1
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Sun JW, Thomas JS, Monkovic JM, Gibson H, Nagapurkar A, Frezzo JA, Katyal P, Punia K, Mahmoudinobar F, Renfrew PD, Montclare JK. Supercharged coiled-coil protein with N-terminal decahistidine tag boosts siRNA complexation and delivery efficiency of a lipoproteoplex. J Pept Sci 2024; 30:e3594. [PMID: 38499991 DOI: 10.1002/psc.3594] [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: 11/30/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Short interfering RNA (siRNA) therapeutics have soared in popularity due to their highly selective and potent targeting of faulty genes, providing a non-palliative approach to address diseases. Despite their potential, effective transfection of siRNA into cells requires the assistance of an accompanying vector. Vectors constructed from non-viral materials, while offering safer and non-cytotoxic profiles, often grapple with lackluster loading and delivery efficiencies, necessitating substantial milligram quantities of expensive siRNA to confer the desired downstream effects. We detail the recombinant synthesis of a diverse series of coiled-coil supercharged protein (CSP) biomaterials systematically designed to investigate the impact of two arginine point mutations (Q39R and N61R) and decahistidine tags on liposomal siRNA delivery. The most efficacious variant, N8, exhibits a twofold increase in its affinity to siRNA and achieves a twofold enhancement in transfection activity with minimal cytotoxicity in vitro. Subsequent analysis unveils the destabilizing effect of the Q39R and N61R supercharging mutations and the incorporation of C-terminal decahistidine tags on α-helical secondary structure. Cross-correlational regression analyses reveal that the amount of helical character in these mutants is key in N8's enhanced siRNA complexation and downstream delivery efficiency.
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Affiliation(s)
- Jonathan W Sun
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph S Thomas
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Julia M Monkovic
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Halle Gibson
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Akash Nagapurkar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph A Frezzo
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Kamia Punia
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Jin Kim Montclare
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Radiology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Biomaterials, NYU College of Dentistry, New York, New York, USA
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2
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Liu Y, Cui S, Ma W, Wu Y, Xin R, Bai Y, Chen Z, Xu J, Ge J. Direct Imaging of Protein Clusters in Metal-Organic Frameworks. J Am Chem Soc 2024; 146:12565-12576. [PMID: 38661569 DOI: 10.1021/jacs.4c01483] [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: 04/26/2024]
Abstract
Protein@metal-organic frameworks (P@MOFs) prepared by coprecipitation of protein, metal ions, and organic ligands represent an effective method for protein stabilization with a wide spectrum of applications. However, the formation mechanism of P@MOFs via the coprecipitation process and the reason why proteins can retain their biological activity in the frameworks with highly concentrated metal ions remain unsettled. Here, by a combined methodology of single molecule localization microscopy and clustering analysis, we discovered that in this process enzyme molecules form clusters with metal ions and organic ligands, contributing to both the nucleation and subsequent crystal growth. We proposed that the clusters played an important role in the retention of overall enzymatic activity by sacrificing protein molecules on the cluster surface. This work offers fresh perspectives on protein behaviors in the formation of P@MOFs, inspiring future endeavors in the design and development of artificial bionanocomposites with high biological activities.
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Affiliation(s)
- Yu Liu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Shitong Cui
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Wenjun Ma
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yibo Wu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ruobing Xin
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yunxiu Bai
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Zhuo Chen
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jianhong Xu
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jun Ge
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
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3
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Zaorska E, Malinska M. Cucurbit[7]uril-mediated Histidine Dimerization: Exploring the Structure and Binding Mechanism. Chemistry 2024; 30:e202302250. [PMID: 38055216 DOI: 10.1002/chem.202302250] [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: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Cucurbit[7,8]urils are known to form inclusion complexes with hydrophobic amino acids such as Trp, Tyr, Phe, and Met, as well as peptides containing these residues at the N-terminus. Despite their widespread use in protein purification, the affinity of histidine (His) for cucurbit[7,8]urils has not been extensively explored. In this study, X-ray diffraction experiments were conducted to investigate the binding of two histidine moieties to the cucurbit[7]uril (CB7) cavity, resulting in a network of π-π and hydrogen bonds. This assembly was found to induce a His pKa shift of ΔpKa=-4. Histidine weakly bound to CB7 or CB8; however, isothermal titration calorimetry revealed micromolar equilibrium dissociation constant values for CB7 and CB8 when bound to dipeptides containing His at the C-terminus. Conversely, dipeptides with His at the N-terminus exhibited millimolar values. Additionally, the His-Gly-Gly tripeptide formed a 2 : 1 complex with CB7. These findings suggest the potential use of histidine and histidine-containing tags in conjunction with CB7 for various biological applications.
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Affiliation(s)
- Ewelina Zaorska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Maura Malinska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
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4
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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5
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Sam S, Sung S, Krem S, Park S, Hwang DS, Kim D. Sum-Frequency Vibrational Spectroscopic Study of the Cation-π Interaction: Amine and Guanidine. J Phys Chem B 2022; 126:7621-7626. [PMID: 36166344 DOI: 10.1021/acs.jpcb.2c05709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cation-π interaction is an interaction between a positively charged cation and π electrons in an aromatic group of a molecule. It is considered to play key roles in signal transduction, stabilization of the protein structure, enzyme catalysis in biology, and wet adhesion and biomolecular condensation. In this study, octadecylguanidine hydrochloride (ODG) and octadecylamine (ODA) having guanidine and amine headgroups, respectively, are found to interact with π molecules (phenol or indole) as investigated by sum-frequency vibrational spectroscopy. ODG is unstable and does not form a neat monolayer on the water surface. However, after adding π molecules into subphase water, it becomes more stable against dissolution as evidenced by the appearance of its CHx peaks and a CH peak of the aromatic ring in the sum-frequency spectrum. Unlike ODG, ODA forms a stable monolayer on the water surface at a neutral pH. After adding π molecules into the solution, the amine-π interaction promotes the protonation of the amine headgroup and the penetration of the π molecules makes the ODA monolayer more disordered. Indole is found to be more effective in binding with the ODG as compared to phenol.
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Affiliation(s)
- Sokhuoy Sam
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Siheon Sung
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Sona Krem
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Sohee Park
- Division of Environmental Science and Engineering (DESE), Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Namgu, Pohang 37673, Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering (DESE), Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Namgu, Pohang 37673, Korea
| | - Doseok Kim
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
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6
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Liang J, Bin Zulkifli MY, Yong J, Du Z, Ao Z, Rawal A, Scott JA, Harmer JR, Wang J, Liang K. Locking the Ultrasound-Induced Active Conformation of Metalloenzymes in Metal-Organic Frameworks. J Am Chem Soc 2022; 144:17865-17875. [PMID: 36075889 DOI: 10.1021/jacs.2c06471] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enhancing the enzymatic activity inside metal-organic frameworks (MOFs) is a critical challenge in chemical technology and bio-technology, which, if addressed, will broaden their scope in energy, food, environmental, and pharmaceutical industries. Here, we report a simple yet versatile and effective strategy to optimize biocatalytic activity by using MOFs to rapidly "lock" the ultrasound (US)-activated but more fragile conformation of metalloenzymes. The results demonstrate that up to 5.3-fold and 9.3-fold biocatalytic activity enhancement of the free and MOF-immobilized enzymes could be achieved compared to those without US pretreatment, respectively. Using horseradish peroxidase as a model, molecular dynamics simulation demonstrates that the improved activity of the enzyme is driven by an opened gate conformation of the heme active site, which allows more efficient substrate binding to the enzyme. The intact heme active site is confirmed by solid-state UV-vis and electron paramagnetic resonance, while the US-induced enzyme conformation change is confirmed by circular dichroism spectroscopy and Fourier-transform infrared spectroscopy. In addition, the improved activity of the biocomposites does not compromise their stability upon heating or exposure to organic solvent and a digestion cocktail. This rapid locking and immobilization strategy of the US-induced active enzyme conformation in MOFs gives rise to new possibilities for the exploitation of highly efficient biocatalysts for diverse applications.
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Affiliation(s)
- Jieying Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney 2052, New South Wale, Australia
| | - Muhammad Yazid Bin Zulkifli
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney 2052, New South Wale, Australia
| | - Joel Yong
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney 2052, New South Wale, Australia.,Graduate School of Biomedical Engineering, The University of New South Wales, Sydney 2052, New South Wale, Australia
| | - Zeping Du
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney 2052, New South Wale, Australia
| | - Zhimin Ao
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai, 519087, China
| | - Aditya Rawal
- Nuclear Magnetic Resonance Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney 2052, New South Wale Australia
| | - Jason A Scott
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney 2052, New South Wale, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, The University of Queensland, Brisbane 4072, Queensland Australia
| | - Joseph Wang
- Department of Nanoengineering, University of California San Diego, La Jolla 92093, California, United States
| | - Kang Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Sydney 2052, New South Wale, Australia.,Graduate School of Biomedical Engineering, The University of New South Wales, Sydney 2052, New South Wale, Australia
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7
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Sahoo BR, Souders CL, Watanabe-Nakayama T, Deng Z, Linton H, Suladze S, Ivanova MI, Reif B, Ando T, Martyniuk CJ, Ramamoorthy A. Conformational Tuning of Amylin by Charged Styrene-Maleic-Acid Copolymers. J Mol Biol 2022; 434:167385. [PMID: 34883118 PMCID: PMC8752516 DOI: 10.1016/j.jmb.2021.167385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 02/01/2023]
Abstract
Human amylin forms structurally heterogeneous amyloids that have been linked to type-2 diabetes. Thus, understanding the molecular interactions governing amylin aggregation can provide mechanistic insights in its pathogenic formation. Here, we demonstrate that fibril formation of amylin is altered by synthetic amphipathic copolymer derivatives of the styrene-maleic-acid (SMAQA and SMAEA). High-speed AFM is used to follow the real-time aggregation of amylin by observing the rapid formation of de novo globular oligomers and arrestment of fibrillation by the positively-charged SMAQA. We also observed an accelerated fibril formation in the presence of the negatively-charged SMAEA. These findings were further validated by fluorescence, SOFAST-HMQC, DOSY and STD NMR experiments. Conformational analysis by CD and FT-IR revealed that the SMA copolymers modulate the conformation of amylin aggregates. While the species formed with SMAQA are α-helical, the ones formed with SMAEA are rich in β-sheet structure. The interacting interfaces between SMAEA or SMAQA and amylin are mapped by NMR and microseconds all-atom MD simulation. SMAEA displayed π-π interaction with Phe23, electrostatic π-cation interaction with His18 and hydrophobic packing with Ala13 and Val17; whereas SMAQA showed a selective interaction with amylin's C terminus (residues 31-37) that belongs to one of the two β-sheet regions (residues 14-19 and 31-36) involved in amylin fibrillation. Toxicity analysis showed both SMA copolymers to be non-toxic in vitro and the amylin species formed with the copolymers showed minimal deformity to zebrafish embryos. Together, this study demonstrates that chemical tools, such as copolymers, can be used to modulate amylin aggregation, alter the conformation of species.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Zhou Deng
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Hunter Linton
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Saba Suladze
- Department of Chemistry, Technische Universität München, Garching 85748, Germany
| | - Magdalena I Ivanova
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Bernd Reif
- Department of Chemistry, Technische Universität München, Garching 85748, Germany
| | - Toshio Ando
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 9201192, Japan
| | - Christopher J Martyniuk
- Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, The University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109, USA.
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8
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Uddin M, Swathi KV, Anil A, Boopathy R, Ramani K, Sekaran G. Biosequestration of lignin in municipal landfill leachate by tailored cationic lipoprotein biosurfactant through Bacillus tropicus valorized tannery solid waste. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 300:113755. [PMID: 34537555 DOI: 10.1016/j.jenvman.2021.113755] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/28/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Bioremediation of municipal landfill leachate (MLL) is often intricate due to presence of refractory lignin. In the present study, it was attempted to tailor the histidine rich protein moiety of cationic lipoprotein biosurfactant (CLB) to sequester the lignin from MLL. Animal fleshing (AF), the solid waste generated in tanning industry was utilized for the production of histidine rich CLB by de novo substrate dependent synthesis pathway involving Bacillus tropicus. The optimum conditions for the maximum production of CLB were determined using response surface methodology. At the optimized conditions, the maximum yield of CLB was 217.4 mg/g AF (on dry basis). The produced histidine rich CLB was purified using Immobilized metal affinity chromatography at the optimum binding and elution conditions. The histidine residues were more pronounced in the CLB, as determined by HPLC analysis. The CLB was further characterized by SDS-PAGE, Zeta potential, XRD, FT-IR, Raman, NMR, GC-MS and TG analyses. The CLB was immobilized onto functionalized nanoporous activated bio carbon (FNABC) and the optimum immobilization capacity was found to be 211.6 mg/g FNABC. The immobilization of CLB onto FNABC was confirmed using SEM, FT-IR, XRD and TG analyses. The isotherm models, kinetic and thermodynamics studies of CLB immobilization onto FNABC were performed to evaluate its field level application. Subsequently, the CLB-FNABC was then applied for the sequestration of lignin in MLL. The maximum lignin sequestration was achieved by 92.5 mg/g CLB-FNABC at the optimized sequestration time, 180 min; pH, 5; temperature, 45 °C and mass of CLB-FNABC, 1.0 g. The sequestration of lignin by CLB- FNABC was confirmed by SEM, FT-IR and UV-Vis analyses. Further, the mechanistic study revealed the anchoring of CLB onto the surface of lignin through electrostatic interaction.
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Affiliation(s)
- Maseed Uddin
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - K V Swathi
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - Ananya Anil
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - R Boopathy
- Environment & Sustainability Department, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, 751013, Odisha, India
| | - K Ramani
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India.
| | - G Sekaran
- SRM Institute of Science and Technology, Ramapuram, 600089, Tamil Nadu, India
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9
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Liu Y, Cao X, Ge J. Antioxidative Composites Based on Multienzyme Systems Encapsulated in Metal-Organic Frameworks. ACS APPLIED MATERIALS & INTERFACES 2021; 13:46431-46439. [PMID: 34551515 DOI: 10.1021/acsami.1c15506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Skin is exposed to ultraviolet radiation from the sun constantly, which may induce overproduction of reactive oxygen species (ROS) causing oxidative stress to cells and tissues. Enzymes and small molecules work together to maintain the redox homeostasis, among which superoxide dismutase (SOD) and catalase (CAT) are two kinds of most important antioxidants that suffer from the fragile nature of proteins. Moreover, the proportion of two enzymes used in products must be precisely controlled to reduce the damage caused by the toxic intermediate H2O2. Metal-organic frameworks (MOFs) are emerging as promising candidates for multiple enzyme encapsulation due to their high porosity, easy synthesis, and good biocompatibility. Herein, we developed enzyme-MOF composites, SC@ZIF-8, which exhibited an excellent antioxidative activity in vitro. Chemically protective cages formed by MOFs endow the encapsulated enzymes the long-term stability under unnatural conditions in cosmetic and biomedical materials. The pH-dependent protein release profile of SC@ZIF-8 facilitated the successful delivery of enzymes into the cytoplasm to scavenge toxic ROS. The nanocomposites protected human cells from paraquat-induced oxidative stress, paving a new path for the stable and efficient application of antioxidative enzymes in cosmetic and dermatological fields.
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Affiliation(s)
- Yu Liu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xun Cao
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jun Ge
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518107, China
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10
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Mutations in PBP2 from ceftriaxone-resistant Neisseria gonorrhoeae alter the dynamics of the β3-β4 loop to favor a low-affinity drug-binding state. J Biol Chem 2021; 297:101188. [PMID: 34529975 PMCID: PMC8503634 DOI: 10.1016/j.jbc.2021.101188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/20/2022] Open
Abstract
Resistance to the extended-spectrum cephalosporin ceftriaxone in the pathogenic bacteria Neisseria gonorrhoeae is conferred by mutations in penicillin-binding protein 2 (PBP2), the lethal target of the antibiotic, but how these mutations exert their effect at the molecular level is unclear. Using solution NMR, X-ray crystallography, and isothermal titration calorimetry, we report that WT PBP2 exchanges dynamically between a low-affinity state with an extended β3–β4 loop conformation and a high-affinity state with an inward β3–β4 loop conformation. Histidine-514, which is located at the boundary of the β4 strand, plays an important role during the exchange between these two conformational states. We also find that mutations present in PBP2 from H041, a ceftriaxone-resistant strain of N. gonorrhoeae, increase resistance to ceftriaxone by destabilizing the inward β3–β4 loop conformation or stabilizing the extended β3–β4 loop conformation to favor the low-affinity drug-binding state. These observations reveal a unique mechanism for ceftriaxone resistance, whereby mutations in PBP2 lower the proportion of target molecules in the high-affinity drug-binding state and thus reduce inhibition at lower drug concentrations.
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11
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Sartor P, Denkhaus L, Gerhardt S, Einsle O, Fetzner S. Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis. J Struct Biol 2021; 213:107794. [PMID: 34506908 DOI: 10.1016/j.jsb.2021.107794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
The S-adenosyl-L-methionine-dependent methyltransferase Rv0560c of Mycobacterium tuberculosis belongs to an orthologous group of heterocyclic toxin methyltransferases (Htm) which likely contribute to resistance of mycobacteria towards antimicrobial natural compounds as well as drugs. HtmM.t. catalyzes the methylation of the Pseudomonas aeruginosa toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one (also known as 2-heptyl-4-hydroxyquinoline N-oxide), a potent inhibitor of respiratory electron transfer, its 1-hydroxyquinolin-4(1H)-one core (QNO), structurally related (iso)quinolones, and some mycobactericidal compounds. In this study, crystal structures of HtmM.t. in complex with S-adenosyl-L-homocysteine (SAH) and the methyl-accepting substrates QNO or 4-hydroxyisoquinoline-1(2H)-one, or the methylated product 1-methoxyquinolin-4(1H)-one, were determined at < 1.9 Å resolution. The monomeric protein exhibits the typical Rossmann fold topology and conserved residues of class I methyltransferases. Its SAH binding pocket is connected via a short tunnel to a large solvent-accessible cavity, which accommodates the methyl-accepting substrate. Residues W44, F168, and F208 in connection with F212 form a hydrophobic clamp around the heteroaromatic ring of the methyl-accepting substrate and likely play a major role in substrate positioning. Structural and biochemical data suggest that H139 and T136 are key active site residues, with H139 acting as general base that activates the methyl-accepting hydroxy group. Our structural data may contribute to the design of Htm inhibitors or of antimycobacterial drugs unamenable for methylation.
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Affiliation(s)
- Pascal Sartor
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
| | - Lukas Denkhaus
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Stefan Gerhardt
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Oliver Einsle
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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12
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Zhang W, Jia Q, Teng Y, Yang M, Zhang H, Zhang XE, Wang P, Ge J, Cao S, Li F. An Ultrastable Virus-Like Particle with a Carbon Dot Core and Expanded Sequence Plasticity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101717. [PMID: 34302443 DOI: 10.1002/smll.202101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/06/2021] [Indexed: 06/13/2023]
Abstract
Ordered bio-inorganic hybridization has evolved for the generation of high-performance materials in living organisms and inspires novel strategies to design artificial hybrid materials. Virus-like particles (VLPs) are attracting extensive interest as self-assembling systems and platforms in the fields of biotechnology and nanotechnology. However, as soft nanomaterials, their structural stability remains a general and fundamental problem in various applications. Here, an ultrastable VLP assembled from the major capsid protein (VP1) of simian virus 40 is reported, which contains a carbon dot (C-dot) core. Co-assembly of VP1 with C-dots led to homogeneous T = 1 VLPs with a fourfold increase in VLP yields. The resultant hybrid VLPs showed markedly enhanced structural stability and sequence plasticity. C-dots and a polyhistidine tag fused to the inner-protruding N-terminus of VP1 contributed synergistically to these enhancements, where extensive and strong noncovalent interactions on the C-dot/VP1 interfaces are responsible according to cryo-EM 3D reconstruction, molecular simulation, and affinity measurements. C-dot-enhanced ultrastable VLPs can serve as a new platform, enabling the fabrication of new architectures for bioimaging, theranostics, nanovaccines, etc. The hybridization strategy is simple and can easily be extended to other VLPs and protein nanoparticle systems.
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Affiliation(s)
- Wenjing Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingyan Jia
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yibo Teng
- Wuhan Ready science and technology corporation Ltd, Wuhan, 430064, China
| | - Mengsi Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-En Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Pengfei Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiechao Ge
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Sheng Cao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Deb I, Wong H, Tacubao C, Frank AT. Quantum Mechanics Helps Uncover Atypical Recognition Features in the Flavin Mononucleotide Riboswitch. J Phys Chem B 2021; 125:8342-8350. [PMID: 34310879 DOI: 10.1021/acs.jpcb.1c02702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Estimating the binding energies of small molecules to RNA could help uncover their molecular recognition characteristics and be used to rationally design RNA-targeting chemical probes. Here, we leveraged the ability of the fragment molecular orbital (FMO) method to provide detailed pairwise energetic information to examine the interactions between the aptamer domain of the flavin mononucleotide (FMN)-responsive riboswitch and small-molecule ligands. After developing an efficient protocol for executing high-level FMO calculations on RNA-ligand complexes, we applied our protocol to nine FMN-aptamer-ligand complexes. We then used the results to identify "hot-spots" within the aptamer and decomposed pairwise interactions between the hot-spot residues and the ligands. Interestingly, we found that several of these hot-spot residues interact with the ligands via atypical CH···O hydrogen bonds and anion-π contacts, as well as (face-to-edge) T-shaped π-π interactions. We envision that our results should pave the way for the wider and more prominent use of FMO calculations to study structure-energy relationships in diverse RNA-ligand systems, which in turn may provide a basis for dissecting the molecular recognition characteristics of RNAs.
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Affiliation(s)
- Indrajit Deb
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hazel Wong
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Colleen Tacubao
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aaron T Frank
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Chemistry Department, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Montiel V, Bella R, Michel LYM, Esfahani H, De Mulder D, Robinson EL, Deglasse JP, Tiburcy M, Chow PH, Jonas JC, Gilon P, Steinhorn B, Michel T, Beauloye C, Bertrand L, Farah C, Dei Zotti F, Debaix H, Bouzin C, Brusa D, Horman S, Vanoverschelde JL, Bergmann O, Gilis D, Rooman M, Ghigo A, Geninatti-Crich S, Yool A, Zimmermann WH, Roderick HL, Devuyst O, Balligand JL. Inhibition of aquaporin-1 prevents myocardial remodeling by blocking the transmembrane transport of hydrogen peroxide. Sci Transl Med 2021; 12:12/564/eaay2176. [PMID: 33028705 DOI: 10.1126/scitranslmed.aay2176] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 12/24/2019] [Accepted: 08/31/2020] [Indexed: 12/31/2022]
Abstract
Pathological remodeling of the myocardium has long been known to involve oxidant signaling, but strategies using systemic antioxidants have generally failed to prevent it. We sought to identify key regulators of oxidant-mediated cardiac hypertrophy amenable to targeted pharmacological therapy. Specific isoforms of the aquaporin water channels have been implicated in oxidant sensing, but their role in heart muscle is unknown. RNA sequencing from human cardiac myocytes revealed that the archetypal AQP1 is a major isoform. AQP1 expression correlates with the severity of hypertrophic remodeling in patients with aortic stenosis. The AQP1 channel was detected at the plasma membrane of human and mouse cardiac myocytes from hypertrophic hearts, where it colocalized with NADPH oxidase-2 and caveolin-3. We show that hydrogen peroxide (H2O2), produced extracellularly, is necessary for the hypertrophic response of isolated cardiac myocytes and that AQP1 facilitates the transmembrane transport of H2O2 through its water pore, resulting in activation of oxidant-sensitive kinases in cardiac myocytes. Structural analysis of the amino acid residues lining the water pore of AQP1 supports its permeation by H2O2 Deletion of Aqp1 or selective blockade of the AQP1 intrasubunit pore inhibited H2O2 transport in mouse and human cells and rescued the myocyte hypertrophy in human induced pluripotent stem cell-derived engineered heart muscle. Treatment of mice with a clinically approved AQP1 inhibitor, Bacopaside, attenuated cardiac hypertrophy. We conclude that cardiac hypertrophy is mediated by the transmembrane transport of H2O2 by the water channel AQP1 and that inhibitors of AQP1 represent new possibilities for treating hypertrophic cardiomyopathies.
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Affiliation(s)
- Virginie Montiel
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Ramona Bella
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Lauriane Y M Michel
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Hrag Esfahani
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Delphine De Mulder
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Emma L Robinson
- Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KULeuven, 3000 Leuven, Belgium
| | - Jean-Philippe Deglasse
- Institute of Experimental and Clinical Research (IREC), Endocrinology, Diabetes and Nutrition (EDIN), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Malte Tiburcy
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Pak Hin Chow
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Jean-Christophe Jonas
- Institute of Experimental and Clinical Research (IREC), Endocrinology, Diabetes and Nutrition (EDIN), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Patrick Gilon
- Institute of Experimental and Clinical Research (IREC), Endocrinology, Diabetes and Nutrition (EDIN), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Benjamin Steinhorn
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 2115, USA
| | - Thomas Michel
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 2115, USA
| | - Christophe Beauloye
- Institute of Experimental and Clinical Research (IREC), Pole of Cardiovascular Research (CARD), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Luc Bertrand
- Institute of Experimental and Clinical Research (IREC), Pole of Cardiovascular Research (CARD), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Charlotte Farah
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Flavia Dei Zotti
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Huguette Debaix
- Institute of Experimental and Clinical Research (IREC), Nephrology (NEFR), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium.,Institute of Physiology, University of Zürich, CH 8057 Zürich, Switzerland
| | - Caroline Bouzin
- 2IP-IREC Imaging Platform, Institute of Experimental and Clinical Research (IREC), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Davide Brusa
- Flow Cytometry Platform, Institute of Experimental and Clinical Research (IREC), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Sandrine Horman
- Institute of Experimental and Clinical Research (IREC), Pole of Cardiovascular Research (CARD), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Jean-Louis Vanoverschelde
- Institute of Experimental and Clinical Research (IREC), Pole of Cardiovascular Research (CARD), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Olaf Bergmann
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01062 Dresden, Germany.,Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Dimitri Gilis
- Computational Biology and Bioinformatics (3BIO-BioInfo), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics (3BIO-BioInfo), Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium
| | - Alessandra Ghigo
- Molecular Biotechnology Center, Università di Torino, 10124 Torino, Italy
| | | | - Andrea Yool
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Wolfram H Zimmermann
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, 37075 Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - H Llewelyn Roderick
- Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KULeuven, 3000 Leuven, Belgium
| | - Olivier Devuyst
- Institute of Experimental and Clinical Research (IREC), Nephrology (NEFR), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium.,Institute of Physiology, University of Zürich, CH 8057 Zürich, Switzerland
| | - Jean-Luc Balligand
- Institute of Experimental and Clinical Research (IREC), Pharmacology and Therapeutics (FATH), Cliniques Universitaires St Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium.
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15
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In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity. Int J Mol Sci 2021; 22:ijms22094516. [PMID: 33925997 PMCID: PMC8123603 DOI: 10.3390/ijms22094516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/10/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022] Open
Abstract
Sphingomyelin phosphodiesterase (SMPD1) is a key enzyme in the sphingolipid metabolism. Genetic SMPD1 variants have been related to the Niemann-Pick lysosomal storage disorder, which has different degrees of phenotypic severity ranging from severe symptomatology involving the central nervous system (type A) to milder ones (type B). They have also been linked to neurodegenerative disorders such as Parkinson and Alzheimer. In this paper, we leveraged structural, evolutionary and stability information on SMPD1 to predict and analyze the impact of variants at the molecular level. We developed the SMPD1-ZooM algorithm, which is able to predict with good accuracy whether variants cause Niemann-Pick disease and its phenotypic severity; the predictor is freely available for download. We performed a large-scale analysis of all possible SMPD1 variants, which led us to identify protein regions that are either robust or fragile with respect to amino acid variations, and show the importance of aromatic-involving interactions in SMPD1 function and stability. Our study also revealed a good correlation between SMPD1-ZooM scores and in vitro loss of SMPD1 activity. The understanding of the molecular effects of SMPD1 variants is of crucial importance to improve genetic screening of SMPD1-related disorders and to develop personalized treatments that restore SMPD1 functionality.
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16
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Wilson KA, Kung RW, D'souza S, Wetmore SD. Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes. Nucleic Acids Res 2021; 49:2213-2225. [PMID: 33544852 PMCID: PMC7913691 DOI: 10.1093/nar/gkab008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 01/07/2023] Open
Abstract
A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protein π–π and sugar–π contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, π–π and sugar–π interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA–protein contacts than DNA–protein interactions. In addition to highlighting distinct differences between RNA and DNA–protein binding, this work has generated the largest dataset of RNA–protein π-interactions to date, thereby underscoring that RNA–protein π-contacts are ubiquitous in nature, and key to the stability and function of RNA–protein complexes.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ryan W Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Simmone D'souza
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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17
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Lei M, Quan C, Wang JY, Kao YH, Schöneich C. Light-Induced Histidine Adducts to an IgG1 Molecule Via Oxidized Histidine Residue and the Potential Impact of Polysorbate-20 Concentration. Pharm Res 2021; 38:491-501. [PMID: 33666838 DOI: 10.1007/s11095-021-03010-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/02/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE Histidine (His) undergoes light-induced reactions such as oxidation, crosslinking and addition. These reactions are initiated by singlet oxygen (1O2) to generate His photo-oxidation products, which are subject to nucleophilic attack by a non-oxidized His residue from another protein or by nucleophilic buffer components such as Tris and His. This report aims to identify light-induced His-adducts to a monoclonal antibody (mAb-1) due to the reaction of His molecules in the buffer with the photooxidized His residues under ICH light conditions. Since polysorbate-20 (PS-20) is a commonly used excipient in biotherapeutics formulation, it is also important to study the impact of PS-20 concentration on protein photostability. RESULTS We identified and characterized light-induced His-adducts of mAb-1 by LC-MS/MS. We showed that the levels of light-induced His-adducts generally correlate with the solvent accessibility of His residues in the protein. In addition, the presence of PS-20 at concentrations commonly used in protein drug formulations can significantly increase the levels of light-induced His-adducts. CONCLUSIONS Since His residues are present in a conserved region in the Fc domain, and may be present in the complementarity-determining region (CDR), the impact on the biological functions of the His-adducts observed here should be further studied to evaluate the risk of their presence.
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Affiliation(s)
- Ming Lei
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA.
| | - Cynthia Quan
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA
| | - John Y Wang
- Late Stage Pharmaceutical Development, Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA
| | - Yung-Hsiang Kao
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA
| | - Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, Kansas, 66047, USA.
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18
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Kropp C, Straub K, Linde M, Babinger P. Hexamerization and thermostability emerged very early during geranylgeranylglyceryl phosphate synthase evolution. Protein Sci 2020; 30:583-596. [PMID: 33342010 PMCID: PMC7888582 DOI: 10.1002/pro.4016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
A large number of archaea live in hyperthermophilic environments. In consequence, their proteins need to adopt to these harsh conditions, including the enzymes that catalyze the synthesis of their membrane ether lipids. The enzyme that catalyzes the formation of the first ether bond in these lipids, geranylgeranylglyceryl phosphate synthase (GGGPS), exists as a hexamer in many hyperthermophilic archaea, and a recent study suggested that hexamerization serves for a fine‐tuning of the flexibility – stability trade‐off under hyperthermophilic conditions. We have recently reconstructed the sequences of ancestral group II GGGPS enzymes and now present a detailed biochemical characterization of nine of these predecessors, which allowed us to trace back the evolution of hexameric GGGPS and to draw conclusions about the properties of extant GGGPS branches that were not accessible to experiments up to now. Almost all ancestral GGGPS proteins formed hexamers, which demonstrates that hexamerization is even more widespread among the GGGPS family than previously assumed. Furthermore, all experimentally studied ancestral proteins showed high thermostability. Our results indicate that the hexameric oligomerization state and thermostability were present very early during the evolution of group II GGGPS, while the fine tuning of the flexibility – stability trade‐off developed very late, independent of the emergence of hexamerization.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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19
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Afrose F, Martfeld AN, Greathouse DV, Koeppe RE. Examination of pH dependency and orientation differences of membrane spanning alpha helices carrying a single or pair of buried histidine residues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183501. [PMID: 33130099 DOI: 10.1016/j.bbamem.2020.183501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/08/2023]
Abstract
We have employed the peptide framework of GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide) to examine the orientation, dynamics and pH dependence of peptides having buried single or pairs of histidine residues. When residue L8 is substituted to yield GWALP23-H8, acetyl-GGALWLAH8ALALALALALWLAGA-amide, the deuterium NMR spectra of 2H-labeled core alanine residues reveal a helix that occupies a single transmembrane orientation in DLPC, or in DMPC at low pH, yet shows multiple states at higher pH or in bilayers of DOPC. Moreover, a single histidine at position 8 or 16 in the GWALP23 framework is sensitive to pH. Titration points are observed near pH 3.5 for the deprotonation of H8 in lipid bilayers of DLPC or DMPC, and for H16 in DOPC. When residues L8 and L16 both are substituted to yield GWALP23-H8,16, the 2H NMR spectra show, interestingly, no titration dependence from pH 2-8, yet bilayer thickness-dependent orientation differences. The helix with H8 and H16 is found to adopt a transmembrane orientation in thin bilayers of DLPC, a combination of transmembrane and surface orientations in DMPC, and then a complete transition to a surface bound orientation in the thicker DPoPC and DOPC lipid bilayers. In the surface orientations, alanine A7 no longer fits within the core helix. These results along with previous studies with different locations of histidine residues suggest that lipid hydrophobic thickness is a first determinant and pH a second determinant for the helical orientation, along with possible side-chain snorkeling, when the His residues are incorporated into the hydrophobic region of a lipid membrane-associated helix.
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Affiliation(s)
- Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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20
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Mondal P. In silico decryption of serotonin-receptor binding: local non-covalent interactions and long-range conformational changes. RSC Adv 2020; 10:37995-38003. [PMID: 35515142 PMCID: PMC9057181 DOI: 10.1039/d0ra05559j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/08/2021] [Accepted: 09/15/2020] [Indexed: 01/10/2023] Open
Abstract
Serotonin-receptor binding is the key step in the process behind serotonin functionality, including several psychological and physiological behaviours. This study is focused on identifying the main non-covalent interactions controlling the stability of serotonin-receptor complexes as well as the main conformational changes in the receptor due to serotonin-receptor binding using classical molecular dynamics simulations and quantum chemical calculations. A qualitative analysis based on two order parameters ((i) the centre of mass distance and (ii) the angle between the surface normals of each aromatic residue and serotonin in the binding site) on the serotonin-receptor complex trajectory suggests that the T-type stacking interaction is predominant in the binding site. Quantum chemical calculations of the stacking interaction energy provide the quantitative contributions of important aromatic residues to the stabilization of the complex. Furthermore, a three body stacking interaction (named 'L'-type) was observed and likely contributes to the stability of the complex. Direct and water-mediated hydrogen bonding between the residues in the binding site and serotonin contributes to the complex stability. Principal component analysis of the molecular dynamics simulation trajectory of the serotonin-receptor complex and the apo-receptor in water indicates that the whole receptor is significantly stabilized due to serotonin binding. An analysis based on the dynamic cross correlation function reflects the strong correlation between trans-membrane (TM)3, TM5, TM6 (containing residues responsible for the stacking interaction and hydrogen bonding) and mini-G0 which may participate in signal transduction leading to the functionality of serotonin.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences and Technologies, Indian Institute of Science Education and Research (IISER) Tirupati Tirupati 517507 Andhra Pradesh India +91 877 2500 926
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21
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Palanisamy K, Prakash M, Rajapandian V. Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids. NEW J CHEM 2020. [DOI: 10.1039/d0nj03085f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The hydrated clusters of protonated imidazole (ImH+) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.
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Affiliation(s)
- Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Varatharaj Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science
- Coimbatore-641020
- India
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22
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Jayawardena BM, Jones MR, Hong Y, Jones CE. Copper ions trigger disassembly of neurokinin B functional amyloid and inhibit de novo assembly. J Struct Biol 2019; 208:107394. [DOI: 10.1016/j.jsb.2019.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/23/2019] [Accepted: 09/23/2019] [Indexed: 01/24/2023]
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23
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Kachaeva MV, Obernikhina NV, Veligina ES, Zhuravlova MY, Prostota YO, Kachkovsky OD, Brovarets VS. Estimation of biological affinity of nitrogen-containing conjugated heterocyclic pharmacophores. Chem Heterocycl Compd (N Y) 2019. [DOI: 10.1007/s10593-019-02478-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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An aluminum adjuvant-integrated nano-MOF as antigen delivery system to induce strong humoral and cellular immune responses. J Control Release 2019; 300:81-92. [PMID: 30826373 DOI: 10.1016/j.jconrel.2019.02.035] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/21/2019] [Accepted: 02/25/2019] [Indexed: 12/21/2022]
Abstract
Metal-organic frameworks (MOFs) have high surface area, tunable pore size, and high loading capacity, making them promising for drug delivery. However, their synthesis requires organic solvents, high temperature and high pressure that are incompatible with biomacromolecules. Zeolitic imidazole frameworks (ZIF-8) which forms through coordination between zinc ions and 2-methylimidazole (MeIM) have emerged as an advanced functional material for drug delivery due to its unique features such as high loading and pH-sensitive degradation. In this study, we took advantage of a natural biomineralization process to create aluminum-containing nanoZIF-8 particles for antigen delivery. Without organic solvents or stabilizing agent, nanoparticles (ZANPs) were synthesized by a mild and facile method with aluminum, model antigen ovalbumin (OVA) and ZIF-8 integrated. A high antigen loading capacity (%) of 30.6% and a pH dependent antigen release were achieved. A Toll-like receptor 9 agonist cytosine-phosphate-guanine oligodeoxynucleotides (CpG) was adsorbed on the surface of ZANPs (hereafter CpG/ZANPs) to boost the immune response. After subcutaneous injection in vivo, CpG/ZANPs targeted lymph nodes (LNs), where their cargo was efficiently internalized by LN-resident antigen-presenting cells (APCs). ZANPs decomposition in lysosomes released antigen into the cytoplasm and enhanced cross-presentation. Moreover, CpG/ZANPs induced strong antigen-specific humoral and cytotoxic T lymphocyte responses that significantly inhibited the growth of EG7-OVA tumors while showing minimal cytotoxicity. We demonstrate that ZANPs may be a safe and effective vehicle for the development of cancer vaccines.
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25
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26
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Vasiliauskaité-Brooks I, Healey RD, Rochaix P, Saint-Paul J, Sounier R, Grison C, Waltrich-Augusto T, Fortier M, Hoh F, Saied EM, Arenz C, Basu S, Leyrat C, Granier S. Structure of a human intramembrane ceramidase explains enzymatic dysfunction found in leukodystrophy. Nat Commun 2018; 9:5437. [PMID: 30575723 PMCID: PMC6303388 DOI: 10.1038/s41467-018-07864-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/03/2018] [Indexed: 02/02/2023] Open
Abstract
Alkaline ceramidases (ACERs) are a class of poorly understood transmembrane enzymes controlling the homeostasis of ceramides. They are implicated in human pathophysiology, including progressive leukodystrophy, colon cancer as well as acute myeloid leukemia. We report here the crystal structure of the human ACER type 3 (ACER3). Together with computational studies, the structure reveals that ACER3 is an intramembrane enzyme with a seven transmembrane domain architecture and a catalytic Zn2+ binding site in its core, similar to adiponectin receptors. Interestingly, we uncover a Ca2+ binding site physically and functionally connected to the Zn2+ providing a structural explanation for the known regulatory role of Ca2+ on ACER3 enzymatic activity and for the loss of function in E33G-ACER3 mutant found in leukodystrophic patients. Alkaline ceramidases (ACERs) are a class of poorly understood transmembrane enzymes controlling the homeostasis of ceramides. Here authors solve the Xray structure of human ACER3 and uncover a Ca2+ binding site providing an explanation for the known regulatory role of Ca2+ on ACER3 activity.
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Affiliation(s)
| | - Robert D Healey
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Pascal Rochaix
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Julie Saint-Paul
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Rémy Sounier
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Claire Grison
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | | | - Mathieu Fortier
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - François Hoh
- CBS, University of Montpellier, CNRS, INSERM, Montpellier, 34090, France
| | - Essa M Saied
- Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.,Chemistry Department, Faculty of Science, Suez Canal University, 41522, Ismailia, Egypt
| | - Christoph Arenz
- Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Shibom Basu
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland
| | - Cédric Leyrat
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France.
| | - Sébastien Granier
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France.
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27
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Iyer BR, Vetal PV, Noordeen H, Zadafiya P, Mahalakshmi R. Salvaging the Thermodynamic Destabilization of Interface Histidine in Transmembrane β-Barrels. Biochemistry 2018; 57:6669-6678. [PMID: 30284812 PMCID: PMC6284319 DOI: 10.1021/acs.biochem.8b00805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The ability of histidine to participate in a wide range of stabilizing polar interactions preferentially populates this residue in functionally important sites of proteins. Histidine possesses an amphiphilic and electrostatic nature that is essential for amino acids residing at membrane interfaces. However, the frequency of occurrence of histidine at membrane interfaces, particularly transmembrane β-barrels, is lower than those of other aromatic residues. Here, we carry out comprehensive energetic measurements using equilibrium folding of the outer membrane enzyme PagP to address the contribution of a C-terminal interface histidine to barrel stability. We show that placing histidine at the C-terminus universally destabilizes PagP by 4.0-8.0 kcal mol-1 irrespective of the neighboring residue. Spectroscopic and electrophoretic measurements indicate that the altered stability may arise from a loss of barrel compaction. Isoleucine, methionine, and valine salvage this destabilization marginally (in addition to tyrosine, which shows an exceptionally high folding free energy value), when placed at the penultimate position, at the expense of an altered folding pathway. Double-mutant cycle analysis indicates that the coupling energy between the terminal and penultimate residues in PagP-X160H161 increases when the level of intrinsic destabilization by the terminal H161 is high. Our observations that neighboring residues cannot salvage the energetic destabilization of histidine may explain why histidine is less abundant at membrane interfaces.
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Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Pallavi Vijay Vetal
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Henna Noordeen
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Punit Zadafiya
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
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28
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Leshem G, Richman M, Lisniansky E, Antman-Passig M, Habashi M, Gräslund A, Wärmländer SKTS, Rahimipour S. Photoactive chlorin e6 is a multifunctional modulator of amyloid-β aggregation and toxicity via specific interactions with its histidine residues. Chem Sci 2018; 10:208-217. [PMID: 30713632 PMCID: PMC6333166 DOI: 10.1039/c8sc01992d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/03/2018] [Indexed: 11/23/2022] Open
Abstract
Photoactive chlorin e6 selectively damage the histidine residues of amyloid-β and reduce its aggregation and toxicity even in the presence of Cu ions.
The self-assembly of Aβ to β-sheet-rich neurotoxic oligomers is a main pathological event leading to Alzheimer's disease (AD). Selective targeting of Aβ oligomers without affecting other functional proteins is therefore an attractive approach to prevent the disease and its progression. In this study, we report that photodynamic treatment of Aβ in the presence of catalytic amounts of chlorin e6 can selectively damage Aβ and inhibit its aggregation and toxicity. Chlorin e6 also reversed the amyloid aggregation process in the dark by binding its soluble and low molecular weight oligomers, as shown by thioflavin T (ThT) fluorescence and photoinduced cross-linking of unmodified protein (PICUP) methods. Using HSQC NMR spectroscopy, ThT assays, amino acid analysis, SDS/PAGE, and EPR spectroscopy, we show that catalytic amounts of photoexcited chlorin e6 selectively damage the Aβ histidine residues H6, H13, and H14, and induce Aβ cross-linking by generating singlet oxygen. In contrast, photoexcited chlorin e6 was unable to cross-link ubiquitin and α-synuclein, demonstrating its high selectivity for Aβ. By binding to the Aβ histidine residues, catalytic amounts of chlorin e6 can also inhibit the Cu2+-induced aggregation and toxicity in darkness, while at stoichiometric amounts it acts as a chelator to reduce the amount of free Cu2+. This study demonstrates the great potential of chlorin e6 as a multifunctional agent for treatment of AD, and shows that the three N-terminal Aβ histidine residues are a suitable target for Aβ-specific drugs.
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Affiliation(s)
- Guy Leshem
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 5290002 , Israel .
| | - Michal Richman
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 5290002 , Israel .
| | - Elvira Lisniansky
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 5290002 , Israel .
| | - Merav Antman-Passig
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 5290002 , Israel .
| | - Maram Habashi
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 5290002 , Israel .
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics , Arrhenius Laboratories , Stockholm University , S-106 91 Stockholm , Sweden .
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics , Arrhenius Laboratories , Stockholm University , S-106 91 Stockholm , Sweden .
| | - Shai Rahimipour
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 5290002 , Israel .
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Hou Q, Bourgeas R, Pucci F, Rooman M. Computational analysis of the amino acid interactions that promote or decrease protein solubility. Sci Rep 2018; 8:14661. [PMID: 30279585 PMCID: PMC6168528 DOI: 10.1038/s41598-018-32988-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/11/2018] [Indexed: 11/24/2022] Open
Abstract
The solubility of globular proteins is a basic biophysical property that is usually a prerequisite for their functioning. In this study, we probed the solubility of globular proteins with the help of the statistical potential formalism, in view of objectifying the connection of solubility with structural and energetic properties and of the solubility-dependence of specific amino acid interactions. We started by setting up two independent datasets containing either soluble or aggregation-prone proteins with known structures. From these two datasets, we computed solubility-dependent distance potentials that are by construction biased towards the solubility of the proteins from which they are derived. Their analysis showed the clear preference of amino acid interactions such as Lys-containing salt bridges and aliphatic interactions to promote protein solubility, whereas others such as aromatic, His-π, cation-π, amino-π and anion-π interactions rather tend to reduce it. These results indicate that interactions involving delocalized π-electrons favor aggregation, unlike those involving no (or few) dispersion forces. Furthermore, using our potentials derived from either highly or weakly soluble proteins to compute protein folding free energies, we found that the difference between these two energies correlates better with solubility than other properties analyzed before such as protein length, isoelectric point and aliphatic index. This is, to the best of our knowledge, the first comprehensive in silico study of the impact of residue-residue interactions on protein solubility properties.The results of this analysis provide new insights that will facilitate future rational protein design applications aimed at modulating the solubility of targeted proteins.
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Affiliation(s)
- Qingzhen Hou
- Department of BioModeling BioInformatics & BioProcesses, Université Libre de Bruxelles, Brussels, 1050, Belgium
| | - Raphaël Bourgeas
- Department of BioModeling BioInformatics & BioProcesses, Université Libre de Bruxelles, Brussels, 1050, Belgium
| | - Fabrizio Pucci
- Department of BioModeling BioInformatics & BioProcesses, Université Libre de Bruxelles, Brussels, 1050, Belgium
| | - Marianne Rooman
- Department of BioModeling BioInformatics & BioProcesses, Université Libre de Bruxelles, Brussels, 1050, Belgium.
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30
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Biswas H, Chattopadhyaya R. Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from α 2β 2 to unfolded state. J Biomol Struct Dyn 2018. [DOI: 10.1080/07391102.2017.1345327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Himadri Biswas
- Department of Biochemistry, Bose Institute, Calcutta 700054, India
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31
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Structural insights into two inorganic-organic hybrids based on chiral amino acids and polyoxomolybdates. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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32
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X-Shaped ZIF-8 for Immobilization Rhizomucor miehei Lipase via Encapsulation and Its Application toward Biodiesel Production. Catalysts 2018. [DOI: 10.3390/catal8030096] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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33
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Kumar K, Woo SM, Siu T, Cortopassi WA, Duarte F, Paton RS. Cation-π interactions in protein-ligand binding: theory and data-mining reveal different roles for lysine and arginine. Chem Sci 2018; 9:2655-2665. [PMID: 29719674 PMCID: PMC5903419 DOI: 10.1039/c7sc04905f] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/20/2018] [Indexed: 12/22/2022] Open
Abstract
The interactions of neutral aromatic ligands with cationic arginine, histidine and lysine amino acid residues have been studied with ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of X-ray structures.
We have studied the cation–π interactions of neutral aromatic ligands with the cationic amino acid residues arginine, histidine and lysine using ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of all available Protein Data Bank (PDB) X-ray structures. Quantum chemical potential energy surfaces (PES) for these interactions were obtained at the DLPNO-CCSD(T) level of theory and compared against the empirical distribution of 2012 unique protein–ligand cation–π interactions found in X-ray crystal structures. We created a workflow to extract these structures from the PDB, filtering by interaction type and residue pKa. The gas phase cation–π interaction of lysine is the strongest by more than 10 kcal mol–1, but the empirical distribution of 582 X-ray structures lies away from the minimum on the interaction PES. In contrast, 1381 structures involving arginine match the underlying calculated PES with good agreement. SAPT analysis revealed that underlying differences in the balance of electrostatic and dispersion contributions are responsible for this behavior in the context of the protein environment. The lysine–arene interaction, dominated by electrostatics, is greatly weakened by a surrounding dielectric medium and causes it to become essentially negligible in strength and without a well-defined equilibrium separation. The arginine–arene interaction involves a near equal mix of dispersion and electrostatic attraction, which is weakened to a much smaller degree by the surrounding medium. Our results account for the paucity of cation–π interactions involving lysine, even though this is a more common residue than arginine. Aromatic ligands are most likely to interact with cationic arginine residues as this interaction is stronger than for lysine in higher polarity surroundings.
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Affiliation(s)
- Kiran Kumar
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Shin M Woo
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Thomas Siu
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Wilian A Cortopassi
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Fernanda Duarte
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , UK .
| | - Robert S Paton
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
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Čapkauskaitė E, Zakšauskas A, Ruibys V, Linkuvienė V, Paketurytė V, Gedgaudas M, Kairys V, Matulis D. Benzimidazole design, synthesis, and docking to build selective carbonic anhydrase VA inhibitors. Bioorg Med Chem 2017; 26:675-687. [PMID: 29305297 DOI: 10.1016/j.bmc.2017.12.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/15/2017] [Accepted: 12/22/2017] [Indexed: 10/18/2022]
Abstract
The similarity of human carbonic anhydrase (CA) active sites makes it difficult to design selective inhibitors for one or several CA isoforms that are drug targets. Here we synthesize a series of compounds that are based on 5-[2-(benzimidazol-1-yl)acetyl]-2-chloro-benzenesulfonamide (1a) which demonstrated picomolar binding affinity and significant selectivity for CA isoform five A (VA), and explain the structural influence of inhibitor functional groups to the binding affinity and selectivity. A series of chloro-substituted benzenesulfonamides bearing a heterocyclic tail, together with molecular docking, was used to build inhibitors that explore substituent influence on the binding affinity to the CA VA isoform.
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Key Words
- 3,4-Dihydro-2H-quinoline
- CA inhibitor
- Carbonic anhydrase isozyme I, II, III, IV, VA, VB, VI, VII, IX, XII, XIII, and XIV
- Docking
- Fluorescent thermal shift assay
- Imidazole
- Indoline
- N-Alkylated benzimidazole
- Sulfonamide
- ThermoFluor®
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Affiliation(s)
- Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Virginijus Ruibys
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, Vilnius LT-03225, Lithuania
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Marius Gedgaudas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.
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35
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Wang Q, Zhang X, Huang L, Zhang Z, Dong S. GOx@ZIF-8(NiPd) Nanoflower: An Artificial Enzyme System for Tandem Catalysis. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710418] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Qingqing Wang
- College of Chemistry; Jilin University; Changchun 130012 P. R. China
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
| | - Xueping Zhang
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
| | - Liang Huang
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
| | - Zhiquan Zhang
- College of Chemistry; Jilin University; Changchun 130012 P. R. China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
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36
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Wang Q, Zhang X, Huang L, Zhang Z, Dong S. GOx@ZIF-8(NiPd) Nanoflower: An Artificial Enzyme System for Tandem Catalysis. Angew Chem Int Ed Engl 2017; 56:16082-16085. [DOI: 10.1002/anie.201710418] [Citation(s) in RCA: 257] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Qingqing Wang
- College of Chemistry; Jilin University; Changchun 130012 P. R. China
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
| | - Xueping Zhang
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
| | - Liang Huang
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
| | - Zhiquan Zhang
- College of Chemistry; Jilin University; Changchun 130012 P. R. China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Changchun 130022 P. R. China
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37
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Brylinski M. Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 2017; 91:380-390. [PMID: 28816025 DOI: 10.1111/cbdd.13084] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/29/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022]
Abstract
The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experimental and computer-generated structures of ligand-protein complexes, considering various combinations of aromatic amino acid residues and ligand rings. The geometry of interfacial π-π stacking in crystal structures accords with experimental and theoretical data collected for simple systems, such as the benzene dimer. Many contemporary ligand docking programs implicitly treat aromatic stacking with van der Waals and Coulombic potentials. Although this approach generally provides a sufficient specificity to model aromatic interactions, the geometry of π-π contacts in high-scoring docking conformations could still be improved. The comprehensive analysis of aromatic geometries at ligand-protein interfaces lies the foundation for the development of type-specific statistical potentials to more accurately describe aromatic interactions in molecular docking. A Perl script to detect and calculate the geometric parameters of aromatic interactions in ligand-protein complexes is available at https://github.com/michal-brylinski/earomatic. The dataset comprising experimental complex structures and computer-generated models is available at https://osf.io/rztha/.
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Affiliation(s)
- Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, USA
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de V C Sinatti V, R Baptista LP, Alves-Ferreira M, Dardenne L, Hermínio Martins da Silva J, Guimarães AC. In silico identification of inhibitors of ribose 5-phosphate isomerase from Trypanosoma cruzi using ligand and structure based approaches. J Mol Graph Model 2017; 77:168-180. [PMID: 28865321 DOI: 10.1016/j.jmgm.2017.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 08/07/2017] [Indexed: 11/25/2022]
Abstract
Chagas disease, caused by the protozoan Trypanosoma cruzi, affects approximately seven million people, mainly in Latin America, and causes about 7000 deaths annually. The available treatments are unsatisfactory and search for more effective drugs against this pathogen is critical. In this context, the ribose 5-phosphate isomerase (Rpi) enzyme is a potential drug target mainly due to its function in the pentose phosphate pathway and its essentiality (previously shown in other trypanosomatids). In this study, we propose novel potential inhibitors for the Rpi of T. cruzi (TcRpi) based on a computer-aided approach, including structure-based and ligand-based pharmacophore modeling. Along with a substructural and similarity search, the selected pharmacophore hypotheses were used to screen the purchasable subset of the ZINC Database, yielding 20,183 candidate compounds. These compounds were submitted to molecular docking studies in the TcRpi and Human Rpi (HsRpi) active sites in order to identify potential selective inhibitors for the T. cruzi enzyme. After the molecular docking and ADME-T (absorption, distribution, metabolism, excretion and toxicity)/PAINS (pan-assay interference compounds) screenings, 211 molecules were selected as potential TcRpi inhibitors. Out of these, three compounds - ZINC36975961, ZINC63480117, and ZINC43763931 - were submitted to molecular dynamics simulations and two of them - ZINC36975961 and ZINC43763931- had good performance and made interactions with important active site residues over all the simulation time. These compounds could be considered potential TcRpi inhibitors candidates and also may be used as leads for developing new TcRpi inhibitors.
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Affiliation(s)
- Vanessa de V C Sinatti
- Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Av. Brasil 4365, Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil.
| | - Luiz Phillippe R Baptista
- Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Av. Brasil 4365, Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
| | - Marcelo Alves-Ferreira
- Fiocruz, Laboratório de Modelagem de Sistemas Biológicos, Centro de Desenvolvimento Tecnológico em Saúde, Av. Brasil 4036, Manguinhos, 21040-361, Rio de Janeiro, Brazil; Instituto Nacional de Ciência e Tecnologia em Inovação em Doenças de Populações Negligenciadas, INCT-IDPN, CNPq, Brazil
| | - Laurent Dardenne
- Laboratório Nacional de Computação Científica, Grupo de Modelagem Molecular de Sistemas Biológicos, Av. Getúlio Vargas, 333, Quitandinha, 25651-075, Petrópolis, RJ, Brazil
| | | | - Ana Carolina Guimarães
- Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Av. Brasil 4365, Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
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Rahman MF, Askwith C, Govindarajan R. Molecular determinants of acidic pH-dependent transport of human equilibrative nucleoside transporter 3. J Biol Chem 2017; 292:14775-14785. [PMID: 28729424 DOI: 10.1074/jbc.m117.787952] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/11/2017] [Indexed: 12/16/2022] Open
Abstract
Equilibrative nucleoside transporters (ENTs) translocate hydrophilic nucleosides across cellular membranes and are essential for salvage nucleotide synthesis and purinergic signaling. Unlike the prototypic human ENT members hENT1 and hENT2, which mediate plasma membrane nucleoside transport at pH 7.4, hENT3 is an acidic pH-activated lysosomal transporter partially localized to mitochondria. Recent studies demonstrate that hENT3 is indispensable for lysosomal homeostasis, and that mutations in hENT3 can result in a spectrum of lysosomal storage-like disorders. However, despite hENT3's prominent role in lysosome pathophysiology, the molecular basis of hENT3-mediated transport is unknown. Therefore, we sought to examine the mechanistic basis of acidic pH-driven hENT3 nucleoside transport with site-directed mutagenesis, homology modeling, and [3H]adenosine flux measurements in mutant RNA-injected Xenopus oocytes. Scanning mutagenesis of putative residues responsible for pH-dependent transport via hENT3 revealed that the ionization states of Asp-219 and Glu-447, and not His, strongly determined the pH-dependent transport permissible-impermissible states of the transporter. Except for substitution with certain isosteric and polar residues, substitution of either Asp-219 or Glu-447 with any other residues resulted in robust activity that was pH-independent. Dual substitution of Asp-219 and Glu-447 to Ala sustained pH-independent activity over a broad range of physiological pH (pH 5.5-7.4), which also maintained stringent substrate selectivity toward endogenous nucleosides and clinically used nucleoside drugs. Our results suggest a putative pH-sensing role for Asp-219 and Glu-447 in hENT3 and that the size, ionization state, or electronegative polarity at these positions is crucial for obligate acidic pH-dependent activity.
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Affiliation(s)
- Md Fazlur Rahman
- From the Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
| | | | - Rajgopal Govindarajan
- From the Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, .,the Translational Therapeutics Program, Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210
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Wilson KA, Wetmore SD. Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature. Struct Chem 2017. [DOI: 10.1007/s11224-017-0954-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Nakarada Đ, Etinski M, Petković M. Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers. J Phys Chem A 2016; 120:7704-7713. [PMID: 27626138 DOI: 10.1021/acs.jpca.6b06493] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stacking interactions in thymine dimers are studied with density functional theory. According to our calculations, six dimers of comparable stability can be prepared at low temperature, but dimerization is impossible at room temperature due to the large entropy contribution that accompanies it. Analysis of vibrational anharmonic coupling terms shows that each of the dimers exhibits distinct vibrational dynamics. Properties of electron density in the intermolecular region are used to analyze neutral stacked species and their ionized forms. Bond paths and critical points in the intermolecular region are identified, but a simple relationship between binding energy and total electron density in the intermolecular critical points could not be found due to an uneven electron distribution in the binding region. The reduced density gradient was confirmed to be a useful tool for analysis of weak stacking interactions. Those interactions also affect vertical and adiabatic ionization energies, which are computed to be slightly lower for the dimers compared to the monomer.
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Affiliation(s)
- Đura Nakarada
- Faculty of Physical Chemistry, University of Belgrade , Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade , Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade , Studentski trg 12-16, 11 158 Belgrade, Serbia
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Wilson KA, Holland DJ, Wetmore SD. Topology of RNA-protein nucleobase-amino acid π-π interactions and comparison to analogous DNA-protein π-π contacts. RNA (NEW YORK, N.Y.) 2016; 22:696-708. [PMID: 26979279 PMCID: PMC4836644 DOI: 10.1261/rna.054924.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 02/13/2016] [Indexed: 06/05/2023]
Abstract
The present work analyzed 120 high-resolution X-ray crystal structures and identified 335 RNA-protein π-interactions (154 nonredundant) between a nucleobase and aromatic (W, H, F, or Y) or acyclic (R, E, or D) π-containing amino acid. Each contact was critically analyzed (including using a visual inspection protocol) to determine the most prevalent composition, structure, and strength of π-interactions at RNA-protein interfaces. These contacts most commonly involve F and U, with U:F interactions comprising one-fifth of the total number of contacts found. Furthermore, the RNA and protein π-systems adopt many different relative orientations, although there is a preference for more parallel (stacked) arrangements. Due to the variation in structure, the strength of the intermolecular forces between the RNA and protein components (as determined from accurate quantum chemical calculations) exhibits a significant range, with most of the contacts providing significant stability to the associated RNA-protein complex (up to -65 kJ mol(-1)). Comparison to the analogous DNA-protein π-interactions emphasizes differences in RNA- and DNA-protein π-interactions at the molecular level, including the greater abundance of RNA contacts and the involvement of different nucleobase/amino acid residues. Overall, our results provide a clearer picture of the molecular basis of nucleic acid-protein binding and underscore the important role of these contacts in biology, including the significant contribution of π-π interactions to the stability of nucleic acid-protein complexes. Nevertheless, more work is still needed in this area in order to further appreciate the properties and roles of RNA nucleobase-amino acid π-interactions in nature.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Devany J Holland
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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São Pedro SL, Alves JMP, Barreto AS, Lima AODS. Evidence of Positive Selection of Aquaporins Genes from Pontoporia blainvillei during the Evolutionary Process of Cetaceans. PLoS One 2015; 10:e0134516. [PMID: 26226365 PMCID: PMC4520692 DOI: 10.1371/journal.pone.0134516] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/10/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Marine mammals are well adapted to their hyperosmotic environment. Several morphological and physiological adaptations for water conservation and salt excretion are known to be present in cetaceans, being responsible for regulating salt balance. However, most previous studies have focused on the unique renal physiology of marine mammals, but the molecular bases of these mechanisms remain poorly explored. Many genes have been identified to be involved in osmotic regulation, including the aquaporins. Considering that aquaporin genes were potentially subject to strong selective pressure, the aim of this study was to analyze the molecular evolution of seven aquaporin genes (AQP1, AQP2, AQP3, AQP4, AQP6, AQP7, and AQP9) comparing the lineages of cetaceans and terrestrial mammals. RESULTS Our results demonstrated strong positive selection in cetacean-specific lineages acting only in the gene for AQP2 (amino acids 23, 83, 107,179, 180, 181, 182), whereas no selection was observed in terrestrial mammalian lineages. We also analyzed the changes in the 3D structure of the aquaporin 2 protein. Signs of strong positive selection in AQP2 sites 179, 180, 181, and 182 were unexpectedly identified only in the baiji lineage, which was the only river dolphin examined in this study. Positive selection in aquaporins AQP1 (45), AQP4 (74), AQP7 (342, 343, 356) was detected in cetaceans and artiodactyls, suggesting that these events are not related to maintaining water and electrolyte homeostasis in seawater. CONCLUSIONS Our results suggest that the AQP2 gene might reflect different selective pressures in maintaining water balance in cetaceans, contributing to the passage from the terrestrial environment to the aquatic. Further studies are necessary, especially those including other freshwater dolphins, who exhibit osmoregulatory mechanisms different from those of marine cetaceans for the same essential task of maintaining serum electrolyte balance.
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Affiliation(s)
- Simone Lima São Pedro
- Laboratório de Genética Molecular, Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí, Itajaí, SC, Brazil
| | - João Marcelo Pereira Alves
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - André Silva Barreto
- Laboratório de Informática da Biodiversidade e Geomática, Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí, Itajaí, SC, Brazil
| | - André Oliveira de Souza Lima
- Laboratório de Genética Molecular, Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí, Itajaí, SC, Brazil
- * E-mail:
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Liang K, Ricco R, Doherty CM, Styles MJ, Bell S, Kirby N, Mudie S, Haylock D, Hill AJ, Doonan CJ, Falcaro P. Biomimetic mineralization of metal-organic frameworks as protective coatings for biomacromolecules. Nat Commun 2015; 6:7240. [PMID: 26041070 PMCID: PMC4468859 DOI: 10.1038/ncomms8240] [Citation(s) in RCA: 811] [Impact Index Per Article: 90.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/20/2015] [Indexed: 12/22/2022] Open
Abstract
Enhancing the robustness of functional biomacromolecules is a critical challenge in biotechnology, which if addressed would enhance their use in pharmaceuticals, chemical processing and biostorage. Here we report a novel method, inspired by natural biomineralization processes, which provides unprecedented protection of biomacromolecules by encapsulating them within a class of porous materials termed metal-organic frameworks. We show that proteins, enzymes and DNA rapidly induce the formation of protective metal-organic framework coatings under physiological conditions by concentrating the framework building blocks and facilitating crystallization around the biomacromolecules. The resulting biocomposite is stable under conditions that would normally decompose many biological macromolecules. For example, urease and horseradish peroxidase protected within a metal-organic framework shell are found to retain bioactivity after being treated at 80 °C and boiled in dimethylformamide (153 °C), respectively. This rapid, low-cost biomimetic mineralization process gives rise to new possibilities for the exploitation of biomacromolecules.
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Affiliation(s)
- Kang Liang
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Raffaele Ricco
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Cara M. Doherty
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Mark J. Styles
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Stephen Bell
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Nigel Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3169, Australia
| | - Stephen Mudie
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3169, Australia
| | - David Haylock
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
- The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Anita J. Hill
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Christian J. Doonan
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paolo Falcaro
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
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Wilson KA, Wells RA, Abendong MN, Anderson CB, Kung RW, Wetmore SD. Landscape of π-π and sugar-π contacts in DNA-protein interactions. J Biomol Struct Dyn 2015; 34:184-200. [PMID: 25723403 DOI: 10.1080/07391102.2015.1013157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There were 1765 contacts identified between DNA nucleobases or deoxyribose and cyclic (W, H, F, Y) or acyclic (R, E, D) amino acids in 672 X-ray structures of DNA-protein complexes. In this first study to compare π-interactions between the cyclic and acyclic amino acids, visual inspection was used to categorize amino acid interactions as nucleobase π-π (according to biological edge) or deoxyribose sugar-π (according to sugar edge). Overall, 54% of contacts are nucleobase π-π interactions, which involve all amino acids, but are more common for Y, F, and R, and involve all DNA nucleobases with similar frequencies. Among binding arrangements, cyclic amino acids prefer more planar (stacked) π-systems than the acyclic counterparts. Although sugar-π interactions were only previously identified with the cyclic amino acids and were found to be less common (38%) than nucleobase-cyclic amino acid contacts, sugar-π interactions are more common than nucleobase π-π contacts for the acyclic series (61% of contacts). Similar to DNA-protein π-π interactions, sugar-π contacts most frequently involve Y and R, although all amino acids adopt many binding orientations relative to deoxyribose. These DNA-protein π-interactions stabilize biological systems, by up to approximately -40 kJ mol(-1) for neutral nucleobase or sugar-amino acid interactions, but up to approximately -95 kJ mol(-1) for positively or negatively charged contacts. The high frequency and strength, despite variation in structure and composition, of these π-interactions point to an important function in biological systems.
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Affiliation(s)
- Katie A Wilson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Rachael A Wells
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Minette N Abendong
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Colin B Anderson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Ryan W Kung
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Stacey D Wetmore
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
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Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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47
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Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
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Chemerovski-Glikman M, Richman M, Rahimipour S. Structure-based study of antiamyloidogenic cyclic d,l-α-peptides. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.07.097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Paasche A, Zipper A, Schäfer S, Ziebuhr J, Schirmeister T, Engels B. Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease. Biochemistry 2014; 53:5930-46. [PMID: 25196915 DOI: 10.1021/bi400604t] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The coronavirus main protease (M(pro)) represents an attractive drug target for antiviral therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome (SARS). The SARS-CoV M(pro) and related CoV proteases have several distinct features, such as an uncharged Cys-His catalytic dyad embedded in a chymotrypsin-like protease fold, that clearly separate these enzymes from archetypical cysteine proteases. To further characterize the catalytic system of CoV main proteases and to obtain information about improved inhibitors, we performed comprehensive simulations of the proton-transfer reactions in the SARS-CoV M(pro) active site that lead to the Cys(-)/His(+) zwitterionic state required for efficient proteolytic activity. Our simulations, comprising the free enzyme as well as substrate-enzyme and inhibitor-enzyme complexes, lead us to predict that zwitterion formation is fostered by substrate binding but not inhibitor binding. This indicates that M(pro) employs a substrate-induced catalytic mechanism that further enhances its substrate specificity. Our computational data are in line with available experimental results, such as X-ray geometries, measured pKa values, mutagenesis experiments, and the measured differences between the kinetic parameters of substrates and inhibitors. The data also provide an atomistic picture of the formerly postulated electrostatic trigger involved in SARS-CoV M(pro) activity. Finally, they provide information on how a specific microenvironment may finely tune the activity of M(pro) toward specific viral protein substrates, which is known to be required for efficient viral replication. Our simulations also indicate that the low inhibition potencies of known covalently interacting inhibitors may, at least in part, be attributed to insufficient fostering of the proton-transfer reaction. These findings suggest ways to achieve improved inhibitors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg , Emil-Fischer-Straße 42, 97074 Würzburg, Germany
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Liu J, Spulber M, Wu D, Talom RM, Palivan CG, Meier W. Poly(N-isopropylacrylamide-co-tris-nitrilotriacetic acid acrylamide) for a Combined Study of Molecular Recognition and Spatial Constraints in Protein Binding and Interactions. J Am Chem Soc 2014; 136:12607-14. [DOI: 10.1021/ja503632w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Liu
- Department of Chemistry, University of Basel, Klingelbergstrasse
80, Basel 4056, Switzerland
| | - Mariana Spulber
- Department of Chemistry, University of Basel, Klingelbergstrasse
80, Basel 4056, Switzerland
| | - Dalin Wu
- Department of Chemistry, University of Basel, Klingelbergstrasse
80, Basel 4056, Switzerland
| | - Renee M. Talom
- Department of Chemistry, University of Basel, Klingelbergstrasse
80, Basel 4056, Switzerland
| | - Cornelia G. Palivan
- Department of Chemistry, University of Basel, Klingelbergstrasse
80, Basel 4056, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel, Klingelbergstrasse
80, Basel 4056, Switzerland
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