two key cytosolic receptors belonging to the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) family sense the viral RNA-derived danger signals: RIG-I and melanoma differentiation-associated protein 5 (MDA5). Their activation establishes an antiviral state by downstream signaling that ultimately activates interferon-stimulated genes (ISGs). While in rare cases RIG-I gene loss has been detected in mammalian and avian species, most notably in the chicken, MDA5 pseudogenization has only been detected once in mammals. We have screened over a hundred publicly available avian genome sequences and describe an independent disruption of MDA5 in two unrelated avian lineages, the storks (Ciconiiformes) and the rallids (Gruiformes). The results of our RELAX analysis confirmed the absence of negative selection in the MDA5 pseudogene. In contrast to our prediction, we have shown, using multiple dN/dS-based approaches, that the MDA5 loss does not appear to have resulted in any compensatory evolution in the RIG-I gene, which may partially share its ligand-binding specificity. Together, our results indicate that the MDA5 pseudogenization may have important functional effects on immune responsiveness in these two avian clades.
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22
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Abstract
Protein structure prediction (PSP) predicts the native conformation for a given protein sequence. Classically, the problem has been shown to belong to the NP-complete complexity class. Its applications range from physics, through bioinformatics to medicine and quantum biology. It is possible however to speed it up with quantum computational methods, as we show in this paper. Here we develop a fast quantum algorithm for PSP in three-dimensional hydrophobic-hydrophilic model on body-centered cubic lattice with quadratic speedup over its classical counterparts. Given a protein sequence of n amino acids, our algorithm reduces the temporal and spatial complexities to, respectively, [Formula: see text] and O(n2 logn) . With respect to oracle-related quantum algorithms for the NP-complete problems, we identify our algorithm as optimal. To justify the feasibility of the proposed algorithm we successfully solve the problem on IBM quantum simulator involving 21 and 25 qubits. We confirm the experimentally obtained high probability of success in finding the desired conformation by calculating the theoretical probability estimations.
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23
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Yap J, Deepak RNVK, Tian Z, Ng WH, Goh KC, Foo A, Tee ZH, Mohanam MP, Sim YRM, Degirmenci U, Lam P, Chen Z, Fan H, Hu J. The stability of R-spine defines RAF inhibitor resistance: A comprehensive analysis of oncogenic BRAF mutants with in-frame insertion of αC-β4 loop. SCIENCE ADVANCES 2021; 7:7/24/eabg0390. [PMID: 34108213 PMCID: PMC8189578 DOI: 10.1126/sciadv.abg0390] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Although targeting BRAF mutants with RAF inhibitors has achieved promising outcomes in cancer therapy, drug resistance remains a remarkable challenge, and underlying molecular mechanisms are not fully understood. Here, we characterized a previously unknown group of oncogenic BRAF mutants with in-frame insertions (LLRins506 or VLRins506) of αC-β4 loop. Using structure modeling and molecular dynamics simulation, we found that these insertions formed a large hydrophobic network that stabilizes R-spine and thus triggers the catalytic activity of BRAF. Furthermore, these insertions disrupted BRAF dimer interface and impaired dimerization. Unlike BRAF(V600E), these BRAF mutants with low dimer affinity were strongly resistant to all RAF inhibitors in clinic or clinical trials, which arises from their stabilized R-spines. As predicted by molecular docking, the stabilized R-spines in other BRAF mutants also conferred drug resistance. Together, our data indicated that the stability of R-spine but not dimer affinity determines the RAF inhibitor resistance of oncogenic BRAF mutants.
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Affiliation(s)
- Jiajun Yap
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - R N V Krishna Deepak
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Zizi Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Kah Chun Goh
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Alicia Foo
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Zi Heng Tee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Manju Payini Mohanam
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Yuen Rong M Sim
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Ufuk Degirmenci
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Paula Lam
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, MD9, Singapore 117593, Singapore
- Cellvec Pte. Ltd., 100 Pasir Panjang Road, #04-02, Singapore 118518, Singapore
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hao Fan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Jiancheng Hu
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
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24
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Wan L, Yi J, Lam SL, Lee HK, Guo P. 5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbells. Chemistry 2021; 27:6740-6747. [PMID: 33501691 DOI: 10.1002/chem.202005410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Indexed: 11/07/2022]
Abstract
Minidumbbell (MDB) is a recently identified non-B DNA structure that has been proposed to associate with genetic instabilities. It also serves as a functional structural motif in DNA nanotechnology. DNA molecular switches constructed using MDBs show instant and complete structural conversions with easy manipulations. The availability of stable MDBs can broaden their applications. In this work, we found that substitutions of cytosine with 5-methylcytosine could lead to a significant enhancement in the thermal stabilities of MDBs. Consecutive methylations of cytosine in MDBs brought about cumulative stabilization with a drastic increase in the melting temperature by 23 °C. NMR solution structures of two MDBs containing 5-methylcytosine residues have been successfully determined and revealed that the enhanced stabilities resulted primarily from favorable hydrophobic contacts, more stable base pairs and enhanced base-base stackings involving the methyl group of 5-methylcytosine.
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Affiliation(s)
- Liqi Wan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jie Yi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Pei Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
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25
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Wan L, Lam SL, Lee HK, Guo P. Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell. Int J Mol Sci 2021; 22:3633. [PMID: 33807305 PMCID: PMC8037738 DOI: 10.3390/ijms22073633] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/17/2022] Open
Abstract
DNA methylation is a prevalent regulatory modification in prokaryotes and eukaryotes. N1-methyladenine (m1A) and N6-methyladenine (m6A) have been found to be capable of altering DNA structures via disturbing Watson-Crick base pairing. However, little has been known about their influences on non-B DNA structures, which are associated with genetic instabilities. In this work, we investigated the effects of m1A and m6A on both the structure and thermodynamic stability of a newly reported DNA minidumbbell formed by two TTTA tetranucleotide repeats. As revealed by the results of nuclear magnetic resonance spectroscopic studies, both m1A and m6A favored the formation of a T·m1A and T·m6A Hoogsteen base pair, respectively. More intriguingly, the m1A and m6A modifications brought about stabilization and destabilization effects on the DNA minidumbbell, respectively. This work provides new biophysical insights into the effects of adenine methylation on the structure and thermodynamic stability of DNA.
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Affiliation(s)
- Liqi Wan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China;
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, China;
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, China;
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, China;
| | - Pei Guo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China;
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26
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Chen D, Zhu X, Ilavsky J, Whitmer T, Hatzakis E, Jones OG, Campanella OH. Polyphenols Weaken Pea Protein Gel by Formation of Large Aggregates with Diminished Noncovalent Interactions. Biomacromolecules 2021; 22:1001-1014. [PMID: 33494594 DOI: 10.1021/acs.biomac.0c01753] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyphenols are well-known native cross-linkers and gel strengthening agents for many animal proteins. However, their role in modifying plant protein gels remains unclear. In this study, multiple techniques were applied to unravel the influence of green tea polyphenols (GTP) on pea protein gels and the underlying mechanisms. We found that the elasticity and viscosity of pea protein gels decreased with increased GTP. The protein backbone became less rigid when GTP was present based on shortened T1ρH in relaxation solid-state NMR measurements. Electron microscopy and small-angle X-ray scattering showed that gels weakened by GTP possessed disrupted networks with the presence of large protein aggregates. Solvent extraction and molecular dynamic simulation revealed a reduction in hydrophobic interactions and hydrogen bonds among proteins in gels containing GTP. The current findings may be applicable to other plant proteins for greater control of gel structures in the presence of polyphenols, expanding their utilization in food and biomedical applications.
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Affiliation(s)
- Da Chen
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Rd, Columbus, Ohio 43210, United States
| | - Xiao Zhu
- Research Computing, Information Technology at Purdue (ITaP), Purdue University, 155 South Grant Street, West Lafayette, Indiana 47907, United States
| | - Jan Ilavsky
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Tanya Whitmer
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Emmanuel Hatzakis
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Rd, Columbus, Ohio 43210, United States
| | - Owen G Jones
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, Indiana 47907, United States
| | - Osvaldo H Campanella
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Rd, Columbus, Ohio 43210, United States
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27
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Tragni V, Cotugno P, De Grassi A, Massari F, Di Ronzo F, Aresta AM, Zambonin C, Sanzani SM, Ippolito A, Pierri CL. Targeting mitochondrial metabolite transporters in Penicillium expansum for reducing patulin production. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:158-181. [PMID: 33250320 DOI: 10.1016/j.plaphy.2020.07.027] [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: 05/16/2020] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 06/12/2023]
Abstract
There is an increasing need of alternative treatments to control fungal infection and consequent mycotoxin accumulation in harvested fruits and vegetables. Indeed, only few biological targets of antifungal agents have been characterized and can be used for limiting fungal spread from decayed fruits/vegetables to surrounding healthy ones during storage. On this concern, a promising target of new antifungal treatments may be represented by mitochondrial proteins due to some species-specific functions played by mitochondria in fungal morphogenesis, drug resistance and virulence. One of the most studied mycotoxins is patulin produced by several species of Penicillium and Aspergillus genera. Patulin is toxic to many biological systems including bacteria, higher plants and animalia. Although precise biochemical mechanisms of patulin toxicity in humans are not completely clarified, its high presence in fresh and processed apple fruits and other apple-based products makes necessary developing a strategy for limiting its presence/accumulation. Patulin biosynthetic pathway consists of an enzymatic cascade, whose first step is represented by the synthesis of 6-methylsalicylic acid, obtained from the condensation of one acetyl-CoA molecule with three malonyl-CoA molecules. The most abundant acetyl-CoA precursor is represented by citrate produced by mitochondria. In the present investigation we report about the possibility to control patulin production through the inhibition of mitochondrial/peroxisome transporters involved in the export of acetyl-CoA precursors from mitochondria and/or peroxisomes, with specific reference to the predicted P. expansum mitochondrial Ctp1p, DTC, Sfc1p, Oac1p and peroxisomal PXN carriers.
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Affiliation(s)
- Vincenzo Tragni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Pietro Cotugno
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy; BROWSer S.r.l. (https://browser-bioinf.com/) c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126, Bari, Italy
| | - Federica Massari
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Francesco Di Ronzo
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
| | - Antonella Maria Aresta
- Chemistry Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Carlo Zambonin
- Chemistry Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | | | - Antonio Ippolito
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy.
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy; BROWSer S.r.l. (https://browser-bioinf.com/) c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126, Bari, Italy.
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28
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Tragni V, Cotugno P, De Grassi A, Cavalluzzi MM, Mincuzzi A, Lentini G, Sanzani SM, Ippolito A, Pierri CL. Targeting Penicillium expansum GMC Oxidoreductase with High Affinity Small Molecules for Reducing Patulin Production. BIOLOGY 2020; 10:biology10010021. [PMID: 33396459 PMCID: PMC7824139 DOI: 10.3390/biology10010021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/21/2022]
Abstract
Simple Summary With the urgent necessity of potential treatments for limiting mycotoxin production and postharvest fungal rots, we propose a combined in silico/in vitro/in vivo strategy for the rapid and effective identification of bioactive small molecules, chosen among a chemical library hosting approved drugs and phytochemicals, to be used after harvest. The molecular target of our analysis was the GMC oxidoreductase from Penicillium expansum involved in the biosynthesis of patulin, a mycotoxin that can contaminate many foods, especially fruits and fruit-based products. The employed in silico/in vitro/in vivo assays described in our study proved the effectiveness of our strategy and in particular of two small molecules, 6-hydroxycoumarin (structurally related to umbelliferon, an already characterized patulin synthase inhibitor) and meticrane (an already approved drug) in reducing patulin accumulation. Our findings highly recommend the mentioned ligands to be subjected to further analysis for being used in the next future in place of other more toxic compounds, in postharvest treatments based on dipping or drenching methods. Abstract Flavine adenine dinucleotide (FAD) dependent glucose methanol choline oxidoreductase (GMC oxidoreductase) is the terminal key enzyme of the patulin biosynthetic pathway. GMC oxidoreductase catalyzes the oxidative ring closure of (E)-ascladiol to patulin. Currently, no protein involved in the patulin biosynthesis in Penicillium expansum has been experimentally characterized or solved by X-ray diffraction. Consequently, nothing is known about P. expansum GMC oxidoreductase substrate-binding site and mode of action. In the present investigation, a 3D comparative model for P. expansum GMC oxidoreductase has been described. Furthermore, a multistep computational approach was used to identify P. expansum GMC oxidoreductase residues involved in the FAD binding and in substrate recognition. Notably, the obtained 3D comparative model of P. expansum GMC oxidoreductase was used for performing a virtual screening of a chemical/drug library, which allowed to predict new GMC oxidoreductase high affinity ligands to be tested in in vitro/in vivo assays. In vitro assays performed in presence of 6-hydroxycoumarin and meticrane, among the highly affinity predicted binders, confirmed a dose-dependent inhibition (17–81%) of patulin production by 6-hydroxycoumarin (10 µM–1 mM concentration range), whereas the approved drug meticrane inhibited patulin production by 43% already at 10 µM. Furthermore, 6-hydroxycoumarin and meticrane caused a 60 and 41% reduction of patulin production, respectively, in vivo on apples at 100 µg/wound.
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Affiliation(s)
- Vincenzo Tragni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
| | - Pietro Cotugno
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy;
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy;
- BROWSer S.r.l., c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Maria Maddalena Cavalluzzi
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy; (M.M.C.); (G.L.)
| | - Annamaria Mincuzzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
| | - Giovanni Lentini
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy; (M.M.C.); (G.L.)
| | - Simona Marianna Sanzani
- CIHEAM Bari, Via Ceglie 9, 70010 Valenzano (BA), Italy
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
| | - Antonio Ippolito
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy;
- BROWSer S.r.l., c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
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Illig AM, Strodel B. Performance of Markov State Models and Transition Networks on Characterizing Amyloid Aggregation Pathways from MD Data. J Chem Theory Comput 2020; 16:7825-7839. [DOI: 10.1021/acs.jctc.0c00727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexander-Maurice Illig
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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30
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Multifaceted targeting of neurodegeneration with bioactive molecules of saffron (Crocus sativus): An insilco evidence-based hypothesis. Med Hypotheses 2020; 143:109872. [DOI: 10.1016/j.mehy.2020.109872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 12/16/2022]
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Guo P, Lam SL. Minidumbbell structures formed by ATTCT pentanucleotide repeats in spinocerebellar ataxia type 10. Nucleic Acids Res 2020; 48:7557-7568. [PMID: 32520333 PMCID: PMC7367182 DOI: 10.1093/nar/gkaa495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 01/02/2023] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is a progressive genetic disorder caused by ATTCT pentanucleotide repeat expansions in intron 9 of the ATXN10 gene. ATTCT repeats have been reported to form unwound secondary structures which are likely linked to large-scale repeat expansions. In this study, we performed high-resolution nuclear magnetic resonance spectroscopic investigations on DNA sequences containing two to five ATTCT repeats. Strikingly, we found the first two repeats of all these sequences well folded into highly compact minidumbbell (MDB) structures. The 3D solution structure of the sequence containing two ATTCT repeats was successfully determined, revealing the MDB comprises a regular TTCTA and a quasi TTCT/A pentaloops with extensive stabilizing loop-loop interactions. We further carried out in vitro primer extension assays to examine if the MDB formed in the primer could escape from the proofreading function of DNA polymerase. Results showed that when the MDB was formed at 5-bp or farther away from the priming site, it was able to escape from the proofreading by Klenow fragment of DNA polymerase I and thus retained in the primer. The intriguing structural findings bring about new insights into the origin of genetic instability in SCA10.
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Affiliation(s)
- Pei Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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32
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Těšický M, Velová H, Novotný M, Kreisinger J, Beneš V, Vinkler M. Positive selection and convergent evolution shape molecular phenotypic traits of innate immunity receptors in tits (Paridae). Mol Ecol 2020; 29:3056-3070. [PMID: 32652716 DOI: 10.1111/mec.15547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/09/2020] [Accepted: 06/26/2020] [Indexed: 01/04/2023]
Abstract
Despite widespread variability and redundancy abounding animal immunity, little is currently known about the rate of evolutionary convergence (functionally analogous traits not inherited from a common ancestor) in host molecular adaptations to parasite selective pressures. Toll-like receptors (TLRs) provide the molecular interface allowing hosts to recognize pathogenic structures and trigger early danger signals initiating an immune response. Using a novel combination of bioinformatic approaches, here we explore genetic variation in ligand-binding regions of bacteria-sensing TLR4 and TLR5 in 29 species belonging to the tit family of passerine birds (Aves: Paridae). Three out of the four consensual positively selected sites in TLR4 and six out of 14 positively selected positions in TLR5 were located on the receptor surface near the functionally important sites, and based on the phylogenetic pattern evolved in a convergent (parallel) manner. This type of evolution was also seen at one N-glycosylation site and two positively selected phosphorylation sites, providing the first evidence of convergence in post-translational modifications in evolutionary immunology. Finally, the overall mismatch between phylogeny and the clustering of surface charge distribution demonstrates that convergence is common in overall TLR4 and TLR5 molecular phenotypes involved in ligand binding. Our analysis did not reveal any broad ecological traits explaining the convergence observed in electrostatic potentials, suggesting that information on microbial symbionts may be needed to explain TLR evolution. Adopting state-of-the-art predictive structural bionformatics, we have outlined a new broadly applicable methodological approach to estimate the functional significance of positively selected variation and test for the adaptive molecular convergence in protein-coding polymorphisms.
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Affiliation(s)
- Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hana Velová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marian Novotný
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vladimír Beneš
- European Molecular Laboratory Heidelberg, Heidelberg, Germany
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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33
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Ngai CK, Lam SL, Lee HK, Guo P. High-Resolution Structures of DNA Minidumbbells Comprising Type II Tetraloops with a Purine Minor Groove Residue. J Phys Chem B 2020; 124:5131-5138. [PMID: 32484672 DOI: 10.1021/acs.jpcb.0c03163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Minidumbbell (MDB) is a newly discovered DNA structure formed by native sequences, which serves as a possible structural intermediate causing repeat expansion mutations in the genome and also a functional structural motif in constructing DNA-based molecular switches. Until now, all the reported MDBs containing two adjacent type II tetraloops were formed by pyrimidine-rich sequences 5'-YYYR YYYR-3' (Y and R represent pyrimidine and purine, respectively), wherein the second and sixth residues folded into the minor groove and interacted with each other. In this study, we have conducted a high-resolution nuclear magnetic resonance (NMR) spectroscopic investigation on alternative MDB-forming sequences and discovered that an MDB could also be formed stably with a purine in the minor groove, which has never been observed in any previously reported DNA type II tetraloops. Our refined NMR solution structures of the two MDBs formed by 5'-CTTG CATG-3' and 5'-CTTG CGTG-3' reveal that the sixth purine residue was driven into the minor groove via base-base stacking with the second thymine residue and adenine stacked better than guanine. The results of our present research work expand the sequence criteria for the formation of MDBs and shed light to explore the significance of MDBs.
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Affiliation(s)
- Cheuk Kit Ngai
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Pei Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
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34
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Hattori LT, Pinheiro BA, Frigori RB, Benítez CMV, Lopes HS. PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model. Comput Biol Chem 2020; 87:107301. [PMID: 32554177 DOI: 10.1016/j.compbiolchem.2020.107301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
Solving the protein folding problem (PFP) is one of the grand challenges still open in computational biophysics. Globular proteins are believed to evolve from initial configurations through folding pathways connecting several thermodynamically accessible states in a free energy landscape until reaching its minimum, inhabited by the stable native structures. Despite its huge computational burden, molecular dynamics (MD) is the leading approach in the PFP studies by preserving the Newtonian temporal evolution in the canonical ensemble. Non-trivial improvements are provided by highly parallel implementations of MD in cost-effective GPUs, concomitant to multiscale descriptions of proteins by coarse-grained minimalist models. In this vein, we present the PathMolD-AB framework, a comprehensive software package for massively parallel MD simulations using the canonical ensemble, structural analysis, and visualization of the folding pathways using the minimalist AB-model. It has, also, a tool to compare the results with proteins re-scaled from the PDB. We simulate and analyze, as case studies, the folding of four proteins: 13FIBO, 2GB1, 1PLC and 5ANZ, with 13, 55, 99 and 223 amino acids, respectively. The datasets generated from simulations correspond to the MD evolution of 3500 folding pathways, encompassing 35×106 states, which contains the spatial amino acid positions, the protein free energies and radii of gyration at each time step. Results indicate that the speedup of our approach grows logarithmically with the protein length and, therefore, it is suited for most of the proteins in the PDB. The predicted structures simulated by PathMolD-AB were similar to the re-scaled biological structures, indicating that it is promising for the study of the PFP study.
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Affiliation(s)
- Leandro Takeshi Hattori
- Bioinformatics and Computational Intelligence Laboratory (LABIC), Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba, PR, Brazil.
| | - Bruna Araujo Pinheiro
- Bioinformatics and Computational Intelligence Laboratory (LABIC), Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba, PR, Brazil.
| | - Rafael Bertolini Frigori
- Bioinformatics and Computational Intelligence Laboratory (LABIC), Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba, PR, Brazil.
| | - César Manuel Vargas Benítez
- Bioinformatics and Computational Intelligence Laboratory (LABIC), Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba, PR, Brazil
| | - Heitor Silvério Lopes
- Bioinformatics and Computational Intelligence Laboratory (LABIC), Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba, PR, Brazil.
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35
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Corley M, Burns MC, Yeo GW. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. Mol Cell 2020; 78:9-29. [PMID: 32243832 PMCID: PMC7202378 DOI: 10.1016/j.molcel.2020.03.011] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we take a look at the components of protein-RNA interaction, from the molecular level to multi-component interaction. We first summarize what is known about protein-RNA molecular interactions based on analyses of solved structures. We additionally describe software currently available for predicting protein-RNA interaction and other resources useful for the study of RBPs. We then review the structure and function of seventeen known RNA-binding domains and analyze the hydrogen bonds adopted by protein-RNA structures on a domain-by-domain basis. We conclude with a summary of the higher-level mechanisms that regulate protein-RNA interactions.
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Affiliation(s)
- Meredith Corley
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Margaret C Burns
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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36
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Hattori LT, Gutoski M, Vargas Benítez CM, Nunes LF, Lopes HS. A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model. Comput Biol Chem 2020; 84:107192. [PMID: 31918170 DOI: 10.1016/j.compbiolchem.2019.107192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/04/2023]
Abstract
The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world, the more the impact of results and their applicability. This work presents 17 real protein sequences extracted from the Protein Data Bank for a benchmark to the PSP problem using the tri-dimensional Hydrophobic-Polar with Side-Chains model (3D-HP-SC). The native structure of these proteins was found by maximizing the number of hydrophobic contacts between the side-chains of amino acids. The problem was treated as an optimization problem and solved by means of an Integer Programming approach. Although the method optimally solves the problem, the processing time has an exponential trend. Therefore, due to computational limitations, the method is a proof-of-concept and it is not applicable to large sequences. For unknown sequences, an upper bound of the number of hydrophobic contacts (using this model) can be found, due to a linear relationship with the number of hydrophobic residues. The comparison between the predicted and the biological structures showed that the highest similarity between them was found with distance thresholds around 5.2-8.2 Å. Both the dataset and the programs developed will be freely available to foster further research in the area.
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Affiliation(s)
- Leandro Takeshi Hattori
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil.
| | - Matheus Gutoski
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil
| | - César Manuel Vargas Benítez
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil
| | - Luiz Fernando Nunes
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil.
| | - Heitor Silvério Lopes
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil.
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37
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Guo P, Lam SL. Unprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell. J Biomol Struct Dyn 2019; 38:1946-1953. [DOI: 10.1080/07391102.2019.1621211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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38
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Singh AR, Perotti LE, Bruinsma RF, Rudnick J, Klug WS. Ground state instabilities of protein shells are eliminated by buckling. SOFT MATTER 2017; 13:8300-8308. [PMID: 29072764 DOI: 10.1039/c7sm01184a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We propose a hybrid discrete-continuum model to study the ground state of protein shells. The model allows for shape transformation of the shell and buckling transitions as well as the competition between states with different symmetries that characterize discrete particle models with radial pair potentials. Our main results are as follows. For large Föppl-von Kármán (FvK) numbers the shells have stable isometric ground states. As the FvK number is reduced, shells undergo a buckling transition resembling that of thin-shell elasticity theory. When the width of the pair potential is reduced below a critical value, then buckling coincides with the onset of structural instability triggered by over-stretched pair potentials. Chiral shells are found to be more prone to structural instability than achiral shells. It is argued that the well-width appropriate for protein shells lies below the structural instability threshold. This means that the self-assembly of protein shells with a well-defined, stable structure is possible only if the bending energy of the shell is sufficiently low so that the FvK number of the assembled shell is above the buckling threshold.
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Affiliation(s)
- Amit R Singh
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA.
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39
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Srivastava KR, Goyal B, Kumar A, Durani S. Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide. RSC Adv 2017. [DOI: 10.1039/c7ra02137b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.
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Affiliation(s)
| | - Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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40
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Livi L, Maiorino E, Giuliani A, Rizzi A, Sadeghian A. A generative model for protein contact networks. J Biomol Struct Dyn 2016; 34:1441-54. [DOI: 10.1080/07391102.2015.1077736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Lorenzo Livi
- Department of Computer Science, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3Canada
| | - Enrico Maiorino
- Department of Information Engineering, Electronics, and Telecommunications, SAPIENZA University of Rome, Via Eudossiana 18, 00184Rome, Italy
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161Rome, Italy
| | - Antonello Rizzi
- Department of Information Engineering, Electronics, and Telecommunications, SAPIENZA University of Rome, Via Eudossiana 18, 00184Rome, Italy
| | - Alireza Sadeghian
- Department of Computer Science, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3Canada
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41
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Goyal B, Srivastava KR, Kumar A, Patwari GN, Durani S. Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models. RSC Adv 2016. [DOI: 10.1039/c6ra22870d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Energetics of folding (ΔHE→F, in kcal mol−1) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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42
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Banach M, Prudhomme N, Carpentier M, Duprat E, Papandreou N, Kalinowska B, Chomilier J, Roterman I. Contribution to the prediction of the fold code: application to immunoglobulin and flavodoxin cases. PLoS One 2015; 10:e0125098. [PMID: 25915049 PMCID: PMC4411048 DOI: 10.1371/journal.pone.0125098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/20/2015] [Indexed: 12/19/2022] Open
Abstract
Background Folding nucleus of globular proteins formation starts by the mutual interaction of a group of hydrophobic amino acids whose close contacts allow subsequent formation and stability of the 3D structure. These early steps can be predicted by simulation of the folding process through a Monte Carlo (MC) coarse grain model in a discrete space. We previously defined MIRs (Most Interacting Residues), as the set of residues presenting a large number of non-covalent neighbour interactions during such simulation. MIRs are good candidates to define the minimal number of residues giving rise to a given fold instead of another one, although their proportion is rather high, typically [15-20]% of the sequences. Having in mind experiments with two sequences of very high levels of sequence identity (up to 90%) but different folds, we combined the MIR method, which takes sequence as single input, with the “fuzzy oil drop” (FOD) model that requires a 3D structure, in order to estimate the residues coding for the fold. FOD assumes that a globular protein follows an idealised 3D Gaussian distribution of hydrophobicity density, with the maximum in the centre and minima at the surface of the “drop”. If the actual local density of hydrophobicity around a given amino acid is as high as the ideal one, then this amino acid is assigned to the core of the globular protein, and it is assumed to follow the FOD model. Therefore one obtains a distribution of the amino acids of a protein according to their agreement or rejection with the FOD model. Results We compared and combined MIR and FOD methods to define the minimal nucleus, or keystone, of two populated folds: immunoglobulin-like (Ig) and flavodoxins (Flav). The combination of these two approaches defines some positions both predicted as a MIR and assigned as accordant with the FOD model. It is shown here that for these two folds, the intersection of the predicted sets of residues significantly differs from random selection. It reduces the number of selected residues by each individual method and allows a reasonable agreement with experimentally determined key residues coding for the particular fold. In addition, the intersection of the two methods significantly increases the specificity of the prediction, providing a robust set of residues that constitute the folding nucleus.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland
| | - Nicolas Prudhomme
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
| | - Mathilde Carpentier
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
- RPBS, 35 rue Hélène Brion, 75013, Paris, France
| | - Elodie Duprat
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
- RPBS, 35 rue Hélène Brion, 75013, Paris, France
| | - Nikolaos Papandreou
- Genetics Department, Agricultural University of Athens, Iera Odos 75, Athens, Greece
| | - Barbara Kalinowska
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland
| | - Jacques Chomilier
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
- RPBS, 35 rue Hélène Brion, 75013, Paris, France
- * E-mail: (JC); (IR)
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland
- * E-mail: (JC); (IR)
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