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Fatima B, Saleem F, Salar U, Chigurupati S, Felemban SG, Ul-Haq Z, Tariq SS, Almahmoud SA, Taha M, Shah STA, Khan KM. Multitargeted inhibition of key enzymes associated with diabetes and Alzheimer's disease by 1,3,4-oxadiazole derivatives: Synthesis, in vitro screening, and computational studies. Arch Pharm (Weinheim) 2023; 356:e2300384. [PMID: 37806747 DOI: 10.1002/ardp.202300384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
A library of 22 derivatives of 1,3,4-oxadiazole-2-thiol was synthesized, structurally characterized, and assessed for its potential to inhibit α-amylase, α-glucosidase, acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and antioxidant activities. Most of the tested compounds demonstrated good to moderate inhibition potential; however, their activity was lower than that of the standard acarbose. Significantly, compound 3f exhibited the highest inhibition potential against α-glucosidase and α-amylase enzymes, with IC50 values of 18.52 ± 0.09 and 20.25 ± 1.05 µM, respectively, in comparison to the standard acarbose (12.29 ± 0.26; 15.98 ± 0.14 µM). Compounds also demonstrated varying degrees of inhibitory potential against AChE (IC50 = 9.25 ± 0.19 to 36.15 ± 0.12 µM) and BChE (IC50 = 10.06 ± 0.43 to 35.13 ± 0.12 µM) enzymes compared to the standard donepezil (IC50 = 2.01 ± 0.12; 3.12 ± 0.06 µM), as well as DPPH (IC50 = 20.98 ± 0.06 to 52.83 ± 0.12 µM) and ABTS radical scavenging activities (IC50 = 22.29 ± 0.18 to 47.98 ± 0.03 µM) in comparison to the standard ascorbic acid (IC50 = 18.12 ± 0.15; 19.19 ± 0.72). The kinetic investigations have demonstrated that the compounds exhibit competitive-type inhibition for α-amylase, noncompetitive-type inhibition for α-glucosidase and AChE, and mixed-type inhibition for BChE. Additionally, a molecular docking study was performed on all synthetic oxadiazoles to explore the interaction details of these compounds with the active sites of the enzymes.
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Affiliation(s)
- Bibi Fatima
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Faiza Saleem
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Uzma Salar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah, Saudi Arabia
| | - Shatha G Felemban
- Department of Medical Laboratory Science, Fakeeh College for Medical Sciences, Jeddah, Saudi Arabia
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Syeda S Tariq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Suliman A Almahmoud
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah, Saudi Arabia
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Syed T A Shah
- Department of Education, Sukkur IBA University, Sukkur, Pakistan
| | - Khalid M Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Sadia K, Sultan S, Khan K, Javeres LM, Rumman B, Shah STA, Batool S, Nurulain SM. Antioxidant enzymes and association of CAT SNP-21 A/T (rs7943316) with male infertility. Mol Reprod Dev 2021; 88:598-604. [PMID: 34427017 DOI: 10.1002/mrd.23530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022]
Abstract
Infertility is a multifactorial and polygenic disease. A vast majority of infertility is still unexplained despite modern diagnostic techniques. Oxidative stress is considered a factor for male infertility but etiology in terms of functional gene polymorphism and experimental studies on human subjects is scarcely reported. The aim of the study was to investigate the status of three antioxidant enzymes; catalase, superoxide dismutase (SOD), and glutathione reduced (GSH) in clinically diagnosed infertile males and find the potential association of CAT gene variant in the promoter region -21 A/T (rs7943316). The study consisted of 55 clinically diagnosed infertile males and 50 non-infertile volunteers. The activity of antioxidant enzymes was measured through a spectrophotometer. Polymerase chain reaction-restriction fragment length polymorphism was performed for genotyping of single-nucleotide polymorphism. Catalase enzyme activity was significantly decreased while SOD and GSH were substantially increased (p ≤ 0.01) in infertile men in comparison to non-infertile. CAT gene variant rs7943316 had shown significant association in dominant, recessive model and allelic frequencies. The study concludes that rs7943316 has a substantial role in male infertility. The outcome of the study may help in resolving idiopathic infertility cases and may help in evolving novel diagnostic and therapeutic approaches. Other variants of CAT and antioxidant genes are suggested to ascertain further insight.
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Affiliation(s)
- Khulah Sadia
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sikandar Sultan
- Bioclinical Laboratory, National Institute of Health Sciences, Islamabad, Pakistan
| | - Kifayatullah Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Leonel M Javeres
- Bioclinical Laboratory, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research, Douala, Cameroon
| | - Baseerat Rumman
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syed T A Shah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sajida Batool
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syed M Nurulain
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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Riaz SK, Rashid R, Shah STA, Wang F, Malik MFA. Abstract P6-07-22: Association of Hedgehog signaling pathway with luminal B sub-type of breast cancer affected patients of Pakistan. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p6-07-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction
Hedgehog pathway dysregulation is observed in different types of cancers including breast. In the present study, expression profiles of hedgehog pathway molecules in breast cancer cohort of Pakistan and their probable association with molecular sub-types were explored.
Methods
The study was preceded with ethical approval and informed consent from respective institutions and participants. During 2013-2015, a total of 150 cancer biopsies along with adjacent normal tissues were prospectively collected immediately after surgery and processed for RNA isolation. Transcriptional profiles of salient members including SHH, DHH, IHH, PTCH-1, SMO and GLI-1 were quantified using qRT-PCR. Cohort was categorized into molecular sub-types following St. Gallen International Expert Consensus System. Association of expression levels of these aforementioned molecules with various clinico-pathological parameters was explored.
Result
Both SHH (p=0.01) and DHH (p<0.001) showed elevated expression among tumors in comparison to their controls. Similarly, PTCH-1 (p<0.001) and GLI-1 (p=0.002) were also significantly up regulated in the cohort. Interestingly, strong positive correlations were observed among the pathway molecules (r-value ranging from 0.45 to 0.81) which highlight their interdependence towards tumor progression. A significant correlation of SHH, DHH, PTCH-1 and GLI-1 was observed with advanced tumor sizes, stages, grades and nodal involvement (p<0.05). Association of IHH, SMO and GLI-1 over expression with cancer metastasis was also established in the cohort. SHH, PTCH-1 and GLI-1 were significantly linked with laterality, age and menopausal status. Expression of SHH (p=0.002) was more related to younger age group (mean age < 45 yrs) patients in comparison to elderly women.
Moreover all hedgehog molecules were strongly related to hormonal receptors (ER and PR) (r-value ranging from 0.51 to 0.86) while over-expression of HER-2 was not associated with any pathway component. Briefly, 53% (79) of the cohort was categorized as Luminal-B, 18% (27) triple negative, 15% (23) Luminal-A and 14% (21) HER-2 for sub-typing of breast cancer patients in the cohort. Expression of SHH was significantly associated with the molecular sub-types (p=0.02) and age (p=0.005) using Pearson Chi-Square test. Elevated expression of SHH was observed in 60% of the patients in Luminal B sub-type.
Conclusion
Hedgehog pathway plays a crucial role in breast cancer progression and is found to be activated in Luminal B sub-type in this cohort. As Luminal B is a more aggressive type of breast cancer having poor prognosis and early-onset, association of SHH with Luminal-B and younger age patients signify it importance as a biomarker for early diagnosis of young patient's. Hence therapeutic interventions for hedgehog pathway can improve the prognosis of patients categorized as Luminal B subtype of breast carcinogenesis.
Citation Format: Riaz SK, Rashid R, Shah STA, Wang F, Malik MFA. Association of Hedgehog signaling pathway with luminal B sub-type of breast cancer affected patients of Pakistan [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-07-22.
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Affiliation(s)
- SK Riaz
- COMSATS Institute of Information Technology, Islamabad, Pakistan; Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan; Centre for Cancer and Stem Cell Biology, Institute of Biosciences and Technology and College of Medicine, Texas A&M Health Science Centre, Houston, TX
| | - R Rashid
- COMSATS Institute of Information Technology, Islamabad, Pakistan; Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan; Centre for Cancer and Stem Cell Biology, Institute of Biosciences and Technology and College of Medicine, Texas A&M Health Science Centre, Houston, TX
| | - STA Shah
- COMSATS Institute of Information Technology, Islamabad, Pakistan; Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan; Centre for Cancer and Stem Cell Biology, Institute of Biosciences and Technology and College of Medicine, Texas A&M Health Science Centre, Houston, TX
| | - F Wang
- COMSATS Institute of Information Technology, Islamabad, Pakistan; Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan; Centre for Cancer and Stem Cell Biology, Institute of Biosciences and Technology and College of Medicine, Texas A&M Health Science Centre, Houston, TX
| | - MFA Malik
- COMSATS Institute of Information Technology, Islamabad, Pakistan; Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan; Centre for Cancer and Stem Cell Biology, Institute of Biosciences and Technology and College of Medicine, Texas A&M Health Science Centre, Houston, TX
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Nosheen A, Bano A, Yasmin H, Keyani R, Habib R, Shah STA, Naz R. Protein Quantity and Quality of Safflower Seed Improved by NP Fertilizer and Rhizobacteria (Azospirillum and Azotobacter spp.). Front Plant Sci 2016; 7:104. [PMID: 26941744 PMCID: PMC4762221 DOI: 10.3389/fpls.2016.00104] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/20/2016] [Indexed: 05/18/2023]
Abstract
HIGHLIGHTS Rhizobacteria (Azotobacter spp.) have improved the quality and quantity of safflower seed protein.Protein quality was confirmed by SDS-PAGE and new bands were found in response to different combinations of rhizobacteria and lower doses of fertilizers.The PGPR application has reduced the use of fertilizers upto 50%. Protein is an essential part of the human diet. The aim of this present study was to improve the protein quality of safflower seed by the application of plant growth promoting rhizobacteria (PGPR) in combination with conventional nitrogen and phosphate (NP) fertilizers. The seeds of two safflower cultivars Thori and Saif-32, were inoculated with Azospirillum and Azotobacter and grown under field conditions. Protein content and quality was assessed by crude protein, amino acid analysis, and SDS-PAGE. Seed crude protein and amino acids (methionine, phenylalanine, and glutamic acid) showed significant improvements (55-1250%) by Azotobacter supplemented with a quarter dose of fertilizers (BTQ) at P ≤ 0.05. Additional protein bands were induced in Thori and Saif-32 by BTQ and BTH (Azotobacter supplemented with a half dose of fertilizer) respectively. The Azospirillum in combination with half dose of fertilizer (SPH) and BTQ enhanced both indole acetic acid (IAA) (90%) and gibberellic acid (GA) (23-27%) content in safflower leaf. Taken together, these data suggest that Azospirillum and Azotobacter along with significantly reduced (up to 75%) use of NP fertilizers could improve the quality and quantity of safflower seed protein.
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Affiliation(s)
- Asia Nosheen
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
| | - Asghari Bano
- Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
- *Correspondence: Asghari Bano
| | - Humaira Yasmin
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
| | - Rumana Keyani
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
| | - Rabia Habib
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
| | - Syed T. A. Shah
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
| | - Rabia Naz
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
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Takeda H, Hattori M, Nishizawa T, Yamashita K, Shah STA, Caffrey M, Maturana AD, Ishitani R, Nureki O. Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg2+ channel MgtE. Nat Commun 2014; 5:5374. [PMID: 25367295 PMCID: PMC4241985 DOI: 10.1038/ncomms6374] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/24/2014] [Indexed: 01/25/2023] Open
Abstract
Magnesium is the most abundant divalent cation in living cells and is crucial to several biological processes. MgtE is a Mg(2+) channel distributed in all domains of life that contributes to the maintenance of cellular Mg(2+) homeostasis. Here we report the high-resolution crystal structures of the transmembrane domain of MgtE, bound to Mg(2+), Mn(2+) and Ca(2+). The high-resolution Mg(2+)-bound crystal structure clearly visualized the hydrated Mg(2+) ion within its selectivity filter. Based on those structures and biochemical analyses, we propose a cation selectivity mechanism for MgtE in which the geometry of the hydration shell of the fully hydrated Mg(2+) ion is recognized by the side-chain carboxylate groups in the selectivity filter. This is in contrast to the K(+)-selective filter of KcsA, which recognizes a dehydrated K(+) ion. Our results further revealed a cation-binding site on the periplasmic side, which regulate channel opening and prevents conduction of near-cognate cations.
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Affiliation(s)
- Hironori Takeda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Motoyuki Hattori
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- School of Life Sciences, Fudan University, 220 Handan Road, Yangpu District, Shanghai 200433, China
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Syed T. A. Shah
- Membrane Structural and Functional Biology Group, School of Medicine, and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine, and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Andrés D. Maturana
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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Abstract
The lipid-based bicontinuous cubic mesophase is a nanoporous membrane mimetic with applications in areas that include medicine, personal care products, foods and the basic sciences. An application of particular note concerns it use as a medium in which to grow crystals of membrane proteins for structure determination by X-ray crystallography. At least two variations of the mesophase exist. One is the highly viscous cubic phase, which has well developed long-range order. The other so-called sponge phase is considerably more fluid and lacks long-range order. The sponge phase has recently been shown to be a convenient vehicle for delivering microcrystals of membrane proteins to an X-ray free-electron laser beam for serial femtosecond crystallography (SFX). Unfortunately, the sponge phase approach calls for large amounts of protein that are not always available in the case of membrane proteins. The cubic phase offers the advantage of requiring significantly less protein for SFX but comes with its own challenges. Here, we describe the physico-chemical bases for these challenges, solutions to them and prospects for future uses of lipidic mesophases in the SFX arena.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Dianfan Li
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Nicole Howe
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Syed T A Shah
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Republic of Ireland
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Lyons JA, Parker JL, Solcan N, Brinth A, Li D, Shah STA, Caffrey M, Newstead S. Structural basis for polyspecificity in the POT family of proton-coupled oligopeptide transporters. EMBO Rep 2014; 15:886-93. [PMID: 24916388 PMCID: PMC4149780 DOI: 10.15252/embr.201338403] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
An enigma in the field of peptide transport is the structural basis for ligand promiscuity, as exemplified by PepT1, the mammalian plasma membrane peptide transporter. Here, we present crystal structures of di- and tripeptide-bound complexes of a bacterial homologue of PepT1, which reveal at least two mechanisms for peptide recognition that operate within a single, centrally located binding site. The dipeptide was orientated laterally in the binding site, whereas the tripeptide revealed an alternative vertical binding mode. The co-crystal structures combined with functional studies reveal that biochemically distinct peptide-binding sites likely operate within the POT/PTR family of proton-coupled symporters and suggest that transport promiscuity has arisen in part through the ability of the binding site to accommodate peptides in multiple orientations for transport.
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Affiliation(s)
- Joseph A Lyons
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Nicolae Solcan
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alette Brinth
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Dianfan Li
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Syed T A Shah
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK
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Liu W, Wacker D, Gati C, Han GW, James D, Wang D, Nelson G, Weierstall U, Katritch V, Barty A, Zatsepin NA, Li D, Messerschmidt M, Boutet S, Williams GJ, Koglin JE, Seibert MM, Wang C, Shah STA, Basu S, Fromme R, Kupitz C, Rendek KN, Grotjohann I, Fromme P, Kirian RA, Beyerlein KR, White TA, Chapman HN, Caffrey M, Spence JCH, Stevens RC, Cherezov V. Serial femtosecond crystallography of G protein-coupled receptors. Science 2014; 342:1521-4. [PMID: 24357322 DOI: 10.1126/science.1244142] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.
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Affiliation(s)
- Wei Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Li D, Lyons JA, Shah STA, Pye VE, Aragão D, Vogeley L, Tan J, Caffrey M. Membrane protein crystallization in lipidic mesophases. The host lipid screen. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313099479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Li D, Shah STA, Caffrey M. Host Lipid and Temperature as Important Screening Variables for Crystallizing Integral Membrane Proteins in Lipidic Mesophases. Trials with Diacylglycerol Kinase. Cryst Growth Des 2013; 13:2846-2857. [PMID: 23956688 PMCID: PMC3743127 DOI: 10.1021/cg400254v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A systematic study of the crystallization of an α-helical, integral membrane enzyme, diacylglycerol kinase, DgkA, using the lipidic cubic mesophase or in meso method is described. These trials have resulted in the production of blocky, rhombohedron-shaped crystals of diffraction quality currently in use for structure determination. Dramatic improvements in crystal quality were obtained when the identity of the lipid used to form the mesophase bilayer into which the protein was reconstituted as a prelude to crystallogenesis was varied. These monoacylglycerol lipids incorporated fatty acyl chains ranging from 14 to 18 carbon atoms long with cis olefinic bonds located toward the middle of the chain. Best crystals were obtained with a lipid that had an acyl chain 15 carbon atoms long with the double bond between carbons 7 and 8. It is speculated that the effectiveness of this lipid derives from hydrophobic mismatch between the target integral membrane protein and the bilayer of the host mesophase. Low temperature (4 °C) worked in concert with the short chain lipid to provide high quality crystals. Recommended screening strategies for crystallizing membrane proteins that include host lipid type and low temperature are made on the basis of this and related in meso crystallization trials.
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Affiliation(s)
| | | | - Martin Caffrey
- Corresponding Author: Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland, Phone: 353-1-896-4253. Fax: 353-1-896-4253, , Web address: http://www.tcd.ie/Biochemistry/research/m_caffrey.php
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Li D, Lyons JA, Pye VE, Vogeley L, Aragão D, Kenyon CP, Shah STA, Doherty C, Aherne M, Caffrey M. Crystal structure of the integral membrane diacylglycerol kinase. Nature 2013; 497:521-4. [PMID: 23676677 PMCID: PMC3740270 DOI: 10.1038/nature12179] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/12/2013] [Indexed: 11/09/2022]
Abstract
Diacylglycerol kinase catalyses the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane-derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria. For half a century, this 121-residue kinase has served as a model for investigating membrane protein enzymology, folding, assembly and stability. Here we present crystal structures for three functional forms of this unique and paradigmatic kinase, one of which is wild type. These reveal a homo-trimeric enzyme with three transmembrane helices and an amino-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site that is of the composite, shared site type. The crystal structures rationalize extensive biochemical and biophysical data on the enzyme. They are, however, at variance with a published solution NMR model in that domain swapping, a key feature of the solution form, is not observed in the crystal structures.
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Affiliation(s)
- Dianfan Li
- School of Biochemistry and Immunology & School of Medicine, Trinity College Dublin, Dublin 2, Ireland
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Shah STA, Khan KM, Hussain H, Hayat S, Voelter W. CsF-Celite, an Efficient Solid State Reagent for the Syntheses of Thioesters and Thioethers. Monatsh Chem 2005. [DOI: 10.1007/s00706-005-0351-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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