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Maliano MR, Yetming KD, Kalejta RF. Triple lysine and nucleosome-binding motifs of the viral IE19 protein are required for human cytomegalovirus S-phase infections. mBio 2024; 15:e0016224. [PMID: 38695580 PMCID: PMC11237493 DOI: 10.1128/mbio.00162-24] [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: 01/19/2024] [Accepted: 02/29/2024] [Indexed: 06/13/2024] Open
Abstract
Herpesvirus genomes are maintained as extrachromosomal plasmids within the nuclei of infected cells. Some herpesviruses persist within dividing cells, putting the viral genome at risk of being lost to the cytoplasm during mitosis because karyokinesis (nuclear division) requires nuclear envelope breakdown. Oncogenic herpesviruses (and papillomaviruses) avoid genome loss during mitosis by tethering their genomes to cellular chromosomes, thereby ensuring viral genome uptake into newly formed nuclei. These viruses use viral proteins with DNA- and chromatin-binding capabilities to physically link viral and cellular genomes together in a process called tethering. The known viral tethering proteins of human papillomavirus (E2), Epstein-Barr virus (EBNA1), and Kaposi's sarcoma-associated herpesvirus (LANA) each contain two independent domains required for genome tethering, one that binds sequence specifically to the viral genome and another that binds to cellular chromatin. This latter domain is called a chromatin tethering domain (CTD). The human cytomegalovirus UL123 gene encodes a CTD that is required for the virus to productively infect dividing fibroblast cells within the S phase of the cell cycle, presumably by tethering the viral genome to cellular chromosomes during mitosis. The CTD-containing UL123 gene product that supports S-phase infections is the IE19 protein. Here, we define two motifs in IE19 required for S-phase infections: an N-terminal triple lysine motif and a C-terminal nucleosome-binding motif within the CTD.IMPORTANCEThe IE19 protein encoded by human cytomegalovirus (HCMV) is required for S-phase infection of dividing cells, likely because it tethers the viral genome to cellular chromosomes, thereby allowing them to survive mitosis. The mechanism through which IE19 tethers viral genomes to cellular chromosomes is not understood. For human papillomavirus, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus, viral genome tethering is required for persistence (latency) and pathogenesis (oncogenesis). Like these viruses, HCMV also achieves latency, and it modulates the properties of glioblastoma multiforme tumors. Therefore, defining the mechanism through which IE19 tethers viral genomes to cellular chromosomes may help us understand, and ultimately combat or control, HCMV latency and oncomodulation.
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Affiliation(s)
- Minor R. Maliano
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Kristen D. Yetming
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Molecular Biology, Charles River Laboratories, Wayne, Pennsylvania, USA
| | - Robert F. Kalejta
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, USA
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2
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Eskandari S, Rezayof A, Asghari SM, Hashemizadeh S. Neurobiochemical characteristics of arginine-rich peptides explain their potential therapeutic efficacy in neurodegenerative diseases. Neuropeptides 2023; 101:102356. [PMID: 37390744 DOI: 10.1016/j.npep.2023.102356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Neurodegenerative diseases, including Alzheimer̕ s disease (AD), Parkinson̕ s disease (PD), Huntington̕ s disease (HD), and Amyotrophic Lateral Sclerosis (ALS) require special attention to find new potential treatment methods. This review aims to summarize the current knowledge of the relationship between the biochemical properties of arginine-rich peptides (ARPs) and their neuroprotective effects to deal with the harmful effects of risk factors. It seems that ARPs have portrayed a promising and fantastic landscape for treating neurodegeneration-associated disorders. With multimodal mechanisms of action, ARPs play various unprecedented roles, including as the novel delivery platforms for entering the central nervous system (CNS), the potent antagonists for calcium influx, the invader molecules for targeting mitochondria, and the protein stabilizers. Interestingly, these peptides inhibit the proteolytic enzymes and block protein aggregation to induce pro-survival signaling pathways. ARPs also serve as the scavengers of toxic molecules and the reducers of oxidative stress agents. They also have anti-inflammatory, antimicrobial, and anti-cancer properties. Moreover, by providing an efficient nucleic acid delivery system, ARPs can play an essential role in developing various fields, including gene vaccines, gene therapy, gene editing, and imaging. ARP agents and ARP/cargo therapeutics can be raised as an emergent class of neurotherapeutics for neurodegeneration. Part of the aim of this review is to present recent advances in treating neurodegenerative diseases using ARPs as an emerging and powerful therapeutic tool. The applications and progress of ARPs-based nucleic acid delivery systems have also been discussed to highlight their usefulness as a broad-acting class of drugs.
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Affiliation(s)
- Sedigheh Eskandari
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ameneh Rezayof
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - S Mohsen Asghari
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
| | - Shiva Hashemizadeh
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences, IPM, Tehran, Iran
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3
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Niu J, Qiu C, Abbott NL, Gellman SH. Formation of versus Recruitment to RNA-Rich Condensates: Controlling Effects Exerted by Peptide Side Chain Identity. J Am Chem Soc 2022; 144:10386-10395. [PMID: 35639776 PMCID: PMC9746169 DOI: 10.1021/jacs.2c02222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Liquid-liquid phase separation (LLPS), the spontaneous formation of contiguous liquid phases with distinct compositions, has been long known in chemical systems and more recently recognized as a ubiquitous feature of cell biology. We describe a system involving biologically relevant components, synthetic peptides, and total yeast RNA, that has enabled us to explore factors that underlie phase separation. Coulombic complementarity between a cationic peptide and anionic RNA is necessary but not sufficient for formation of a condensed phase in our system. In addition to a net positive charge, the peptide must present the proper type of cationic moiety. Guanidinium groups, as found in the Arg side chain, support phase separation, but ammonium groups, as found in the Lys side chain, or dimethylguanidinium groups, as found in post-translationally modified Arg side chains, do not support phase separation in our system. However, the cationic groups that do not support phase separation via interaction with RNA can nevertheless enable recruitment to a condensed phase, which reveals that the network of forces governing condensed phase formation can differ from the network of forces governing recruitment to such a phase. We introduce a new method for measuring the concentrations of components in condensed phases based on fluorine-containing additives and 19F NMR.
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Affiliation(s)
- Jiani Niu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Cindy Qiu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, New York 14853, USA
| | - Nicholas L. Abbott
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, New York 14853, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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4
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Xie Y, Calabrese Barton S. Infrequent metadynamics study of rare-event electrostatic channeling. Phys Chem Chem Phys 2021; 23:13381-13388. [PMID: 34105559 DOI: 10.1039/d1cp01304a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The efficiency of cascade reactions, which consist of multiple chemical transformations that occur in a single pot without purification steps, is limited by the transport efficiency of intermediates between adjacent steps. Electrostatic channeling is a proven strategy for intermediate transfer in natural chemical cascades, but implementation into artificial cascades remains a challenge. Here, we combine infrequent metadynamics (InMetaD), umbrella sampling (US), and kinetic Monte Carlo (KMC) models to computationally study the transfer mechanism of glucose-6-phosphate (G6P) on a poly-arginine peptide bridging hexokinase (HK) and glucose-6-dehydrogenase (G6PDH). Transport of G6P by hopping in the presence of poly-arginine peptides is shown to be a rare event, and InMetaD is used to compute the hopping activation energy. US simulations capture the configurational change in the desorption process and enable the determination of the desorption energy. Parameterized by these results, a KMC model is used to estimate transport efficiency for the bridged enzyme complex. Results are compared to a similar complex using a poly-lysine bridge, using kinetic lag time as a metric. Even at a high ionic strength of 120 mM, poly-arginine peptides may be capable of more efficient transport as compared to poly-lysine, with a predicted lag time of 6 seconds for poly-arginine, compared to a previously reported lag time of 59 seconds for poly-lysine. This work indicates that poly-arginine peptides may be an improved bridge structure for electrostatic channeling of anionic intermediates.
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Affiliation(s)
- Yan Xie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA.
| | - Scott Calabrese Barton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA.
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5
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Kibria MG, Fukutani A, Akazawa-Ogawa Y, Hagihara Y, Kuroda Y. Anti-EGFR V HH Antibody under Thermal Stress Is Better Solubilized with a Lysine than with an Arginine SEP Tag. Biomolecules 2021; 11:biom11060810. [PMID: 34072518 PMCID: PMC8229009 DOI: 10.3390/biom11060810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/15/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
In this study, we assessed the potential of arginine and lysine solubility-enhancing peptide (SEP) tags to control the solubility of a model protein, anti-EGFR VHH-7D12, in a thermally denatured state at a high temperature. We produced VHH-7D12 antibodies attached with a C-terminal SEP tag made of either five or nine arginines or lysines (7D12-C5R, 7D12-C9R, 7D12-C5K and 7D12-C9K, respectively). The 5-arginine and 5-lysine SEP tags increased the E. coli expression of VHH-7D12 by over 80%. Biophysical and biochemical analysis confirmed the native-like secondary and tertiary structural properties and the monomeric nature of all VHH-7D12 variants. Moreover, all VHH-7D12 variants retained a full binding activity to the EGFR extracellular domain. Finally, thermal stress with 45-minute incubation at 60 and 75 °C, where VHH-7D12 variants are unfolded, showed that the untagged VHH-7D12 formed aggregates in all of the four buffers, and the supernatant protein concentration was reduced by up to 35%. 7D12-C5R and 7D12-C9R did not aggregate in Na-acetate (pH 4.7) and Tris-HCl (pH 8.5) but formed aggregates in phosphate buffer (PB, pH 7.4) and phosphate buffer saline (PBS, pH 7.4). The lysine tags (either C5K or C9K) had the strongest solubilization effect, and both 7D12-C5K and 7D12-C9K remained in the supernatant. Altogether, our results indicate that, under a thermal stress condition, the lysine SEP tags solubilization effect is more potent than that of an arginine SEP tags, and the SEP tags did not affect the structural and functional properties of the protein.
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Affiliation(s)
- Md. Golam Kibria
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan; (M.G.K.); (A.F.)
| | - Akari Fukutani
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan; (M.G.K.); (A.F.)
| | - Yoko Akazawa-Ogawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan; (Y.A.-O.); (Y.H.)
| | - Yoshihisa Hagihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan; (Y.A.-O.); (Y.H.)
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan; (M.G.K.); (A.F.)
- Correspondence: ; Tel./Fax: +81-42-388-7794
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Mink C, Strandberg E, Wadhwani P, Melo MN, Reichert J, Wacker I, Castanho MARB, Ulrich AS. Overlapping Properties of the Short Membrane-Active Peptide BP100 With (i) Polycationic TAT and (ii) α-helical Magainin Family Peptides. Front Cell Infect Microbiol 2021; 11:609542. [PMID: 33981626 PMCID: PMC8107365 DOI: 10.3389/fcimb.2021.609542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/09/2021] [Indexed: 01/04/2023] Open
Abstract
BP100 is a short, designer-made membrane-active peptide with multiple functionalities: antimicrobial, cell-penetrating, and fusogenic. Consisting of five lysines and 6 hydrophobic residues, BP100 was shown to bind to lipid bilayers as an amphipathic α-helix, but its mechanism of action remains unclear. With these features, BP100 embodies the characteristics of two distinctly different classes of membrane-active peptides, which have been studied in detail and where the mechanism of action is better understood. On the one hand, its amphiphilic helical structure is similar to the pore forming magainin family of antimicrobial peptides, though BP100 is much too short to span the membrane. On the other hand, its length and high charge density are reminiscent of the HIV-TAT family of cell penetrating peptides, for which inverted micelles have been postulated as translocation intermediates, amongst other mechanisms. Assays were performed to test the antimicrobial and hemolytic activity, the induced leakage and fusion of lipid vesicles, and cell uptake. From these results the functional profiles of BP100, HIV-TAT, and the magainin-like peptides magainin 2, PGLa, MSI-103, and MAP were determined and compared. It is observed that the activity of BP100 resembles most closely the much longer amphipathic α-helical magainin-like peptides, with high antimicrobial activity along with considerable fusogenic and hemolytic effects. In contrast, HIV-TAT shows almost no antimicrobial, fusogenic, or hemolytic effects. We conclude that the amphipathic helix of BP100 has a similar membrane-based activity as magainin-like peptides and may have a similar mechanism of action.
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Affiliation(s)
- Christian Mink
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, Germany
| | - Manuel N Melo
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Irene Wacker
- Cryo EM, Centre for Advanced Materials, Universität Heidelberg, Heidelberg, Germany
| | - Miguel A R B Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Anne S Ulrich
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Biological Interfaces (IBG-2), KIT, Karlsruhe, Germany
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7
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Lenton S, Hervø-Hansen S, Popov AM, Tully MD, Lund M, Skepö M. Impact of Arginine-Phosphate Interactions on the Reentrant Condensation of Disordered Proteins. Biomacromolecules 2021; 22:1532-1544. [PMID: 33730849 PMCID: PMC8045028 DOI: 10.1021/acs.biomac.0c01765] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Re-entrant condensation results in the formation of a condensed protein regime between two critical ion concentrations. The process is driven by neutralization and inversion of the protein charge by oppositely charged ions. Re-entrant condensation of cationic proteins by the polyvalent anions, pyrophosphate and tripolyphosphate, has previously been observed, but not for citrate, which has similar charge and size compared to the polyphosphates. Therefore, besides electrostatic interactions, other specific interactions between the polyphosphate ions and proteins must contribute. Here, we show that additional attractive interactions between arginine and tripolyphosphate determine the re-entrant condensation and decondensation boundaries of the cationic, intrinsically disordered saliva protein, histatin 5. Furthermore, we show by small-angle X-ray scattering (SAXS) that polyvalent anions cause compaction of histatin 5, as would be expected based solely on electrostatic interactions. Hence, we conclude that arginine-phosphate-specific interactions not only regulate solution properties but also influence the conformational ensemble of histatin 5, which is shown to vary with the number of arginine residues. Together, the results presented here provide further insight into an organizational mechanism that can be used to tune protein interactions in solution of both naturally occurring and synthetic proteins.
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Affiliation(s)
- Samuel Lenton
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Stefan Hervø-Hansen
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Anton M Popov
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mark D Tully
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mikael Lund
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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8
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Sane M, Dighe V, Patil R, Hassan PA, Gawali S, Patravale V. Bivalirudin and sirolimus co-eluting coronary stent: Potential strategy for the prevention of stent thrombosis and restenosis. Int J Pharm 2021; 600:120403. [PMID: 33711467 DOI: 10.1016/j.ijpharm.2021.120403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/19/2022]
Abstract
Localized drug delivery with sustained elution characteristics from nanocarrier coated stents represents a viable therapeutic approach to circumvent concerns related to coronary stent therapy. We fabricated a Sirolimus (SRL) and Bivalirudin (BIV) releasing nanoparticles (NPs) coated stent for concurrent mitigation of vascular restenosis and acute stent thrombosis. SRL NPs were prepared by nanoprecipitation method whereas the BIV vesicles were generated using hydrophobic ion pair approach followed by micellization phenomenon. MTT assay and confocal microscopic analysis indicated superior anti-proliferative activity and higher cellular uptake of SRL NPs into human coronary artery smooth muscle cells, respectively. DSC and ATR-FTIR techniques confirmed the formation of complex between BIV and phosphatidylglycerol via some weak physical interactions. More than 2 fold rise in log P value was obtained for DSPG-BIV at 3:1 M ratio compared with native BIV solution. The SAXS analysis indicated formation of oligolamellar vesicles of DSPG-BIV complex which was preferentially entrapped into lipophilic lamellae of vesicles. APTT, PT, and TT tests revealed that the BIV vesicles caused significant prolongation of clotting time compared to native BIV solution. The SEM analysis showed uniform and defect free stent coating. In vitro release study demonstrated that SRL and BIV were eluted in a sustained manner from coated stents.
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Affiliation(s)
- Mangesh Sane
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, N.P. Marg, Matunga, Mumbai 400 019, Maharashtra, India
| | - Vikas Dighe
- National Centre for Preclinical Reproductive and Genetic Toxicology, National Institute for Research in Reproductive Health, J. M. Street, Parel, Mumbai 400 012, Maharashtra, India
| | - Rucha Patil
- Department of Haemostasis & Thrombosis, National Institute of Immunohaematology, Indian Council of Medical Research, 13th Floor, New Multi-storeyed Building, KEM Hospital Campus, Parel, Mumbai 400 012, India
| | | | - Santosh Gawali
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, N.P. Marg, Matunga, Mumbai 400 019, Maharashtra, India.
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9
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Fuchi Y, Murase H, Kai R, Kurata K, Karasawa S, Sasaki S. Artificial Host Molecules to Covalently Capture 8-Nitro-cGMP in Neutral Aqueous Solutions and in Cells. Bioconjug Chem 2021; 32:385-393. [PMID: 33529519 DOI: 10.1021/acs.bioconjchem.1c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New 1,3-diazaphenoxazine derivatives (nitroG-Grasp-Guanidine, NGG) have been developed to covalently capture 8-nitro-cGMP in neutral aqueous solutions, which furnish a thiol reactive group to displace the 8-nitro group and a guanidine unit for interaction with the cyclic phosphate. The thiol group was introduced to the 1,3-diazaphenoxazine skeleton through a 2-aminobenzylthiol group (NGG-H) and its 4-methyl (NGG-pMe) and 6-methyl (NGG-oMe) substituted derivatives. The covalent adducts were formed between the NGG derivatives and 8-nitro-cGMP in neutral aqueous solutions. Among the NGG derivatives, the one with the 6-methyl group (NGG-oMe) exhibited the most efficient capture reaction. Furthermore, NGG-H showed a cell permeability into HEK-293 and RAW 264.7 cells and reduced the intracellular 8-nitro-cGMP level. The NGG derivatives developed in this study would become a valuable tool to study the intracellular role of 8-nitro-cGMP.
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Affiliation(s)
- Yasufumi Fuchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.,Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3-3165 Higashi-tamagawagakuen, Machida 194-8543, Japan.,Graduate School of Pharmaceutical Sciences, Tokushima Bunri University, 180 Yamashiro-cho, Tokushima 770-8514, Japan
| | - Hirotaka Murase
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo 859-3298, Japan
| | - Ryosuke Kai
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Kakeru Kurata
- Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3-3165 Higashi-tamagawagakuen, Machida 194-8543, Japan
| | - Satoru Karasawa
- Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3-3165 Higashi-tamagawagakuen, Machida 194-8543, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.,Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo 859-3298, Japan
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10
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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11
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Wiegand T, Schledorn M, Malär AA, Cadalbert R, Däpp A, Terradot L, Meier BH, Böckmann A. Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy. Chembiochem 2020; 21:324-330. [PMID: 31310428 PMCID: PMC7318265 DOI: 10.1002/cbic.201900439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 12/16/2022]
Abstract
Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.
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Affiliation(s)
- Thomas Wiegand
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Maarten Schledorn
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander A. Malär
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Riccardo Cadalbert
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander Däpp
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Laurent Terradot
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRS/Université de Lyon7 Passage du vercors69367LyonFrance
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12
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Müller WEG, Neufurth M, Schepler H, Wang S, Tolba E, Schröder HC, Wang X. The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor. Biomater Sci 2020; 8:6603-6610. [DOI: 10.1039/d0bm01244k] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
The polymer polyphosphate, abundant in blood platelets, blocks the binding of the receptor-binding domain (RBD) of the SARS- spike (S)-protein to the angiotensin-converting enzyme 2 (ACE2) at low concentrations.
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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
- 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
- 55128 Mainz
- Germany
| | - Hadrian Schepler
- Department of Dermatology
- University Clinic Mainz
- 55131 Mainz
- Germany
| | - Shunfeng Wang
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry
- University Medical Center of the Johannes Gutenberg University
- 55128 Mainz
- Germany
| | - Emad Tolba
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry
- University Medical Center of the Johannes Gutenberg University
- 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
- 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
- 55128 Mainz
- Germany
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13
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Wiegand T, Cadalbert R, Lacabanne D, Timmins J, Terradot L, Böckmann A, Meier BH. The conformational changes coupling ATP hydrolysis and translocation in a bacterial DnaB helicase. Nat Commun 2019; 10:31. [PMID: 30604765 PMCID: PMC6318325 DOI: 10.1038/s41467-018-07968-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/10/2018] [Indexed: 11/08/2022] Open
Abstract
DnaB helicases are motor proteins that couple ATP-hydrolysis to the loading of the protein onto DNA at the replication fork and to translocation along DNA to separate double-stranded DNA into single strands during replication. Using a network of conformational states, arrested by nucleotide mimics, we herein characterize the reaction coordinates for ATP hydrolysis, DNA loading and DNA translocation using solid-state NMR spectroscopy. AMP-PCP is used as pre-hydrolytic, ADP:AlF4- as transition state, and ADP as post-hydrolytic ATP mimic. 31P and 13C NMR spectra reveal conformational and dynamic responses to ATP hydrolysis and the resulting DNA loading and translocation with single amino-acid resolution. This allows us to identify residues guiding the DNA translocation process and to explain the high binding affinities for DNA observed for ADP:AlF4-, which turns out to be optimally preconfigured to bind DNA.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Denis Lacabanne
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Joanna Timmins
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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14
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Wiegand T, Liao WC, Ong TC, Däpp A, Cadalbert R, Copéret C, Böckmann A, Meier BH. Protein-nucleotide contacts in motor proteins detected by DNP-enhanced solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 69:157-164. [PMID: 29119516 DOI: 10.1007/s10858-017-0144-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
DNP (dynamic nuclear polarization)-enhanced solid-state NMR is employed to directly detect protein-DNA and protein-ATP interactions and identify the residue type establishing the intermolecular contacts. While conventional solid-state NMR can detect protein-DNA interactions in large oligomeric protein assemblies in favorable cases, it typically suffers from low signal-to-noise ratios. We show here, for the oligomeric DnaB helicase from Helicobacter pylori complexed with ADP and single-stranded DNA, that this limitation can be overcome by using DNP-enhanced spectroscopy. Interactions are established by DNP-enhanced 31P-13C polarization-transfer experiments followed by the recording of a 2D 13C-13C correlation experiment. The NMR spectra were obtained in less than 2 days and allowed the identification of residues of the motor protein involved in nucleotide binding.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Wei-Chih Liao
- Department of Chemistry and Applied Biosciences - Inorganic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Ta Chung Ong
- Department of Chemistry and Applied Biosciences - Inorganic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Alexander Däpp
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Christophe Copéret
- Department of Chemistry and Applied Biosciences - Inorganic Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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15
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Yusufaly TI, Li Y, Singh G, Olson WK. Arginine-phosphate salt bridges between histones and DNA: intermolecular actuators that control nucleosome architecture. J Chem Phys 2015; 141:165102. [PMID: 25362343 DOI: 10.1063/1.4897978] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.
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Affiliation(s)
- Tahir I Yusufaly
- Department of Physics and Astronomy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Yun Li
- Department of Chemistry and Biochemistry, Delaware Valley College, Doylestown, Pennsylvania 18901, USA
| | - Gautam Singh
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
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16
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Vener MV, Odinokov AV, Wehmeyer C, Sebastiani D. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. J Chem Phys 2015; 142:215106. [DOI: 10.1063/1.4922165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. V. Vener
- Mendeleev University of Chemical Technology, Moscow, Russia
| | - A. V. Odinokov
- Photochemistry Center of the Russian Academy of Sciences, Moscow, Russia
| | | | - D. Sebastiani
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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17
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Xue Y, Yuwen T, Zhu F, Skrynnikov NR. Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos. Biochemistry 2014; 53:6473-95. [PMID: 25207671 DOI: 10.1021/bi500904f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intrinsically disordered proteins (IDPs) often rely on electrostatic interactions to bind their structured targets. To obtain insight into the mechanism of formation of the electrostatic encounter complex, we investigated the binding of the peptide Sos (PPPVPPRRRR), which serves as a minimal model for an IDP, to the c-Crk N-terminal SH3 domain. Initially, we measured ¹⁵N relaxation rates at two magnetic field strengths and determined the binding shifts for the complex of Sos with wild-type SH3. We have also recorded a 3 μs molecular dynamics (MD) trajectory of this complex using the Amber ff99SB*-ILDN force field. The comparison of the experimental and simulated data shows that MD simulation consistently overestimates the strength of salt bridge interactions at the binding interface. The series of simulations using other advanced force fields also failed to produce any satisfactory results. To address this issue, we have devised an empirical correction to the Amber ff99SB*-ILDN force field whereby the Lennard-Jones equilibrium distance for the nitrogen-oxygen pair across the Arg-to-Asp and Arg-to-Glu salt bridges has been increased by 3%. Implementing this correction resulted in a good agreement between the simulations and the experiment. Adjusting the strength of salt bridge interactions removed a certain amount of strain contained in the original MD model, thus improving the binding of the hydrophobic N-terminal portion of the peptide. The arginine-rich C-terminal portion of the peptide, freed from the effect of the overstabilized salt bridges, was found to interconvert more rapidly between its multiple conformational states. The modified MD protocol has also been successfully used to simulate the entire binding process. In doing so, the peptide was initially placed high above the protein surface. It then arrived at the correct bound pose within ∼2 Å of the crystallographic coordinates. This simulation allowed us to analyze the details of the dynamic binding intermediate, i.e., the electrostatic encounter complex. However, an experimental characterization of this transient, weakly populated state remains out of reach. To overcome this problem, we designed the double mutant of c-Crk N-SH3 in which mutations Y186L and W169F abrogate tight Sos binding and shift the equilibrium toward the intermediate state resembling the electrostatic encounter complex. The results of the combined NMR and MD study of this engineered system will be reported in the next part of this paper.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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18
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Li L, Vorobyov I, Allen TW. The different interactions of lysine and arginine side chains with lipid membranes. J Phys Chem B 2013; 117:11906-20. [PMID: 24007457 DOI: 10.1021/jp405418y] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The basic amino acids lysine (Lys) and arginine (Arg) play important roles in membrane protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin, and cell-penetrating peptides. These roles are thought to stem from the strong interactions and disruptive influences of these amino acids on lipid membranes. In this study, we employ fully atomistic molecular dynamics simulations to observe, quantify, and compare the interactions of Lys and Arg with saturated phosphatidylcholine membranes of different thickness. We make use of both charged (methylammonium and methylguanidinium) and neutral (methylamine and methylguanidine) analogue molecules, as well as Lys and Arg side chains on transmembrane helix models. We find that the free energy barrier experienced by a charged Lys crossing the membrane is strikingly similar to that of a charged Arg (to within 2 kcal/mol), despite the two having different chemistries, H-bonding capability, and hydration free energies that differ by ∼10 kcal/mol. In comparison, the barrier for neutral Arg is higher than that for neutral Lys by around 5 kcal/mol, being more selective than that for the charged species. This can be explained by the different transport mechanisms for charged or neutral amino acid side chains in the membrane, involving membrane deformations or simple dehydration, respectively. As a consequence, we demonstrate that Lys would be deprotonated in the membrane, whereas Arg would maintain its charge. Our simulations also reveal that Arg attracts more phosphate and water in the membrane, and can form extensive H-bonding with its five H-bond donors to stabilize Arg-phosphate clusters. This leads to enhanced interfacial binding and membrane perturbations, including the appearance of a trans-membrane pore in a thinner membrane. These results highlight the special role played by Arg as an amino acid to bind to, disrupt, and permeabilize lipid membranes, as well as to sense voltages for a range of peptide and protein activities in nature and in engineered bionanodevices.
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Affiliation(s)
- Libo Li
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
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19
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Ahmedli NB, Gribanova Y, Njoku CC, Naidu A, Young A, Mendoza E, Yamashita CK, Özgül RK, Johnson JE, Fox DA, Farber DB. Dynamics of the rhomboid-like protein RHBDD2 expression in mouse retina and involvement of its human ortholog in retinitis pigmentosa. J Biol Chem 2013; 288:9742-9754. [PMID: 23386608 DOI: 10.1074/jbc.m112.419960] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The novel rhomboid-like protein RHBDD2 is distantly related to rhomboid proteins, a group of highly specialized membrane-bound proteases that catalyze regulated intramembrane proteolysis. In retina, RHBDD2 is expressed from embryonic stages to adulthood, and its levels show age-dependent changes. RHBDD2 is distinctly abundant in the perinuclear region of cells, and it localizes to their Golgi. A glycine zipper motif present in one of the transmembrane domains of RHBDD2 is important for its packing into the Golgi membranes. Its deletion causes dislodgment of RHBDD2 from the Golgi. A specific antibody against RHBDD2 recognizes two forms of the protein, one with low (39 kDa; RHBDD2(L)) and the other with high (117 kDa; RHBDD2H) molecular masses in mouse retinal extracts. RHBDD2(L) seems to be ubiquitously expressed in all retinal cells. In contrast, RHBDD2H seems to be present only in the outer segments of cone photoreceptors and may correspond to a homotrimer of RHBDD2(L). This protein consistently co-localizes with S- and M-types of cone opsins. We identified a homozygous mutation in the human RHBDD2 gene, R85H, that co-segregates with disease in affected members of a family with autosomal recessive retinitis pigmentosa. Our findings suggest that the RHBDD2 protein plays important roles in the development and normal function of the retina.
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Affiliation(s)
| | | | - Collins C Njoku
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | - Akash Naidu
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | - Alejandra Young
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | | | | | - Riza Köksal Özgül
- Department of Molecular Biology, Hacettepe University, 06230 Beytepe-Ankara, Turkey
| | - Jerry E Johnson
- Department of Natural Sciences, University of Houston-Downtown, Houston, Texas 77002
| | - Donald A Fox
- College of Optometry, University of Houston, Houston, Texas 77004; Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004; Department of Pharmacology and Pharmaceutical Sciences, University of Houston, Houston, Texas 77004
| | - Debora B Farber
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095; Brain Research Institute, UCLA, Los Angeles, California 90095
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20
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Zhou JY, Lu GX. L-Arginine and zinc ion effect on recognition and hydrolysis rate of adenosine 5′-triphosphate. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.713943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jin-Ying Zhou
- a State Key Laboratory for Oxo Synthesis and Selective Oxidation , Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences , Lanzhou , Gansu 730000 , China
- b Graduate University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Gong-Xuan Lu
- a State Key Laboratory for Oxo Synthesis and Selective Oxidation , Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences , Lanzhou , Gansu 730000 , China
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21
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Chen CT, Wang LY, Ho YP. Use of polyethylenimine-modified magnetic nanoparticles for highly specific enrichment of phosphopeptides for mass spectrometric analysis. Anal Bioanal Chem 2011; 399:2795-806. [DOI: 10.1007/s00216-010-4623-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 11/25/2010] [Accepted: 12/17/2010] [Indexed: 10/18/2022]
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22
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New SY, Thio Y, Koh LL, Andy Hor TS, Xue F. Supramolecular assembly of a new series of copper-l-arginine Schiff bases. CrystEngComm 2011. [DOI: 10.1039/c0ce00444h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Sun VZ, Li Z, Deming TJ, Kamei DT. Intracellular fates of cell-penetrating block copolypeptide vesicles. Biomacromolecules 2010; 12:10-3. [PMID: 21128599 DOI: 10.1021/bm101036f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The block copolypeptide poly(l-homoarginine)(60)-b-poly(l-leucine)(20) (R(60)L(20)) was previously found to self-assemble into versatile vesicles with controllable size and encapsulate hydrophilic cargo. These R(60)L(20) vesicles also demonstrated the ability to cross the cell membrane and transport encapsulated cargo into different cell lines. To assess the potential for using the R(60)L(20) vesicles as drug delivery vehicles further, we have investigated their endocytosis and intracellular trafficking behavior. Using drugs that inhibit different endocytosis pathways, we identified macropinocytosis to be a major process by which the R(60)L(20) vesicles enter HeLa cells. Subsequent immunostaining experiments demonstrated that the vesicles entered the early endosomes but not the lysosomes, suggesting that they recycle back to the cell surface. Overall, our studies indicate that the R(60)L(20) vesicles are able to enter cells intact with their cargos, and although some manage to escape from early endosomes, most are trapped within these intracellular compartments.
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Affiliation(s)
- Victor Z Sun
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
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24
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Jezierska A, Panek J, Borstnik U, Mavri J, Janezic D. Car−Parrinello Molecular Dynamics Study of Anharmonic Systems: A Mannich Base in Solution. J Phys Chem B 2007; 111:5243-8. [PMID: 17447809 DOI: 10.1021/jp068676p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A Car-Parrinello molecular dynamics study was performed for 4,5-dimethyl-2-(N,N-dimethylaminomethyl)phenol, a Mannich base, to investigate the vibrational properties in solution of its intramolecular hydrogen bond. The dynamic behavior of this hydrogen-bonded system was investigated using an explicit solvent model. Addition of a nonpolar solvent permitted inclusion of delicate environmental effects on the strongly anharmonic system which was studied from first principles. Molecular dynamics and a posteriori quantization of the O-H motion were applied to reproduce the vibrational features of the O-H stretching mode. Consistent application of Car-Parrinello dynamics based on the density functional theory with subsequent solution of the vibrational Schrödinger equation for the O-H stretching motion offers an effective method for strongly anharmonic systems, and this is supported by the comparison of the results with experimental spectra. As a further element of the intramolecular hydrogen bond study, the effects of deuteration were taken into account and a successful application of the O-H stretching mode quantization technique to the liquid phase is demonstrated. This provides a valuable computational methodology for investigations incorporating nuclear quantum effects in the liquid phase and enzyme active centers and can be used to investigate numerous systems that are not readily susceptible to experimental analysis.
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Affiliation(s)
- Aneta Jezierska
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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25
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Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP. Strengths of hydrogen bonds involving phosphorylated amino acid side chains. J Am Chem Soc 2007; 129:820-7. [PMID: 17243818 DOI: 10.1021/ja063019w] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational phosphorylation plays a key role in regulating protein function. Here, we provide a quantitative assessment of the relative strengths of hydrogen bonds involving phosphorylated amino acid side chains (pSer, pAsp) with several common donors (Arg, Lys, and backbone amide groups). We utilize multiple levels of theory, consisting of explicit solvent molecular dynamics, implicit solvent molecular mechanics, and quantum mechanics with a self-consistent reaction field treatment of solvent. Because the approximately 6 pKa of phosphate suggests that -1 and -2 charged species may coexist at physiological pH, hydrogen bonds involving both protonated and deprotonated phosphates for all donor-acceptor pairs are considered. Multiple bonding geometries for the charged-charged interactions are also considered. Arg is shown to be capable of substantially stronger salt bridges with phosphorylated side chains than Lys. A pSer hydrogen-bond acceptor tends to form more stable interactions than a pAsp acceptor. The effect of phosphate protonation state on the strengths of the hydrogen bonds is remarkably subtle, with a more pronounced effect on pAsp than on pSer.
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Affiliation(s)
- Daniel J Mandell
- Graduate Program in Biological and Medical Informatics, Department of Pharmaceutical Chemistry, and Graduate Group in Biophysics, University of California, San Francisco, California 94143, USA
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26
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Pradhan P, Ghose R, Green ME. Voltage gating and anions, especially phosphate: a model system. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1717:97-103. [PMID: 16289371 DOI: 10.1016/j.bbamem.2005.09.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 09/19/2005] [Accepted: 09/21/2005] [Indexed: 11/29/2022]
Abstract
The voltage sensor of voltage gated sodium and potassium channels consists of four sets of transmembrane segments, of which one, called S4, contains at least four arginines; these are presumed to each carry positive charges. The channel opening is usually attributed to the outward (i.e., toward the extracellular side of the membrane) motion of S4. The evidence for this motion is based on certain experiments that appear to show differential access to parts of S4 from the intracellular and extracellular sides of the membrane in the open and closed states. A newly available structure [S.B. Long, E.B. Campbell and R. MacKinnon, Crystal structure of a mammalian voltage-dependent Shaker family K(+) channel. Science 309 (2005) 897-903; S.B. Long, E.B. Campbell, R. MacKinnon, Voltage sensor of Kv1.2: structural basis of electromechanical coupling. Science 309 (2005) 903-908][1,2] has now been used to argue for a large scale motion, although, as a static structure, it is not conclusive. In this paper, we consider the effect of anions in the surrounding medium. Phosphate is present in the intracellular as well as the extracellular fluid, apparently at hundreds of micromolar concentration, or more. There is evidence in the literature suggesting that phosphate-arginine complexes are rather strong. In a recent calculation one of us [M.E. Green, A possible role for phosphate in complexing the arginines of S4 in voltage gated channels J. Theor. Biol. 233 (2005) 337-341][3] has shown that a model peptide with a 2:1 arg:phosphate complex should have a favorable geometry. Here, we present NMR evidence of the existence of phosphate complexes of a model peptide with two arginines separated by two hydrophobic residues, the same spacing as in S4 segments. The complexes (there are different complexes for HPO(4)(2-) and for H(2)PO(4)(-) [3]) form with concentrations of peptide in the range of hundreds of micromolar, making it significant in the biological context. NMR spectra provide changes in chemical shift as functions of both phosphate concentration and pH. The resulting curves show titration of the phosphate, with its standard pK. Possible implications for other anion-S4 interactions, including ion pairs rather than complexes, as with Cl(-), are also discussed.
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Affiliation(s)
- Padmanava Pradhan
- Department of Chemistry, City College of the City University of New York, New York, NY 10031, USA
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27
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Schug KA, Lindner W. Noncovalent binding between guanidinium and anionic groups: focus on biological- and synthetic-based arginine/guanidinium interactions with phosph[on]ate and sulf[on]ate residues. Chem Rev 2005; 105:67-114. [PMID: 15720152 DOI: 10.1021/cr040603j] [Citation(s) in RCA: 459] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin A Schug
- University of Vienna, Department of Analytical Chemistry, Währingerstrasse 38, A-1090 Vienna, Austria.
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28
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Green ME. A possible role for phosphate in complexing the arginines of S4 in voltage gated channels. J Theor Biol 2004; 233:337-41. [PMID: 15652143 DOI: 10.1016/j.jtbi.2004.10.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 09/24/2004] [Accepted: 10/08/2004] [Indexed: 11/19/2022]
Abstract
Phosphate ions are known to complex guanidinium groups, which are the side chains of arginine. Voltage gated channels that allow passage of ions through cell membranes, producing, for example the nerve impulse, are in many cases composed of four domains, each with six transmembrane segments. The S4 transmembrane segments of these channels have arginines placed in such a way that they would be expected to complex phosphate. Known phosphate-arginine complexes are reasonably strong. Here, an ab initio calculation reinforces the expectation that a strong complex could form. As a consequence, if the S4 moved, it would carry either no charge, or at most half of what is expected from fully charged arginines. This suggests that it may be necessary to rethink voltage gating models in which the gating current is produced by physical motion of the S4 transmembrane segments.
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Affiliation(s)
- Michael E Green
- Department of Chemistry, City College of the City University of New York, New York, NY 10031, USA.
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29
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Saiz L, Klein ML. The transmembrane domain of the acetylcholine receptor: insights from simulations on synthetic peptide models. Biophys J 2004; 88:959-70. [PMID: 15556982 PMCID: PMC1305168 DOI: 10.1529/biophysj.104.049726] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the structure and properties of a bundle of alpha-helical peptides embedded in a 1,2-dimyristoyl-3-phosphatidylcholine phospholipid bilayer by molecular dynamics simulations. The bundle of five transmembrane deltaM2 segments constitutes the model for the pore region of the nicotinic acetylcholine receptor, which is the neurotransmitter-gated ion-channel responsible for the fast propagation of electrical signals between cells at the nerve-muscle synapse. The deltaM2 segments were shown to oligomerize in biomembranes resulting in ion-channel activity with characteristics similar to the native protein, and the structure of the isolated peptides was studied in 1,2-dimyristoyl-3-phosphatidylcholine bilayers and micelles by NMR experiments (Opella, S. J., et al. 1999. Nat. Struct. Biol. 6:374-379). Our analyses indicate that the structure, helix tilt, and the overall shape of the channel are in good agreement with the NMR experiments and the proposed model for the channel, which we show is formed by rings of functional residues. The studied geometry resulted in a closed pore state, where the channel is partially dehydrated at the hydrophobic extracellular half and the extracellular mouth of the channel blocked by the hydrocarbon chains of Arg+ residues. The arginine amino acids form intermolecular salt-bridges with the C-terminus, which contribute as well to the bundle stabilization.
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Affiliation(s)
- Leonor Saiz
- Center for Molecular Modeling, Chemistry Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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