1
|
Fossat MJ. MEDOC: A fast, scalable and mathematically exact algorithm for the site-specific prediction of the protonation degree in large disordered proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.08.617153. [PMID: 39416064 PMCID: PMC11482746 DOI: 10.1101/2024.10.08.617153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Intrinsically disordered regions are found in most eukaryotic proteins and are enriched in positively and negatively charged residues. While it is often convenient to assume these residues follow their model-compound pKa values, recent work has shown that local charge effects (charge regulation) can upshift or downshift sidechain pKa values with major consequences for molecular function. Despite this, charge regulation is rarely considered when investigating disordered regions. The number of potential charge microstates that can be populated through acid/base regulation of a given number of ionizable residues in a sequence, N , scales as~ 2 N . This exponential scaling makes the assessment of the full charge landscape of most proteins computationally intractable. To address this problem, we developed MEDOC (Multisite Extent of Deprotonation Originating from Context) to determine the degree of protonation of a protein based on the local sequence context of each ionizable residue. We show that we can drastically reduce the number of parameters necessary to determine the full, analytic, Boltzmann partition function of the charge landscape at both global and site-specific levels. Our algorithm applies the structure of the q-canonical ensemble, combined with novel strategies to rapidly obtain the minimal set of parameters, thereby circumventing the combinatorial explosion of the number of charge microstates even for proteins containing a large number of ionizable amino acids. We apply MEDOC to several sequences, including a global analysis of the distribution of pKa values across the entire DisProt database. Our results show differences in the distribution of predicted pKa values for different amino acids, in agreement with NMR-measured distributions in proteins.
Collapse
Affiliation(s)
- Martin J Fossat
- Max-Planck-Institut für Immunbiologie und Epigenetik (MPI-IE) Stübeweg 51, 79108 Freiburg im Breisgau, Germany
| |
Collapse
|
2
|
Galindo AV, Raj M. Solvent-Dependent Chemoselectivity Switch to Arg-Lys Imidazole Cross-Links. Org Lett 2024; 26:8356-8360. [PMID: 39303223 PMCID: PMC11459505 DOI: 10.1021/acs.orglett.4c03101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 09/10/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Herein, we report a trifluoroethanol-mediated, chemoselective method for the formation of Arg-Lys imidazole cross-links with methylglyoxal and its application in the selective macrocyclization of peptides between Lys and Arg and the late-stage diversification of Lys-containing peptides with guanidine. Our findings highlight the critical role of solvent choice in controlling chemoselectivity, providing valuable insights into solvent-dependent peptide modification.
Collapse
Affiliation(s)
| | - Monika Raj
- Department of Chemistry, Emory
University, Atlanta, Georgia 30322, United States
| |
Collapse
|
3
|
Antipov A, Okorokova N, Mordkovich N, Safonova T, Veiko V. Role of phosphate-coordinating arginine residues in the thermal stability of uridine phosphorylase from Shewanella oneidensis MR-1. Biochimie 2024; 225:19-25. [PMID: 38723939 DOI: 10.1016/j.biochi.2024.05.008] [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: 01/23/2024] [Revised: 03/15/2024] [Accepted: 05/06/2024] [Indexed: 05/24/2024]
Abstract
The role of phosphate-coordinating arginine residues in the thermal stability of uridine phosphorylase from Shewanella oneidensis MR-1 was investigated by mutation analysis. Uridine phosphorylase mutant genes were constructed by site-directed mutagenesis. The enzyme mutants were prepared and isolated, and their kinetic parameters were determined. It was shown that all these arginine residues play an important role both in the catalysis and thermal stability. The arginine residues 176 were demonstrated to form a kind of a phosphate pore in the hexameric structure of uridine phosphorylase, and they not only contribute to thermal stabilization of the enzyme but also have a regulatory function. The replacement of arginine 176 with an alanine residue resulted in a significant decrease in the kinetic stability of the enzyme but led to a twofold increase in its specific activity.
Collapse
Affiliation(s)
- Alexey Antipov
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia.
| | - Natalya Okorokova
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Nadezhda Mordkovich
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Tatyana Safonova
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Vladimir Veiko
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| |
Collapse
|
4
|
Ying ANJ, Tan YF, Wong YS, Venkatraman S. Sustained intra-cellular siRNA release from poly(L-arginine) multilayered nanoparticles for prolonged gene silencing. Expert Opin Drug Deliv 2024; 21:1513-1522. [PMID: 39290161 DOI: 10.1080/17425247.2024.2405206] [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: 04/29/2024] [Revised: 09/07/2024] [Accepted: 09/10/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUND Sustained siRNA release from nanocarriers is difficult to achieve inside the cell after entry: typically, all nanocarriers exhibit burst release of the cargo into the cytoplasm. RESEARCH DESIGN AND METHODS Layer-by-layer (LbL) nanoparticles (NPs) can be constructed so that they escape endosomes intact, and subsequently exhibit sustained release of the cargo. Our work quantifies intra-cellular siRNA release from multilayered NPs, evaluates mechanism behind the sustained release, and optimizes the duration of release. RESULTS Intra-cellular studies showed that NPs developed with four layers of poly-L-arginine, alternated with three layers of siRNA layers, were able to elicit effective and prolonged SPARC knockdown activity over 21 days with a single-dose treatment. For the first time, we have quantified the amounts of released siRNA in the cytoplasm and the amount of siRNA remaining inside the NPs at each timepoint. Furthermore, we have correlated the amount of released siRNA within cells by LbL NPs to the cellular knockdown efficiency of multilayered delivery system. CONCLUSIONS This methodology may provide an excellent screening tool for assessing the duration of gene silencing by various nanocarrier formulations.
Collapse
Affiliation(s)
- Alice Ng Jie Ying
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yang Fei Tan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yee Shan Wong
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
- NTU-Northwestern University, Institute for Nanomedicine, Singapore, Singapore
| | - Subbu Venkatraman
- Material Science & Engineering, National University of Singapore, Singapore, Singapore
- Investigator, iHealthTech, National University of Singapore, Singapore, Singapore
| |
Collapse
|
5
|
Calinsky R, Levy Y. Aromatic Residues in Proteins: Re-Evaluating the Geometry and Energetics of π-π, Cation-π, and CH-π Interactions. J Phys Chem B 2024; 128:8687-8700. [PMID: 39223472 PMCID: PMC11403661 DOI: 10.1021/acs.jpcb.4c04774] [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: 09/04/2024]
Abstract
Aromatic residues can participate in various biomolecular interactions, such as π-π, cation-π, and CH-π interactions, which are essential for protein structure and function. Here, we re-evaluate the geometry and energetics of these interactions using quantum mechanical (QM) calculations, focusing on pairwise interactions involving the aromatic amino acids Phe, Tyr, and Trp and the cationic amino acids Arg and Lys. Our findings reveal that π-π interactions, while energetically favorable, are less abundant in structured proteins than commonly assumed and are often overshadowed by previously underappreciated, yet prevalent, CH-π interactions. Cation-π interactions, particularly those involving Arg, show strong binding energies and a specific geometric preference toward stacked conformations, despite the global QM minimum, suggesting that a rather perpendicular T-shape conformation should be more favorable. Our results support a more nuanced understanding of protein stabilization via interactions involving aromatic residues. On the one hand, our results challenge the traditional emphasis on π-π interactions in structured proteins by showing that CH-π and cation-π interactions contribute significantly to their structure. On the other hand, π-π interactions appear to be key stabilizers in solvated regions and thus may be particularly important to the stabilization of intrinsically disordered proteins.
Collapse
Affiliation(s)
- Rivka Calinsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
6
|
Rekhi S, Garcia CG, Barai M, Rizuan A, Schuster BS, Kiick KL, Mittal J. Expanding the molecular language of protein liquid-liquid phase separation. Nat Chem 2024; 16:1113-1124. [PMID: 38553587 PMCID: PMC11230844 DOI: 10.1038/s41557-024-01489-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024]
Abstract
Understanding the relationship between a polypeptide sequence and its phase separation has important implications for analysing cellular function, treating disease and designing novel biomaterials. Several sequence features have been identified as drivers for protein liquid-liquid phase separation (LLPS), schematized as a 'molecular grammar' for LLPS. Here we further probe how sequence modulates phase separation and the material properties of the resulting condensates, targeting sequence features previously overlooked in the literature. We generate sequence variants of a repeat polypeptide with either no charged residues, high net charge, no glycine residues or devoid of aromatic or arginine residues. All but one of 12 variants exhibited LLPS, albeit to different extents, despite substantial differences in composition. Furthermore, we find that all the condensates formed behaved like viscous fluids, despite large differences in their viscosities. Our results support the model of multiple interactions between diverse residue pairs-not just a handful of residues-working in tandem to drive the phase separation and dynamics of condensates.
Collapse
Affiliation(s)
- Shiv Rekhi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Mayur Barai
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA.
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
7
|
Visibelli A, Finetti R, Niccolai N, Spiga O, Santucci A. Molecular Origins of the Mendelian Rare Diseases Reviewed by Orpha.net: A Structural Bioinformatics Investigation. Int J Mol Sci 2024; 25:6953. [PMID: 39000061 PMCID: PMC11241713 DOI: 10.3390/ijms25136953] [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: 03/28/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
The study of rare diseases is important not only for the individuals affected but also for the advancement of medical knowledge and a deeper understanding of human biology and genetics. The wide repertoire of structural information now available from reliable and accurate prediction methods provides the opportunity to investigate the molecular origins of most of the rare diseases reviewed in the Orpha.net database. Thus, it has been possible to analyze the topology of the pathogenic missense variants found in the 2515 proteins involved in Mendelian rare diseases (MRDs), which form the database for our structural bioinformatics study. The amino acid substitutions responsible for MRDs showed different mutation site distributions at different three-dimensional protein depths. We then highlighted the depth-dependent effects of pathogenic variants for the 20,061 pathogenic variants that are present in our database. The results of this structural bioinformatics investigation are relevant, as they provide additional clues to mitigate the damage caused by MRD.
Collapse
Affiliation(s)
- Anna Visibelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
| | - Rebecca Finetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
- Le Ricerche del BarLume Free Association, Ville di Corsano, 53014 Monteroni d’Arbia, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
- Industry 4.0 Competence Center ARTES 4.0, Viale Rinaldo Piaggio, 56025 Pontedera, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
- Industry 4.0 Competence Center ARTES 4.0, Viale Rinaldo Piaggio, 56025 Pontedera, Italy
| |
Collapse
|
8
|
Bonanata J. The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase. Comput Biol Chem 2024; 110:108075. [PMID: 38678729 DOI: 10.1016/j.compbiolchem.2024.108075] [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: 11/22/2023] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.
Collapse
Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay.
| |
Collapse
|
9
|
Lv H, Cao Y, Zhu J, Liang Q. Molecular Insights into the Effect of Cholesterol on the Binding of Bicarbonate Ions in Band 3 Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10908-10915. [PMID: 38739034 DOI: 10.1021/acs.langmuir.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Band 3, or anion exchanger 1 (AE1), is one of the indispensable transmembrane proteins involved in the effective respiratory process of the human body and is primarily responsible for the exchange of bicarbonate and chloride anions across the plasma membrane of erythrocyte. However, the molecular mechanism of ion transport of Band 3 is not completely understood, yet. In this work, we systematically investigate the key binding sites of bicarbonate ions in Band 3 and the impact of cholesterol (CHOL) in lipid bilayers on bicarbonate ion binding using all-atom molecular dynamics (MD) simulations. We examine the dynamics of interactions of bicarbonate ions with Band 3 in the microsecond time scale and calculate the binding free energy of the anion in Band 3. The results indicate that the residue R730 of Band 3 is the most probable binding site for bicarbonate ions. CHOL enhances the bicarbonate ion binding by influencing the conformational stability of Band 3 and compressing the volume of the Band 3 cavity. These findings provide some insights into the bicarbonate ion binding in Band 3 and are helpful for understanding the anion exchange of Band 3.
Collapse
Affiliation(s)
- Haiying Lv
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
| | - Yu Cao
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
| | - Jin Zhu
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua 321004, China
| |
Collapse
|
10
|
Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [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: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
Collapse
Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| |
Collapse
|
11
|
Nersesova L, Petrosyan M, Tsakanova G. Review of the evidence of radioprotective potential of creatine and arginine as dietary supplements. Int J Radiat Biol 2024; 100:849-864. [PMID: 38683545 DOI: 10.1080/09553002.2024.2345098] [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: 12/29/2022] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
PURPOSE Creatine (Cr) and l-arginine are naturally occurring guanidino compounds, commonly used as ergogenic dietary supplements. Creatine and l-arginine exhibit also a number of non-energy-related features, such as antioxidant, anti-apoptotic, and anti-inflammatory properties, which contribute to their protective action against oxidative stress (OS). In this regard, there are a number of studies emphasizing the protective effect of Cr against OS, which develops in the process of aging, increased physical loads as part of athletes' workouts, as well as a number of neurological diseases and toxic effects associated with xenobiotics and UV irradiation. Against this backdrop, and since ionizing radiation causes OS in cells, leading to radiotoxicity, there is an increasing interest to understand whether Cr has the full potential to serve as an effective radioprotective agent. The extensive literature search did not provide any data on this issue. In this narrative review, we have summarized some of our own experimental data published over the last years addressing the respective radioprotective effects of Cr. Next, we have additionally reviewed the existing data on the radiomodifying effects of l-arginine presented earlier by other research groups. CONCLUSIONS Creatine possesses significant radioprotective potential including: (1) radioprotective effect on the survival rate of rats subjected to acute whole-body X-ray irradiation in a LD70/30 dose of 6.5 Gy, (2) radioprotective effect on the population composition of peripheral blood cells, (3) radioprotective effect on the DNA damage of peripheral blood mononuclear cells, (4) radioprotective effect on the hepatocyte nucleus-nucleolar apparatus, and (5) radioprotective effect on the brain and liver Cr-Cr kinase systems of the respective animals. Taking into account these cytoprotective, gene-protective, hepatoprotective and energy-stimulating features of Cr, as well as its significant radioprotective effect on the survival rate of rats, it can be considered as a potentially promising radioprotector for further preclinical and clinical studies. The review of the currently available data on radiomodifying effects of l-arginine has indicated its significant potential as a radioprotector, radiomitigator, and radiosensitizer. However, to prove the effectiveness of arginine (Arg) as a radioprotective agent, it appears necessary to expand and deepen the relevant preclinical studies, and, most importantly, increase the number of proof-of-concept clinical trials, which are evidently lacking as of now.
Collapse
Affiliation(s)
| | | | - Gohar Tsakanova
- Institute of Molecular Biology NAS RA, Yerevan, Armenia
- CANDLE Synchrotron Research Institute, Yerevan, Armenia
| |
Collapse
|
12
|
Egger T, Morano L, Blanchard MP, Basbous J, Constantinou A. Spatial organization and functions of Chk1 activation by TopBP1 biomolecular condensates. Cell Rep 2024; 43:114064. [PMID: 38578830 DOI: 10.1016/j.celrep.2024.114064] [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: 10/03/2023] [Revised: 02/14/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024] Open
Abstract
Assembly of TopBP1 biomolecular condensates triggers activation of the ataxia telangiectasia-mutated and Rad3-related (ATR)/Chk1 signaling pathway, which coordinates cell responses to impaired DNA replication. Here, we used optogenetics and reverse genetics to investigate the role of sequence-specific motifs in the formation and functions of TopBP1 condensates. We propose that BACH1/FANCJ is involved in the partitioning of BRCA1 within TopBP1 compartments. We show that Chk1 is activated at the interface of TopBP1 condensates and provide evidence that these structures arise at sites of DNA damage and in primary human fibroblasts. Chk1 phosphorylation depends on the integrity of a conserved arginine motif within TopBP1's ATR activation domain (AAD). Its mutation uncouples Chk1 activation from TopBP1 condensation, revealing that optogenetically induced Chk1 phosphorylation triggers cell cycle checkpoints and slows down replication forks in the absence of DNA damage. Together with previous work, these data suggest that the intrinsically disordered AAD encodes distinct molecular steps in the ATR/Chk1 pathway.
Collapse
Affiliation(s)
- Tom Egger
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Laura Morano
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Marie-Pierre Blanchard
- Montpellier Ressources Imageries, BioCampus, Université de Montpellier, CNRS, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| |
Collapse
|
13
|
Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| |
Collapse
|
14
|
Remm S, De Vecchis D, Schöppe J, Hutter CAJ, Gonda I, Hohl M, Newstead S, Schäfer LV, Seeger MA. Structural basis for triacylglyceride extraction from mycobacterial inner membrane by MFS transporter Rv1410. Nat Commun 2023; 14:6449. [PMID: 37833269 PMCID: PMC10576003 DOI: 10.1038/s41467-023-42073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Mycobacterium tuberculosis is protected from antibiotic therapy by a multi-layered hydrophobic cell envelope. Major facilitator superfamily (MFS) transporter Rv1410 and the periplasmic lipoprotein LprG are involved in transport of triacylglycerides (TAGs) that seal the mycomembrane. Here, we report a 2.7 Å structure of a mycobacterial Rv1410 homologue, which adopts an outward-facing conformation and exhibits unusual transmembrane helix 11 and 12 extensions that protrude ~20 Å into the periplasm. A small, very hydrophobic cavity suitable for lipid transport is constricted by a functionally important ion-lock likely involved in proton coupling. Combining mutational analyses and MD simulations, we propose that TAGs are extracted from the core of the inner membrane into the central cavity via lateral clefts present in the inward-facing conformation. The functional role of the periplasmic helix extensions is to channel the extracted TAG into the lipid binding pocket of LprG.
Collapse
Affiliation(s)
- Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Dario De Vecchis
- Center for Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany
| | - Jendrik Schöppe
- Institute of Biochemistry, University of Zurich, Zürich, Switzerland
- Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
- Linkster Therapeutics, Zürich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Michael Hohl
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland.
- National Center for Mycobacteria, Zurich, Switzerland.
| |
Collapse
|
15
|
Chatterjee R, Jindal G. Role of mutations in a chemoenzymatic enantiodivergent C(sp 3)-H insertion: exploring the mechanism and origin of stereoselectivity. Chem Sci 2023; 14:8810-8822. [PMID: 37621422 PMCID: PMC10445471 DOI: 10.1039/d3sc02788k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/23/2023] [Indexed: 08/26/2023] Open
Abstract
New-to-nature enzymes have emerged as powerful catalysts in recent years for streamlining various stereoselective organic transformations. While synthetic strategies employing engineered enzymes have witnessed proliferating success, there is limited clarity on the mechanistic front and more so when considering molecular-level insights into the role of selected mutations, dramatically escalating catalytic competency and selectivity. We have investigated the mechanism and correlation between mutations and exquisite stereoselectivity of a lactone carbene insertion into the C(sp3)-H bond of substituted aniline, catalyzed by two mutants of a cytochrome P450 variant, "P411" (engineered through directed evolution) in which the axial cysteine has been mutated to serine, utilizing various computational tools. The pivotal role of S264 and L/R328 mutations in the active site has been delineated computationally using two cluster models, thus rationalizing the enantiodivergence. This report provides much-needed insights into the origin of enantiodivergence, furnishing a mechanistic framework for understanding the anchoring effects of H-bond donor residues with the lactone ring. This study is expected to have important implications in the rational design of stereodivergent enzymes and toward successful in silico enzyme designing.
Collapse
Affiliation(s)
- Ritwika Chatterjee
- Department of Organic Chemistry, Chemical Sciences Division, Indian Institute of Science Bangalore 560012 India
| | - Garima Jindal
- Department of Organic Chemistry, Chemical Sciences Division, Indian Institute of Science Bangalore 560012 India
| |
Collapse
|
16
|
Li X, Singh NK, Collins DR, Ng R, Zhang A, Lamothe-Molina PA, Shahinian P, Xu S, Tan K, Piechocka-Trocha A, Urbach JM, Weber JK, Gaiha GD, Takou Mbah OC, Huynh T, Cheever S, Chen J, Birnbaum M, Zhou R, Walker BD, Wang JH. Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide. Nat Commun 2023; 14:2929. [PMID: 37217466 DOI: 10.1038/s41467-023-38573-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Cytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.
Collapse
Affiliation(s)
- Xiaolong Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Nishant Kumar Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Robert Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Peter Shahinian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Shutong Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | | | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | | | - Tien Huynh
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
| | - Sophia Cheever
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - James Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Michael Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02142, USA
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
- Department of Chemistry, Columbia University, New York, NY, 10025, USA
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
- Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Jia-Huai Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02215, USA.
| |
Collapse
|
17
|
Curtolo F, Arantes GM. Dissecting Reaction Mechanisms and Catalytic Contributions in Flavoprotein Fumarate Reductases. J Chem Inf Model 2023. [PMID: 37196341 DOI: 10.1021/acs.jcim.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The interconversion between fumarate and succinate is fundamental to the energy metabolism of nearly all organisms. This redox reaction is catalyzed by a large family of enzymes, fumarate reductases and succinate dehydrogenases, using hydride and proton transfers from a flavin cofactor and a conserved Arg side-chain. These flavoenzymes also have substantial biomedical and biotechnological importance. Therefore, a detailed understanding of their catalytic mechanisms is valuable. Here, calibrated electronic structure calculations in a cluster model of the active site of the Fcc3 fumarate reductase were employed to investigate various reaction pathways and possible intermediates in the enzymatic environment and to dissect interactions that contribute to catalysis of fumarate reduction. Carbanion, covalent adduct, carbocation, and radical intermediates were examined. Significantly lower barriers were obtained for mechanisms via carbanion intermediates, with similar activation energies for hydride and proton transfers. Interestingly, the carbanion bound to the active site is best described as an enolate. Hydride transfer is stabilized by a preorganized charge dipole in the active site and by the restriction of the C1-C2 bond in a twisted conformation of the otherwise planar fumarate dianion. But, protonation of a fumarate carboxylate and quantum tunneling effects are not critical for catalysis of the hydride transfer. Calculations also suggest that the driving force for enzyme turnover is provided by regeneration of the catalytic Arg, either coupled with flavin reduction and decomposition of a proposed transient state or directly from the solvent. The detailed mechanistic description of enzymatic reduction of fumarate provided here clarifies previous contradictory views and provides new insights into catalysis by essential flavoenzyme reductases and dehydrogenases.
Collapse
Affiliation(s)
- Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
| |
Collapse
|
18
|
Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
Collapse
Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
19
|
Banerjee N, Chatterjee O, Roychowdhury T, Basu D, Dutta A, Chowdhury M, Dastidar SG, Chatterjee S. Sequence driven interaction of amino acids in de-novo designed peptides determines c-Myc G-quadruplex unfolding inducing apoptosis in cancer cells. Biochim Biophys Acta Gen Subj 2023; 1867:130267. [PMID: 36334788 DOI: 10.1016/j.bbagen.2022.130267] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
c-MYC proto-oncogene harbors a putative G-quadruplex structure (Pu27) at the NHEIII1 domain, which can shuffle between transcriptional inhibitor quadruplex and transcriptionally active duplex. In cancer cells this quadruplex destabilization is preferred and NHEIII1 domain assume a duplex topology thereby inducing c-MYC overexpression and tumorigenesis. Hence, the c-MYC quadruplex acts as an excellent target for anti-cancer therapy. Though researcher have tried to develop G-quadruplex targeted small molecules, work with G-quadruplex targeting peptides is very limited. Here we present a peptide that can bind to c-MYC quadruplex, destabilize the tetrad core, and permit the formation of a substantially different structure from the quartet core seen in the canonical G-quadruplexes. Such conformation potentially acted as a roadblock for transcription factors thereby reducing cMYC expression. This event sensitizes the cancer cell to activate apoptotic cascade via the c-MYC-VEGF-A-BCL2 axis. This study provides a detailed insight into the peptide-quadruplex interface that encourages better pharmacophore design to target dynamic quadruplex structure. We believe that our results will contribute to the development, characterization, and optimization of G-quadruplex binding peptides for potential clinical application.
Collapse
Affiliation(s)
- Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Oishika Chatterjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Tanaya Roychowdhury
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Debadrita Basu
- Division of Bioinformatics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Madhurima Chowdhury
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India.
| |
Collapse
|
20
|
Bhoite SS, Kolli D, Gomulinski MA, Chapman MR. Electrostatic interactions mediate the nucleation and growth of a bacterial functional amyloid. Front Mol Biosci 2023; 10:1070521. [PMID: 36756360 PMCID: PMC9900396 DOI: 10.3389/fmolb.2023.1070521] [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: 10/14/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Bacterial biofilm formation can have severe impacts on human and environmental health. Enteric bacteria produce functional amyloid fibers called curli that aid in biofilm formation and host colonization. CsgA is the major proteinaceous component of curli amyloid fibers and is conserved in many gram-negative enteric bacteria. The CsgA amyloid core consists of five imperfect repeats (R1-R5). R2, R3, and R4 have aspartic acid (D) and glycine (G) residues that serve as "gatekeeper" residues by modulating the intrinsic aggregation propensity of CsgA. Here, using mutagenesis, salt-mediated charge screening, and by varying pH conditions, we show that the ability of CsgA variants to nucleate and form amyloid fibers is dictated by the charge state of the gatekeeper residues. We report that in Citrobacter youngae CsgA, certain arginine (R) and lysine (K) residues also act as gatekeeper residues. A mechanism of gatekeeping is proposed wherein R and K residues electrostatically interact with negatively charged D residues, tempering CsgA fiber formation.
Collapse
|
21
|
Mohammed EH, Lohan S, Ghaffari T, Gupta S, Tiwari RK, Parang K. Membrane-Active Cyclic Amphiphilic Peptides: Broad-Spectrum Antibacterial Activity Alone and in Combination with Antibiotics. J Med Chem 2022; 65:15819-15839. [PMID: 36442155 PMCID: PMC9743092 DOI: 10.1021/acs.jmedchem.2c01469] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We designed a library of 24 cyclic peptides containing arginine (R) and tryptophan (W) residues in a sequential manner [RnWn] (n = 2-7) to study the impact of the hydrophilic/hydrophobic ratio, charge, and ring size on the antibacterial activity against Gram-positive and Gram-negative strains. Among peptides, 5a and 6a demonstrated the highest antimicrobial activity. In combination with 11 commercially available antibiotics, 5a and 6a showed remarkable synergism against a large panel of resistant pathogens. Hemolysis (HC50 = 340 μg/mL) and cell viability against mammalian cells demonstrated the selective lethal action of 5a against bacteria over mammalian cells. Calcein dye leakage and scanning electron microscopy studies revealed the membranolytic effect of 5a. Moreover, the stability in human plasma (t1/2 = 3 h) and the negligible ability of pathogens to develop resistance further reflect the potential of 5a for further development as a peptide-based antibiotic.
Collapse
Affiliation(s)
- Eman H.
M. Mohammed
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy,
Harry and Diane Rinker Health Science Campus, Irvine, California92618, United States,Department
of Chemistry, Faculty of Science, Menoufia
University, Shebin
El-Koam51132, Egypt,AJK
Biopharmaceutical, Irvine, California92617, United States
| | - Sandeep Lohan
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy,
Harry and Diane Rinker Health Science Campus, Irvine, California92618, United States,AJK
Biopharmaceutical, Irvine, California92617, United States
| | - Tarra Ghaffari
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy,
Harry and Diane Rinker Health Science Campus, Irvine, California92618, United States
| | - Shilpi Gupta
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy,
Harry and Diane Rinker Health Science Campus, Irvine, California92618, United States
| | - Rakesh K. Tiwari
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy,
Harry and Diane Rinker Health Science Campus, Irvine, California92618, United States,. Fax: +1-714-516-548. Phone: +1-714-516-5483
| | - Keykavous Parang
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy,
Harry and Diane Rinker Health Science Campus, Irvine, California92618, United States,. Fax: +1-714-516-5481. Phone: +1-714-516-5489
| |
Collapse
|
22
|
Aggarwal S, Tanwar N, Singh A, Munde M. Formation of Protamine and Zn-Insulin Assembly: Exploring Biophysical Consequences. ACS OMEGA 2022; 7:41044-41057. [PMID: 36406544 PMCID: PMC9670714 DOI: 10.1021/acsomega.2c04419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The insulin-protamine interaction is at the core of the mode of action in many insulin formulations (Zn + insulin + protamine) and to treat diabetes, in which protamine is added to the stable form of hexameric insulin (Zn-insulin). However, due to the unavailability of quantitative data and a high-resolution structure, the binding mechanism of the insulin-protamine complex remains unknown. In this study, it was observed that Zn-insulin experiences destabilization as observed by the loss of secondary structure in circular dichroism (CD), and reduction in thermal stability in melting study, upon protamine binding. In isothermal titration calorimetry (ITC), it was found that the interactions were mostly enthalpically driven. This is in line with the positive ΔC m value (+880 cal mol-1), indicating the role of hydrophilic interactions in the complex formation, with the exposure of hydrophobic residues to the solvent, which was firmly supported by the 8-anilino-1-naphthalene sulfonate (ANS) binding study. The stoichiometry (N) value in ITC suggests the multiple insulin molecules binding to the protamine chain, which is consistent with the picture of the condensation of insulin in the presence of protamine. Atomic force microscopy (AFM) suggested the formation of a heterogeneous Zn-insulin-protamine complex. In fluorescence, Zn-insulin experiences strong Tyr quenching, suggesting that the location of the protamine-binding site is near Tyr, which is also supported by the molecular docking study. Since Tyr is critical in the stabilization of insulin self-assembly, its interaction with protamine may impair insulin's self-association ability and thermodynamic stability while at the same time promoting its flexible conformation desired for better biological activity.
Collapse
|
23
|
Harrison SA, Palmeira RN, Halpern A, Lane N. A biophysical basis for the emergence of the genetic code in protocells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148597. [PMID: 35868450 DOI: 10.1016/j.bbabio.2022.148597] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022]
Abstract
The origin of the genetic code is an abiding mystery in biology. Hints of a 'code within the codons' suggest biophysical interactions, but these patterns have resisted interpretation. Here, we present a new framework, grounded in the autotrophic growth of protocells from CO2 and H2. Recent work suggests that the universal core of metabolism recapitulates a thermodynamically favoured protometabolism right up to nucleotide synthesis. Considering the genetic code in relation to an extended protometabolism allows us to predict most codon assignments. We show that the first letter of the codon corresponds to the distance from CO2 fixation, with amino acids encoded by the purines (G followed by A) being closest to CO2 fixation. These associations suggest a purine-rich early metabolism with a restricted pool of amino acids. The second position of the anticodon corresponds to the hydrophobicity of the amino acid encoded. We combine multiple measures of hydrophobicity to show that this correlation holds strongly for early amino acids but is weaker for later species. Finally, we demonstrate that redundancy at the third position is not randomly distributed around the code: non-redundant amino acids can be assigned based on size, specifically length. We attribute this to additional stereochemical interactions at the anticodon. These rules imply an iterative expansion of the genetic code over time with codon assignments depending on both distance from CO2 and biophysical interactions between nucleotide sequences and amino acids. In this way the earliest RNA polymers could produce non-random peptide sequences with selectable functions in autotrophic protocells.
Collapse
Affiliation(s)
- Stuart A Harrison
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Raquel Nunes Palmeira
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Aaron Halpern
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland.
| |
Collapse
|
24
|
Stachurski O, Neubauer D, Walewska A, Iłowska E, Bauer M, Bartoszewska S, Sikora K, Hać A, Wyrzykowski D, Prahl A, Kamysz W, Sikorska E. Understanding the Role of Self-Assembly and Interaction with Biological Membranes of Short Cationic Lipopeptides in the Effective Design of New Antibiotics. Antibiotics (Basel) 2022; 11:1491. [PMID: 36358146 PMCID: PMC9686977 DOI: 10.3390/antibiotics11111491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 10/22/2023] Open
Abstract
This study investigates short cationic antimicrobial lipopeptides composed of 2-4 amino acid residues and C12-C18 fatty acids attached to the N-terminal part of the peptides. The findings were discussed in the context of the relationship among biological activity, self-assembly, stability, and membrane interactions. All the lipopeptides showed the ability to self-assemble in PBS solution. In most cases, the critical aggregation concentration (CAC) much surpassed the minimal inhibitory concentration (MIC) values, suggesting that monomers are the main active form of lipopeptides. The introduction of β-alanine into the peptide sequence resulted in a compound with a high propensity to fibrillate, which increased the peptide stability and activity against S. epidermidis and C. albicans and reduced the cytotoxicity against human keratinocytes. The results of our study indicated that the target of action of lipopeptides is the bacterial membrane. Interestingly, the type of peptide counterion may affect the degree of penetration of the lipid bilayer. In addition, the binding of the lipopeptide to the membrane of Gram-negative bacteria may lead to the release of calcium ions necessary for stabilization of the lipopolysaccharide layer.
Collapse
Affiliation(s)
- Oktawian Stachurski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Damian Neubauer
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Aleksandra Walewska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Emilia Iłowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Bauer
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Sylwia Bartoszewska
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Karol Sikora
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Aleksandra Hać
- Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Adam Prahl
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Wojciech Kamysz
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Emilia Sikorska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| |
Collapse
|
25
|
Dual contribution of the mTOR pathway and of the metabolism of amino acids in prostate cancer. Cell Oncol (Dordr) 2022; 45:831-859. [PMID: 36036882 DOI: 10.1007/s13402-022-00706-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Prostate cancer is the leading cause of cancer in men, and its incidence increases with age. Among other risk factors, pre-existing metabolic diseases have been recently linked with prostate cancer, and our current knowledge recognizes prostate cancer as a condition with important metabolic anomalies as well. In malignancies, metabolic disorders are commonly associated with aberrations in mTOR, which is the master regulator of protein synthesis and energetic homeostasis. Although there are reports demonstrating the high dependency of prostate cancer cells for lipid derivatives and even for carbohydrates, the understanding regarding amino acids, and the relationship with the mTOR pathway ultimately resulting in metabolic aberrations, is still scarce. CONCLUSIONS AND PERSPECTIVES In this review, we briefly provide evidence supporting prostate cancer as a metabolic disease, and discuss what is known about mTOR signaling and prostate cancer. Next, we emphasized on the amino acids glutamine, leucine, serine, glycine, sarcosine, proline and arginine, commonly related to prostate cancer, to explore the alterations in their regulatory pathways and to link them with the associated metabolic reprogramming events seen in prostate cancer. Finally, we display potential therapeutic strategies for targeting mTOR and the referred amino acids, as experimental approaches to selectively attack prostate cancer cells.
Collapse
|
26
|
Asokan-Sheeja H, Yang S, A Adones A, Chen W, B Fulton B, K Chintapula U, T Nguyen K, J Lovely C, A Brautigam C, Nam K, Dong H. Self‐assembling Peptides with Internal Ionizable Unnatural Amino Acids: A New and General Approach to pH‐responsive Peptide Materials. Chem Asian J 2022; 17:e202200724. [DOI: 10.1002/asia.202200724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/11/2022] [Indexed: 11/06/2022]
Affiliation(s)
| | - Su Yang
- The University of Texas at Arlington Chemistry UNITED STATES
| | - Ashley A Adones
- The University of Texas at Arlington Chemistry UNITED STATES
| | - Weike Chen
- The University of Texas at Arlington Chemistry UNITED STATES
| | | | | | - Kytai T Nguyen
- The University of Texas at Arlington Bioengineering UNITED STATES
| | - Carl J Lovely
- The University of Texas at Arlington Chemistry UNITED STATES
| | - Chad A Brautigam
- UT Southwestern: The University of Texas Southwestern Medical Center Biophysics UNITED STATES
| | - Kwangho Nam
- The University of Texas at Arlington Chemistry UNITED STATES
| | - He Dong
- University of Texas at Arlington Chemistry 700 Planetarium Place 76019 Arlington UNITED STATES
| |
Collapse
|
27
|
Biembengut ÍV, Shigunov P, Frota NF, Lourenzoni MR, de Souza TACB. Molecular Dynamics of CYFIP2 Protein and Its R87C Variant Related to Early Infantile Epileptic Encephalopathy. Int J Mol Sci 2022; 23:8708. [PMID: 35955843 PMCID: PMC9368851 DOI: 10.3390/ijms23158708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 12/05/2022] Open
Abstract
The CYFIP2 protein (cytoplasmic FMR1-interacting protein 2) is part of the WAVE regulatory complex (WRC). CYFIP2 was recently correlated to neurological disorders by the association of the R87C variant with early infantile epileptic encephalopathy (EIEE) patients. In this set of syndromes, the epileptic spasms and seizures since early childhood lead to impaired neurological development in children. Inside the WRC, the variant residue is at the CYFIP2 and WAVE1 protein interface. Thus, the hypothesis is that the R87C modification weakens this interaction, allowing the WRC complex's constant activation. This work aimed to investigate the impacts of the mutation on the structure of the WRC complex through molecular dynamics simulation. For that, we constructed WRC models containing WAVE1-NCKAP1 proteins complexed with WT or R87C CYFIP2. Our simulations showed a flexibilization of the loop comprising residues 80-110 due to the loss of contacts between internal residues in the R87C CYFIP2 as well as the key role of residues R/C87, E624, and E689 in structural modification. These data could explain the mechanism by which the mutation impairs the stability and proper regulation of the WRC.
Collapse
Affiliation(s)
- Ísis V. Biembengut
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fundação Oswaldo Cruz Paraná (Fiocruz-PR), Curitiba 80320-290, Brazil
| | - Patrícia Shigunov
- Laboratory of Basic Biology of Stem Cells, Carlos Chagas Institute, Fundação Oswaldo Cruz Paraná (Fiocruz-PR), Curitiba 80320-290, Brazil
| | - Natalia F. Frota
- Campus do Pici (Bloco 873), Federal University of Ceara (UFC), Fortaleza 60440-970, Brazil
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, Eusébio 61773-270, Brazil
| | - Marcos R. Lourenzoni
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, Eusébio 61773-270, Brazil
| | - Tatiana A. C. B. de Souza
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fundação Oswaldo Cruz Paraná (Fiocruz-PR), Curitiba 80320-290, Brazil
| |
Collapse
|
28
|
Bücker R, Seuring C, Cazey C, Veith K, García-Alai M, Grünewald K, Landau M. The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Nat Commun 2022; 13:4356. [PMID: 35896552 PMCID: PMC9329304 DOI: 10.1038/s41467-022-32039-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids.
Collapse
Grants
- Joachim Herz Foundation (Add-on fellowship, R.B.).
- This research was supported by the Ministry of Science, Research, Equalities and Districts of the Free and Hanseatic City of Hamburg (K.G., M.L., R.B.), Israel Science Foundation (grant no. 2111/20, M.L.), Israel Ministry of Science, Technology & Space (grant no. 3-15517, M.L.), U.S.-Israel Binational Science Foundation (BSF) (grant no. 2017280, M.L.),
Collapse
Affiliation(s)
- Robert Bücker
- Centre for Structural Systems Biology, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Rigaku Europe SE, Neu-Isenburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Cornelia Cazey
- Centre for Structural Systems Biology, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Maria García-Alai
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Hamburg, Germany.
- Department of Chemistry, University of Hamburg, Hamburg, Germany.
- Leibniz Institute of Virology, Hamburg, Germany.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Meytal Landau
- Centre for Structural Systems Biology, Hamburg, Germany.
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany.
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
| |
Collapse
|
29
|
Allen WJ, Corey RA, Watkins DW, Oliveira ASF, Hards K, Cook GM, Collinson I. Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion. eLife 2022; 11:e77586. [PMID: 35486093 PMCID: PMC9110029 DOI: 10.7554/elife.77586] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Transport of proteins across and into membranes is a fundamental biological process with the vast majority being conducted by the ubiquitous Sec machinery. In bacteria, this is usually achieved when the SecY-complex engages the cytosolic ATPase SecA (secretion) or translating ribosomes (insertion). Great strides have been made towards understanding the mechanism of protein translocation. Yet, important questions remain - notably, the nature of the individual steps that constitute transport, and how the proton-motive force (PMF) across the plasma membrane contributes. Here, we apply a recently developed high-resolution protein transport assay to explore these questions. We find that pre-protein transport is limited primarily by the diffusion of arginine residues across the membrane, particularly in the context of bulky hydrophobic sequences. This specific effect of arginine, caused by its positive charge, is mitigated for lysine which can be deprotonated and transported across the membrane in its neutral form. These observations have interesting implications for the mechanism of protein secretion, suggesting a simple mechanism through which the PMF can aid transport by enabling a 'proton ratchet', wherein re-protonation of exiting lysine residues prevents channel re-entry, biasing transport in the outward direction.
Collapse
Affiliation(s)
- William J Allen
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Robin A Corey
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - A Sofia F Oliveira
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
- School of Chemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Kiel Hards
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Ian Collinson
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| |
Collapse
|
30
|
Chen AY, Lee J, Damjanovic A, Brooks BR. Protein p Ka Prediction by Tree-Based Machine Learning. J Chem Theory Comput 2022; 18:2673-2686. [PMID: 35289611 PMCID: PMC10510853 DOI: 10.1021/acs.jctc.1c01257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protonation states of ionizable protein residues modulate many essential biological processes. For correct modeling and understanding of these processes, it is crucial to accurately determine their pKa values. Here, we present four tree-based machine learning models for protein pKa prediction. The four models, Random Forest, Extra Trees, eXtreme Gradient Boosting (XGBoost), and Light Gradient Boosting Machine (LightGBM), were trained on three experimental PDB and pKa datasets, two of which included a notable portion of internal residues. We observed similar performance among the four machine learning algorithms. The best model trained on the largest dataset performs 37% better than the widely used empirical pKa prediction tool PROPKA and 15% better than the published result from the pKa prediction method DelPhiPKa. The overall root-mean-square error (RMSE) for this model is 0.69, with surface and buried RMSE values being 0.56 and 0.78, respectively, considering six residue types (Asp, Glu, His, Lys, Cys, and Tyr), and 0.63 when considering Asp, Glu, His, and Lys only. We provide pKa predictions for proteins in human proteome from the AlphaFold Protein Structure Database and observed that 1% of Asp/Glu/Lys residues have highly shifted pKa values close to the physiological pH.
Collapse
Affiliation(s)
- Ada Y. Chen
- Department of Physics & Astronomy, Johns Hopkins
University, Baltimore, Maryland, 21218
- Laboratory of Computational Biology, National Heart, Lung
and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Juyong Lee
- Department of Chemistry, Division of Chemistry and
Biochemistry, Kangwon National University, 1 Gangwondaehak-gil, Chuncheon, 24341,
Republic of Korea
| | - Ana Damjanovic
- Department of Biophysics, Johns Hopkins University,
Baltimore, Maryland, 21218
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung
and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| |
Collapse
|
31
|
Koo CW, Tucci FJ, He Y, Rosenzweig AC. Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Science 2022; 375:1287-1291. [PMID: 35298269 PMCID: PMC9357287 DOI: 10.1126/science.abm3282] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.
Collapse
Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Frank J. Tucci
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
32
|
Deng J, Cui Q. Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants. J Am Chem Soc 2022; 144:4594-4610. [PMID: 35239338 PMCID: PMC9616648 DOI: 10.1021/jacs.2c00312] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Buried charged residues play important roles in the modulation of protein stabilities and conformational dynamics and make crucial contributions to protein functions. Considering the generally nonpolar nature of protein interior, a key question concerns the contribution of electronic polarization to the stabilization and properties of buried charges. We answer this question by conducting free energy simulations using the latest polarizable CHARMM force field based on Drude oscillators for a series of Staphylococcal nuclease mutants that involve a buried Glu-Lys pair in different titration states and orientations. While a nonpolarizable model suggests that the ionized form of the buried Glu-Lys pair is more than 40 kcal/mol less stable than the charge-neutral form, the two titration states are comparable in stability when electronic polarization is included explicitly, a result better reconcilable with available experimental data. Analysis of free energy components suggests that additional stabilization of the ionized Glu-Lys pair has contributions from both the enhanced salt-bridge strength and stronger interaction between the ion-pair and surrounding protein residues and penetrated water. Despite the stronger direct interaction between Glu and Lys, the ion-pair exhibits considerably larger and faster structural fluctuations when polarization is included, due to compensation of interactions in the cavity. Collectively, observations from this work provide compelling evidence that electronic polarization is essential to the stability, hydration, dynamics, and therefore function of buried charges in proteins. Therefore, our study advocates for the explicit consideration of electronic polarization for mechanistic and engineering studies that implicate buried charged residues, such as enzymes and ion transporters.
Collapse
Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| |
Collapse
|
33
|
Hernández-Pérez JM, González Carracedo MA, García AC, Pérez JAP. Molecular characterization of PI * S hangzhou , a SERPINA1 allele from continental China encoding a defective alpha-1-antitrypsin. Front Pediatr 2022; 10:985892. [PMID: 36186645 PMCID: PMC9518693 DOI: 10.3389/fped.2022.985892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Alpha-1-antitrypsin deficiency (AATD) is a heritable condition that predisposes to respiratory and hepatic complications. Screenings in East Asia human populations for the AATD alleles most commonly found among Caucasians have yielded poor outcomes. Serum alpha-1-antitrypsin (AAT) levels, AAT phenotypes, and sequences of SERPINA1 gene were examined in a Chinese child with a moderate deficit of serum AAT, who had suffered several episodes of liver disease, as well as in his first-order relatives. Results allowed the identification of PI * S hangzhou , a novel SERPINA1 defective allele, which has been characterized by a L276R substitution, found in a SERPINA1-M3 genetic background. Moreover, potential effects of PI * S hangzhou mutation over the AAT structure were studied by 3D homology modeling. The presence of an arginine residue at position 276 could destabilize the tertiary structure of AAT, since it occurs at a highly conserved hydrophobic cavity in the protein surface, and very close to two positively-charged lysine residues. Attending to the frequency of R276 variant reported in databases for individuals of East Asian ancestry, the PI * S hangzhou allele may explain the global prevalence of the PiS phenotype observed in China.
Collapse
Affiliation(s)
| | - Mario A González Carracedo
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), University of La Laguna, San Cristóbal de La Laguna, Spain
| | | | - José A Pérez Pérez
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands (IUETSPC), University of La Laguna, San Cristóbal de La Laguna, Spain
| |
Collapse
|
34
|
Wang X, Tan M, Wang M, Zhou G, Liu F, Zhang Y. Porphyrin thin-film composite cation exchange membranes enable high retention of amino acids in electrodialysis. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.119729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
35
|
Müller WEG, Schröder HC, Neufurth M, Wang X. An unexpected biomaterial against SARS-CoV-2: Bio-polyphosphate blocks binding of the viral spike to the cell receptor. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2021; 51:504-524. [PMID: 34366696 PMCID: PMC8326012 DOI: 10.1016/j.mattod.2021.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 05/15/2023]
Abstract
No other virus after the outbreak of the influenza pandemic of 1918 affected the world's population as hard as the coronavirus SARS-CoV-2. The identification of effective agents/materials to prevent or treat COVID-19 caused by SARS-CoV-2 is an urgent global need. This review aims to survey novel strategies based on inorganic polyphosphate (polyP), a biologically formed but also synthetically available polyanionic polymeric material, which has the potential of being a potent inhibitor of the SARS-CoV-2 virus-cell-docking machinery. This virus attaches to the host cell surface receptor ACE2 with its receptor binding domain (RBD), which is present at the tips of the viral envelope spike proteins. On the surface of the RBD an unusually conserved cationic groove is exposed, which is composed of basic amino acids (Arg, Lys, and His). This pattern of cationic amino acids, the cationic groove, matches spatially with the anionic polymeric material, with polyP, allowing an electrostatic interaction. In consequence, the interaction between the RBD and ACE2 is potently blocked. PolyP is a physiological inorganic polymer, synthesized by cells and especially enriched in the blood platelets, which releases metabolically useful energy through enzymatic degradation and coupled ADP/ATP formation. In addition, this material upregulates the steady-state-expression of the mucin genes in the epithelial cells. We propose that polyP, with its two antiviral properties (blocking the binding of the virus to the cells and reinforcing the defense barrier against infiltration of the virus) has the potential to be a novel protective/therapeutic anti-COVID-19 agent.
Collapse
Affiliation(s)
- Werner E G Müller
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, 55128 Mainz, Germany
| | - Heinz C Schröder
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, 55128 Mainz, Germany
| | - Meik Neufurth
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, 55128 Mainz, Germany
| | - Xiaohong Wang
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, 55128 Mainz, Germany
| |
Collapse
|
36
|
Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
Collapse
Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
37
|
Kono F, Tamada T. Neutron crystallography for the elucidation of enzyme catalysis. Curr Opin Struct Biol 2021; 71:36-42. [PMID: 34214927 DOI: 10.1016/j.sbi.2021.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/08/2021] [Accepted: 05/22/2021] [Indexed: 11/26/2022]
Abstract
Hydrogen atoms and hydration water molecules in proteins are indispensable for many biochemical processes, especially enzymatic catalysis. The locations of hydrogen atoms in proteins are usually predicted based on X-ray structures, but it is still very difficult to know the ionization states of the catalytic residues, the hydration structure of the protein, and the characteristics of hydrogen-bonding interactions. Neutron crystallography allows the direct observation of hydrogen atoms that play crucial roles in molecular recognition and the catalytic reactions of enzymes. In this review, we present the current status of neutron crystallography in structural biology and recent neutron structural analyses of three enzymes: ascorbate peroxidase, the main protease of severe acute respiratory syndrome coronavirus 2, and copper-containing nitrite reductase.
Collapse
Affiliation(s)
- Fumiaki Kono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan.
| |
Collapse
|
38
|
Hernández VM, Arteaga A, Dunn MF. Diversity, properties and functions of bacterial arginases. FEMS Microbiol Rev 2021; 45:6308370. [PMID: 34160574 DOI: 10.1093/femsre/fuab034] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
The metalloenzyme arginase hydrolyzes L-arginine to produce L-ornithine and urea. In bacteria, arginase has important functions in basic nitrogen metabolism and redistribution, production of the key metabolic precursor L-ornithine, stress resistance and pathogenesis. We describe the regulation and specific functions of the arginase pathway as well as summarize key characteristics of related arginine catabolic pathways. The use of arginase-derived ornithine as a precursor molecule is reviewed. We discuss the biochemical and transcriptional regulation of arginine metabolism, including arginase, with the latter topic focusing on the RocR and AhrC transcriptional regulators in the model organism Bacillus subtilis. Finally, we consider similarities and contrasts in the structure and catalytic mechanism of the arginases from Bacillus caldovelox and Helicobacter pylori. The overall aim of this review is to provide a panorama of the diversity of physiological functions, regulation, and biochemical features of arginases in a variety of bacterial species.
Collapse
Affiliation(s)
- Victor M Hernández
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Alejandra Arteaga
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| |
Collapse
|
39
|
Do Kwon Y, Wang XE, Bender MF, Yang R, Li Y, McKee K, Rawi R, O’Dell S, Schneck NA, Shaddeau A, Zhang B, Arnold FJ, Connors M, Doria-Rose NA, Kwong PD, Lei QP. Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography. Antibodies (Basel) 2021; 10:antib10020023. [PMID: 34200826 PMCID: PMC8293163 DOI: 10.3390/antib10020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/20/2021] [Accepted: 05/30/2021] [Indexed: 11/16/2022] Open
Abstract
Antibody 10E8 is capable of effectively neutralizing HIV through its recognition of the membrane-proximal external region (MPER), and a suitably optimized version of 10E8 might have utility in HIV therapy and prophylaxis. However, 10E8 displays a three-peak profile on size-exclusion chromatography (SEC), complicating its manufacture. Here we show cis-trans conformational isomerization of the Tyr-Pro-Pro (YPP) motif in the heavy chain 3rd complementarity-determining region (CDR H3) of antibody 10E8 to be the mechanistic basis of its multipeak behavior. We observed 10E8 to undergo slow conformational isomerization and delineate a mechanistic explanation for effective comodifiers that were able to resolve its SEC heterogeneity and to allow an evaluation of the critical quality attribute of aggregation. We determined crystal structures of single and double alanine mutants of a key di-proline motif and of a light chain variant, revealing alternative conformations of the CDR H3. We also replicated both multi-peak and delayed SEC behavior with MPER-antibodies 4E10 and VRC42, by introducing a Tyr-Pro (YP) motif into their CDR H3s. Our results show how a conformationally dynamic CDR H3 can provide the requisite structural plasticity needed for a highly hydrophobic paratope to recognize its membrane-proximal epitope.
Collapse
Affiliation(s)
- Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Xiangchun E. Wang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Michael F. Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Rong Yang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Yile Li
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Nicole A. Schneck
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Andrew Shaddeau
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Frank J. Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Mark Connors
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
- Correspondence: (P.D.K.); (Q.P.L.)
| | - Q. Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
- Correspondence: (P.D.K.); (Q.P.L.)
| |
Collapse
|
40
|
Cho H, Lee CS, Kim TH. Label-Free Assay of Protein Kinase A Activity and Inhibition Using a Peptide-Based Electrochemical Sensor. Biomedicines 2021; 9:biomedicines9040423. [PMID: 33924719 PMCID: PMC8069798 DOI: 10.3390/biomedicines9040423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 12/27/2022] Open
Abstract
We propose a simple label-free electrochemical biosensor for monitoring protein kinase activity and inhibition using a peptide-modified electrode. The biosensor employs cys-kemptide (CLRRASLG) as a substrate peptide which was immobilized on the surface of a gold electrode via the self-assembly of the thiol terminals in cysteine (C) residues. The interaction between protein kinase A (PKA) and adenosine 5′-triphosphate (ATP) on the cys-kemptide immobilized electrode can cause the transfer of ATP terminal phosphates to the peptide substrates at serine (S) residues, which alters the surface charge of the electrode, thus enabling monitoring of the PKA activity via measuring the interfacial electron transfer resistance with electrochemical impedance spectroscopy. The proposed sensor showed reliable, sensitive, and selective detection of PKA activity with a wide dynamic range of 0.1–100 U/mL and a detection limit of 56 mU/mL. The sensor also exhibited high selectivity, rendering it possible to screen PKA inhibitors. Moreover, the sensor can be employed to evaluate the activity and inhibition of PKA in real samples.
Collapse
Affiliation(s)
- Hyunju Cho
- Department of ICT Environmental Health System, Graduate School, Soonchunhyang University, Asan 31538, Korea; (H.C.); (C.-S.L.)
| | - Chang-Seuk Lee
- Department of ICT Environmental Health System, Graduate School, Soonchunhyang University, Asan 31538, Korea; (H.C.); (C.-S.L.)
| | - Tae Hyun Kim
- Department of ICT Environmental Health System, Graduate School, Soonchunhyang University, Asan 31538, Korea; (H.C.); (C.-S.L.)
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
- Correspondence: ; Tel.: +82-41-530-4722; Fax: +82-41-530-1247
| |
Collapse
|
41
|
Arias HR, Targowska-Duda KM, García-Colunga J, Ortells MO. Is the Antidepressant Activity of Selective Serotonin Reuptake Inhibitors Mediated by Nicotinic Acetylcholine Receptors? Molecules 2021; 26:molecules26082149. [PMID: 33917953 PMCID: PMC8068400 DOI: 10.3390/molecules26082149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 12/05/2022] Open
Abstract
It is generally assumed that selective serotonin reuptake inhibitors (SSRIs) induce antidepressant activity by inhibiting serotonin (5-HT) reuptake transporters, thus elevating synaptic 5-HT levels and, finally, ameliorates depression symptoms. New evidence indicates that SSRIs may also modulate other neurotransmitter systems by inhibiting neuronal nicotinic acetylcholine receptors (nAChRs), which are recognized as important in mood regulation. There is a clear and strong association between major depression and smoking, where depressed patients smoke twice as much as the normal population. However, SSRIs are not efficient for smoking cessation therapy. In patients with major depressive disorder, there is a lower availability of functional nAChRs, although their amount is not altered, which is possibly caused by higher endogenous ACh levels, which consequently induce nAChR desensitization. Other neurotransmitter systems have also emerged as possible targets for SSRIs. Studies on dorsal raphe nucleus serotoninergic neurons support the concept that SSRI-induced nAChR inhibition decreases the glutamatergic hyperstimulation observed in stress conditions, which compensates the excessive 5-HT overflow in these neurons and, consequently, ameliorates depression symptoms. At the molecular level, SSRIs inhibit different nAChR subtypes by noncompetitive mechanisms, including ion channel blockade and induction of receptor desensitization, whereas α9α10 nAChRs, which are peripherally expressed and not directly involved in depression, are inhibited by competitive mechanisms. According to the functional and structural results, SSRIs bind within the nAChR ion channel at high-affinity sites that are spread out between serine and valine rings. In conclusion, SSRI-induced inhibition of a variety of nAChRs expressed in different neurotransmitter systems widens the complexity by which these antidepressants may act clinically.
Collapse
Affiliation(s)
- Hugo R. Arias
- Department of Pharmacology and Physiology, Oklahoma State University College of Osteopathic Medicine, Tahlequah, OK 74464, USA
- Correspondence: ; Tel.: +1-918-525-6324; Fax: +1-918-280-2515
| | | | - Jesús García-Colunga
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Campus Juriquilla, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico;
| | - Marcelo O. Ortells
- Facultad de Medicina, Universidad de Morón, CONICET, Morón 1708, Argentina;
| |
Collapse
|
42
|
An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity. Biochem J 2021; 477:2999-3018. [PMID: 32729927 DOI: 10.1042/bcj20200311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/19/2022]
Abstract
Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to α-ketoglutarate (αKG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasing kcat values for αKG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKa values. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKa value upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue ∼12 Å from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.
Collapse
|
43
|
Pan Y, Barba‐Bon A, Tian H, Ding F, Hennig A, Nau WM, Guo D. An Amphiphilic Sulfonatocalix[5]arene as an Activator for Membrane Transport of Lysine‐rich Peptides and Proteins. Angew Chem Int Ed Engl 2020; 60:1875-1882. [DOI: 10.1002/anie.202011185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/24/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andrea Barba‐Bon
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Han‐Wen Tian
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Fei Ding
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andreas Hennig
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
- Institute of Chemistry of New Materials and School of Biology/Chemistry Universität Osnabrück Osnabrück Germany
- Center of Cellular Nanoanalytics (CellNanOs) Universität Osnabrück Osnabrück Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Dong‐Sheng Guo
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| |
Collapse
|
44
|
Pan Y, Barba‐Bon A, Tian H, Ding F, Hennig A, Nau WM, Guo D. An Amphiphilic Sulfonatocalix[5]arene as an Activator for Membrane Transport of Lysine‐rich Peptides and Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andrea Barba‐Bon
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Han‐Wen Tian
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Fei Ding
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andreas Hennig
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
- Institute of Chemistry of New Materials and School of Biology/Chemistry Universität Osnabrück Osnabrück Germany
- Center of Cellular Nanoanalytics (CellNanOs) Universität Osnabrück Osnabrück Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Dong‐Sheng Guo
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| |
Collapse
|
45
|
Thermodynamics and Mechanism of the Membrane Permeation of Hv1 Channel Blockers. J Membr Biol 2020; 254:5-16. [PMID: 33196887 DOI: 10.1007/s00232-020-00149-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/14/2020] [Indexed: 02/08/2023]
Abstract
The voltage-gated proton channel Hv1 mediates efflux of protons from the cell. Hv1 integrally contributes to various physiological processes including pH homeostasis and the respiratory burst of phagocytes. Inhibition of Hv1 may provide therapeutic avenues for the treatment of inflammatory diseases, breast cancer, and ischemic brain damage. In this work, we investigate two prototypical Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI), and 5-chloro-2-guanidinobenzimidazole (GBIC), from an experimentally screened class of guanidine derivatives. Both compounds block proton conduction by binding the same site located on the intracellular side of the channel. However, when added to the extracellular medium, the compounds strongly differ in their ability to inhibit proton conduction, suggesting substantial differences in membrane permeability. Here, we compute the potential of mean force for each compound to permeate through the membrane using atomistic molecular dynamics simulations with the adaptive biasing force method. Our results rationalize the putative distinction between these two blockers with respect to their abilities to permeate the cellular membrane.
Collapse
|
46
|
Tian Y, Chen S, Shan Q. Charged residues at the pore extracellular half of the glycine receptor facilitate channel gating: a potential role played by electrostatic repulsion. J Physiol 2020; 598:4643-4661. [PMID: 32844405 DOI: 10.1113/jp279288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 07/29/2020] [Indexed: 02/05/2023] Open
Abstract
KEY POINTS The Arg271Gln mutation of the glycine receptor (GlyR) causes hereditary hyperekplexia. This mutation dramatically compromises GlyR function; however, the underlying mechanism is not yet known. This study, by employing function and computation methods, proposes that charged residues (including the Arg residue) at the pore extracellular half from each of the five subunits of the homomeric α1 GlyR, create an electrostatic repulsive potential to widen the pore, thereby facilitating channel opening. This mechanism explains how the Arg271Gln mutation, in which the positively charged Arg residue is substituted by the neutral Gln residue, compromises GlyR function. This study furthers our understanding of the biophysical mechanism underlying the Arg271Gln mutation compromising GlyR function. ABSTRACT The R271(19')Q mutation in the α1 subunit of the glycine receptor (GlyR) chloride channel causes hereditary hyperekplexia. This mutation dramatically compromises channel function; however, the underlying mechanism is not yet known. The R271 residue is located at the extracellular half of the channel pore. In this study, an Arg-scanning mutagenesis was performed at the pore extracellular half from the 262(10') to the 272(20') position on the background of the α1 GlyR carrying the hyperekplexia-causing mutation R271(19')Q. It was found that the placement of the Arg residue rescued channel function to an extent inversely correlated with the distance between the residue and the pore central axis (perpendicular to the plane of the lipid bilayer). Accordingly, it was hypothesized that the placed Arg residues from each of the five subunits of the homomeric α1 GlyR create an electrostatic repulsive potential to widen the pore, thereby facilitating channel opening. This hypothesis was quantitatively verified by theoretical computation via exploiting basic laws of electrostatics and thermodynamics, and further supported by more experimental findings that the placement of another positively charged Lys residue or even a negatively charged Asp residue also rescued channel function in the same manner. This study provides a novel mechanism via which charged residues in the pore region facilitate channel gating, not only for the disease-causing 19'R residue in the GlyR, but also potentially for charged residues in the same region of other ion channels.
Collapse
Affiliation(s)
- Yao Tian
- Chern Institute of Mathematics, Nankai University, Tianjin, 300071, China
| | - Shijie Chen
- Laboratory for Synaptic Plasticity, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Qiang Shan
- Laboratory for Synaptic Plasticity, Shantou University Medical College, Shantou, Guangdong, 515041, China
| |
Collapse
|
47
|
Fabre L, Ntreh AT, Yazidi A, Leus IV, Weeks JW, Bhattacharyya S, Ruickoldt J, Rouiller I, Zgurskaya HI, Sygusch J. A "Drug Sweeping" State of the TriABC Triclosan Efflux Pump from Pseudomonas aeruginosa. Structure 2020; 29:261-274.e6. [PMID: 32966762 DOI: 10.1016/j.str.2020.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/30/2020] [Accepted: 08/29/2020] [Indexed: 12/01/2022]
Abstract
The structure of the TriABC inner membrane component of the triclosan/SDS-specific efflux pump from Pseudomonas aeruginosa was determined by cryoelectron microscopy to 4.5 Å resolution. The complete structure of the inner membrane transporter TriC of the resistance-nodulation-division (RND) superfamily was solved, including a partial structure of the fused periplasmic membrane fusion subunits, TriA and TriB. The substrate-free conformation of TriABC represents an intermediate step in efflux complex assembly before the engagement of the outer membrane channel. Structural analysis identified a tunnel network whose constriction impedes substrate efflux, indicating inhibition of TriABC in the unengaged state. Blind docking studies revealed binding to TriC at the same loci by substrates and bulkier non-substrates. Together with functional analyses, we propose that selective substrate translocation involves conformational gating at the tunnel narrowing that, together with conformational ordering of TriA and TriB, creates an engaged state capable of mediating substrate efflux.
Collapse
Affiliation(s)
- Lucien Fabre
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada
| | - Abigail T Ntreh
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Amira Yazidi
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Inga V Leus
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Jon W Weeks
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Jakob Ruickoldt
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Isabelle Rouiller
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada; Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA.
| | - Jurgen Sygusch
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada.
| |
Collapse
|
48
|
Luca S, Seal P, Parekh HS, Tupally KR, Smith SC. Cell Membrane Penetration without Pore Formation: Chameleonic Properties of Dendrimers in Response to Hydrophobic and Hydrophilic Environments. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.201900152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sergio Luca
- Integrated Materials Design LaboratoryDepartment of Applied MathematicsResearch School of PhysicsAustralian National University Acton ACT 2601 Australia
| | - Prasenjit Seal
- Department of ChemistryUniversity of Helsinki P.O. Box 55 (A.I. Virtasen aukio 1) Helsinki 00014 Finland
| | - Harendra S. Parekh
- School of PharmacyThe University of Queensland Brisbane QLD 4072 Australia
| | | | - Sean C. Smith
- Integrated Materials Design LaboratoryDepartment of Applied MathematicsResearch School of PhysicsAustralian National University Acton ACT 2601 Australia
| |
Collapse
|
49
|
Hiller DA, Dunican BF, Nallur S, Li NS, Piccirilli JA, Strobel SA. The Positively Charged Active Site of the Bacterial Toxin RelE Causes a Large Shift in the General Base p Ka. Biochemistry 2020; 59:1665-1671. [PMID: 32320214 DOI: 10.1021/acs.biochem.9b01047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial toxin RelE cleaves mRNA in the ribosomal A site. Although it shares a global fold with other microbial RNases, the active site contains several positively charged residues instead of histidines and glutamates that are typical of ribonucleases. The pH dependences of wild-type and mutant RelE indicate it uses general acid-base catalysis, but either the general acid (proposed to be R81) or the general base must have a substantially downshifted pKa. However, which group is shifted cannot be determined using available structural and biochemical data. Here, we use a phosphorothiolate at the scissile phosphate to remove the need for a general acid. We show this modification rescues nearly all of the defect of the R81A mutation, supporting R81 as the general acid. We also find that the observed pKa of the general base is dependent on the charge of the side chain at position 81. This indicates that positive charge in the active site contributes to a general base pKa downshifted by more than 5 units. Although this modestly reduces the effectiveness of general acid-base catalysis, it is strongly supplemented by the role of the positive charge in stabilizing the transition state for cleavage. Furthermore, we show that the ribosome is required for cleavage but not binding of mRNA by RelE. Ribosome functional groups do not directly contact the scissile phosphate, indicating that positioning and charge interactions dominate RelE catalysis. The unusual RelE active site catalyzes phosphoryl transfer at a rate comparable to those of similar enzymes, but in a ribosome-dependent fashion.
Collapse
Affiliation(s)
- David A Hiller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Chemistry and Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Brian F Dunican
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Sunitha Nallur
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Chemistry and Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Nan-Sheng Li
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Chemistry and Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| |
Collapse
|
50
|
Polyionic complexes of chitosan-N-arginine with alginate as pH responsive and mucoadhesive particles for oral drug delivery applications. Int J Biol Macromol 2020; 148:550-564. [DOI: 10.1016/j.ijbiomac.2020.01.160] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/26/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022]
|