1
|
Iqbal T, Murugan S, Das D. A chimeric membrane enzyme and an engineered whole-cell biocatalyst for efficient 1-alkene production. SCIENCE ADVANCES 2024; 10:eadl2492. [PMID: 38924395 PMCID: PMC11204201 DOI: 10.1126/sciadv.adl2492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Bioproduction of 1-alkenes from naturally abundant free fatty acids offers a promising avenue toward the next generation of hydrocarbon-based biofuels and green commodity chemicals. UndB is the only known membrane-bound 1-alkene-producing enzyme, with great potential for 1-alkene bioproduction, but the enzyme exhibits limited turnovers, thus restricting its widespread usage. Here, we explore the molecular basis of the limitation of UndB activity and substantially improve its catalytic power. We establish that the enzyme undergoes peroxide-mediated rapid inactivation during catalysis. To counteract this inactivation, we engineered a chimeric membrane enzyme by conjugating UndB with catalase that protected UndB against peroxide and enhanced its number of turnovers tremendously. Notably, our chimeric enzyme is the only example of a membrane enzyme successfully engineered with catalase. We subsequently constructed a whole-cell biocatalytic system and achieved remarkable efficiencies (up to 95%) in the biotransformation of a wide range of fatty acids (both aliphatic and aromatic) into corresponding 1-alkenes with numerous biotechnological applications.
Collapse
Affiliation(s)
- Tabish Iqbal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | | | | |
Collapse
|
2
|
Wang B, Tieleman DP. The structure, self-assembly and dynamics of lipid nanodiscs revealed by computational approaches. Biophys Chem 2024; 309:107231. [PMID: 38569455 DOI: 10.1016/j.bpc.2024.107231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
Nanodisc technology is increasingly being used in structural, biochemical and biophysical studies of membrane proteins. The computational approaches have revealed many important features of nanodisc assembly, structures and dynamics. Therefore, we reviewed the application of computational approaches, especially molecular modeling and molecular dyncamics (MD) simulations, to characterize nanodiscs, including the structural models, assembly and disassembly, protocols for modeling, structural properties and dynamics, and protein-lipid interactions in nanodiscs. More amazing computational studies about nanodiscs are looked forward to in the future.
Collapse
Affiliation(s)
- Beibei Wang
- Centre for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China.
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary T2N 1N4, Canada.
| |
Collapse
|
3
|
Fang Y, Zhang Y, Bi S, Peng B, Wang C, Ju H, Liu Y. Securing LYTAC with Logic-Identification System for Cancer Cell-Selective Membrane Protein Degradation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2310039. [PMID: 38431928 DOI: 10.1002/smll.202310039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/18/2024] [Indexed: 03/05/2024]
Abstract
Lysosome-targeting chimera (LYTAC) links proteins of interest (POIs) with lysosome-targeting receptors (LTRs) to achieve membrane protein degradation, which is becoming a promising therapeutic modality. However, cancer cell-selective membrane protein degradation remains a big challenge considering expressions of POIs in both cancer cells and normal cells, as well as broad tissue distribution of LTRs. Here a logic-identification system is designed, termed Logic-TAC, based on cell membrane-guided DNA calculations to secure LYTAC selectively for cancer cells. Logic-TAC is designed as a duplex DNA structure, with both POI and LTR recognition regions sealed to avoid systematic toxicity during administration. MCF-7 and MCF-10A are chosen as sample cancer cell and normal cell respectively. As input 1 for logic-identification, membrane proteins EpCAM, which is highly expressed by MCF-7 but barely by MCF-10A, reacts with Logic-TAC to expose POI recognition region. As input 2 for logic-identification, Logic-TAC binds to POI, membrane protein MUC1, to expose LTR recognition region. As output, MUC1 is connected to LTR and degraded via lysosome pathway selectively for cancer cell MCF-7 with little side effect on normal cell MCF-10A. The logic-identification system also demonstrated satisfactory in vivo therapeutic results, indicating its promising potential in precise targeted therapy.
Collapse
Affiliation(s)
- Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yue Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shiyi Bi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Bo Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Caixia Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
4
|
Scheyer MW, Campbell C, William PL, Hussain M, Begum A, Fonseca SE, Asare IK, Dabney P, Dabney-Smith C, Lorigan GA, Sahu ID. Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins. Biophys Chem 2023; 301:107080. [PMID: 37531799 DOI: 10.1016/j.bpc.2023.107080] [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: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
One of the major challenges in solubilization of membrane proteins is to find the optimal physiological environment for their biophysical studies. EPR spectroscopy is a powerful biophysical technique for studying the structural and dynamic properties of macromolecules. However, the challenges in the membrane protein sample preparation and flexible motion of the spin label limit the utilization of EPR spectroscopy to a majority of membrane protein systems in a physiological membrane-bound state. Recently, lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have emerged as a membrane mimetic system for investigating the structural studies of membrane proteins. However, its detail characterization for membrane protein studies is still poorly understood. Recently, we characterized the potassium channel membrane protein KCNQ1 voltage sensing domain (KCNQ1-VSD) and KCNE1 reconstituted into lipodisq nanoparticles using EPR spectroscopy. In this study, the potassium channel accessory protein KCNE3 containing flexible N- and C-termini was encapsulated into proteoliposomes and lipodisq nanoparticles and characterized for studying its structural and dynamic properties using nitroxide based site-directed spin labeling EPR spectroscopy. CW-EPR lineshape analysis data indicated an increase in spectral line broadenings with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated an enhanced quality of distance measurements with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles, when compared to proteoliposomes. These results agree with the solution NMR structural structure of the KCNE3 and EPR studies of other membrane proteins in lipodisq nanoparticles. This study along with our earlier studies will provide the reference characterization data that will provide benefit to the membrane protein researchers for studying structural dynamics of challenging membrane proteins.
Collapse
Affiliation(s)
- Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Patrick L William
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mustakim Hussain
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Afsana Begum
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Peyton Dabney
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
| |
Collapse
|
5
|
Scherhag A, Räschle M, Unbehend N, Venn B, Glueck D, Mühlhaus T, Keller S, Pérez Patallo E, Zehner S, Frankenberg-Dinkel N. Characterization of a soluble library of the Pseudomonas aeruginosa PAO1 membrane proteome with emphasis on c-di-GMP turnover enzymes. MICROLIFE 2023; 4:uqad028. [PMID: 37441524 PMCID: PMC10335732 DOI: 10.1093/femsml/uqad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/30/2023] [Indexed: 07/15/2023]
Abstract
Studies of protein-protein interactions in membranes are very important to fully understand the biological function of a cell. The extraction of proteins from the native membrane environment is a critical step in the preparation of membrane proteins that might affect the stability of protein complexes. In this work, we used the amphiphilic diisobutylene/maleic acid copolymer to extract the membrane proteome of the opportunistic pathogen Pseudomonas aeruginosa, thereby creating a soluble membrane-protein library within a native-like lipid-bilayer environment. Size fractionation of nanodisc-embedded proteins and subsequent mass spectrometry enabled the identification of 3358 proteins. The native membrane-protein library showed a very good overall coverage compared to previous proteome data. The pattern of size fractionation indicated that protein complexes were preserved in the library. More than 20 previously described complexes, e.g. the SecYEG and Pili complexes, were identified and analyzed for coelution. Although the mass-spectrometric dataset alone did not reveal new protein complexes, combining pulldown assays with mass spectrometry was successful in identifying new protein interactions in the native membrane-protein library. Thus, we identified several candidate proteins for interactions with the membrane phosphodiesterase NbdA, a member of the c-di-GMP network. We confirmed the candidate proteins CzcR, PA4200, SadC, and PilB as novel interaction partners of NbdA using the bacterial adenylate cyclase two-hybrid assay. Taken together, this work demonstrates the usefulness of the native membrane-protein library of P. aeruginosa for the investigation of protein interactions and membrane-protein complexes. Data are available via ProteomeXchange with identifiers PXD039702 and PXD039700.
Collapse
Affiliation(s)
- Anna Scherhag
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Markus Räschle
- Department of Molecular Genetics, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Niklas Unbehend
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Benedikt Venn
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - David Glueck
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Timo Mühlhaus
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Sandro Keller
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Eugenio Pérez Patallo
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | | | - Nicole Frankenberg-Dinkel
- Corresponding author. RPTU Kaiserslautern-Landau, Microbiology, Kaiserslautern 67655, Germany. E-mail:
| |
Collapse
|
6
|
Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
Collapse
Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| |
Collapse
|
7
|
López-Lara IM, Govorunova EG. Editorial: In celebration of women in science: Lipids, membranes, and membranous organelles. Front Mol Biosci 2023; 10:1187356. [PMID: 37122568 PMCID: PMC10133683 DOI: 10.3389/fmolb.2023.1187356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Affiliation(s)
- Isabel M. López-Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Isabel M. López-Lara, ; Elena G. Govorunova,
| | - Elena G. Govorunova
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
- *Correspondence: Isabel M. López-Lara, ; Elena G. Govorunova,
| |
Collapse
|
8
|
Cho SG, Song M, Chuon K, Shim JG, Meas S, Jung KH. Heliorhodopsin binds and regulates glutamine synthetase activity. PLoS Biol 2022; 20:e3001817. [PMID: 36190943 PMCID: PMC9529153 DOI: 10.1371/journal.pbio.3001817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022] Open
Abstract
Photoreceptors are light-sensitive proteins found in various organisms that respond to light and relay signals into the cells. Heliorhodopsin, a retinal-binding membrane protein, has been recently discovered, however its function remains unknown. Herein, we investigated the relationship between Actinobacteria bacterium IMCC26103 heliorhodopsin (AbHeR) and an adjacent glutamine synthetase (AbGS) in the same operon. We demonstrate that AbHeR binds to AbGS and regulates AbGS activity. More specifically, the dissociation constant (Kd) value of the binding between AbHeR and AbGS is 6.06 μM. Moreover, the absence of positively charged residues within the intracellular loop of AbHeR impacted Kd value as they serve as critical binding sites for AbGS. We also confirm that AbHeR up-regulates the biosynthetic enzyme activity of AbGS both in vitro and in vivo in the presence of light. GS is a key enzyme involved in nitrogen assimilation that catalyzes the conversion of glutamate and ammonia to glutamine. Hence, the interaction between AbHeR and AbGS may be critical for nitrogen assimilation in Actinobacteria bacterium IMCC26103 as it survives in low-nutrient environments. Overall, the findings of our study describe, for the first time, to the best of our knowledge, a novel function of heliorhodopsin as a regulatory rhodopsin with the capacity to bind and regulate enzyme activity required for nitrogen assimilation. A study of heliorhodopsin, an actinobacterial photoreceptor of unknown function, reveals that it interacts with glutamine synthetase, an enzyme involved in nitrogen assimilation, and regulates its activity in the presence of light, highlighting the diverse functions of rhodopsins in different organisms.
Collapse
Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Myungchul Song
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Jin-gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,Department of Biology, Faculty of Science, Royal University of Phnom Penh, Phnom Penh, Cambodia
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,* E-mail:
| |
Collapse
|
9
|
Zhang Y, Zhu X, Zhang H, Yan J, Xu P, Wu P, Wu S, Bai C. Mechanism Study of Proteins under Membrane Environment. MEMBRANES 2022; 12:membranes12070694. [PMID: 35877897 PMCID: PMC9322369 DOI: 10.3390/membranes12070694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
Membrane proteins play crucial roles in various physiological processes, including molecule transport across membranes, cell communication, and signal transduction. Approximately 60% of known drug targets are membrane proteins. There is a significant need to deeply understand the working mechanism of membrane proteins in detail, which is a challenging work due to the lack of available membrane structures and their large spatial scale. Membrane proteins carry out vital physiological functions through conformational changes. In the current study, we utilized a coarse-grained (CG) model to investigate three representative membrane protein systems: the TMEM16A channel, the family C GPCRs mGlu2 receptor, and the P4-ATPase phospholipid transporter. We constructed the reaction pathway of conformational changes between the two-end structures. Energy profiles and energy barriers were calculated. These data could provide reasonable explanations for TMEM16A activation, the mGlu2 receptor activation process, and P4-ATPase phospholipid transport. Although they all belong to the members of membrane proteins, they behave differently in terms of energy. Our work investigated the working mechanism of membrane proteins and could give novel insights into other membrane protein systems of interest.
Collapse
Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Xiaohong Zhu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Honghui Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Junfang Yan
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peiyi Xu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China;
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
- Correspondence: (S.W.); (C.B.)
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
- Chenzhu Biotechnology Co., Ltd., Hangzhou 310005, China
- Correspondence: (S.W.); (C.B.)
| |
Collapse
|
10
|
Formation of styrene maleic acid lipid nanoparticles (SMALPs) using SMA thin film on a substrate. Anal Biochem 2022; 647:114692. [DOI: 10.1016/j.ab.2022.114692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022]
|
11
|
Wang Q, Zhang Q, He H, Feng Z, Mao J, Hu X, Wei X, Bi S, Qin G, Wang X, Ge B, Yu D, Ren H, Huang F. Carbon Dot Blinking Fingerprint Uncovers Native Membrane Receptor Organizations via Deep Learning. Anal Chem 2022; 94:3914-3921. [PMID: 35188385 DOI: 10.1021/acs.analchem.1c04947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oligomeric organization of G protein-coupled receptors is proposed to regulate receptor signaling and function, yet rapid and precise identification of the oligomeric status especially for native receptors on a cell membrane remains an outstanding challenge. By using blinking carbon dots (CDs), we now develop a deep learning (DL)-based blinking fingerprint recognition method, named deep-blinking fingerprint recognition (BFR), which allows automatic classification of CD-labeled receptor organizations on a cell membrane. This DL model integrates convolutional layers, long-short-term memory, and fully connected layers to extract time-dependent blinking features of CDs and is trained to a high accuracy (∼95%) for identifying receptor organizations. Using deep blinking fingerprint recognition, we found that CXCR4 mainly exists as 87.3% monomers, 12.4% dimers, and <1% higher-order oligomers on a HeLa cell membrane. We further demonstrate that the heterogeneous organizations can be regulated by various stimuli at different degrees. The receptor-binding ligands, agonist SDF-1α and antagonist AMD3100, can induce the dimerization of CXCR4 to 33.1 and 20.3%, respectively. In addition, cytochalasin D, which inhibits actin polymerization, similarly prompts significant dimerization of CXCR4 to 30.9%. The multi-pathway organization regulation will provide an insight for understanding the oligomerization mechanism of CXCR4 as well as for elucidating their physiological functions.
Collapse
Affiliation(s)
- Qian Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Zhang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Zhenzhen Feng
- Technical Center of Qingdao Customs District, Qingdao 266500, China
| | - Jian Mao
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiang Hu
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaoyun Wei
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Simin Bi
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Guangyong Qin
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Daoyong Yu
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| |
Collapse
|
12
|
Exploring the Conformational Changes Induced by Nanosecond Pulsed Electric Fields on the Voltage Sensing Domain of a Ca 2+ Channel. MEMBRANES 2021; 11:membranes11070473. [PMID: 34206827 PMCID: PMC8303878 DOI: 10.3390/membranes11070473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/11/2021] [Accepted: 06/13/2021] [Indexed: 12/21/2022]
Abstract
Nanosecond Pulsed Electric Field (nsPEF or Nano Pulsed Stimulation, NPS) is a technology that delivers a series of pulses of high-voltage electric fields during a short period of time, in the order of nanoseconds. The main consequence of nsPEF upon cells is the formation of nanopores, which is followed by the gating of ionic channels. Literature is conclusive in that the physiological mechanisms governing ion channel gating occur in the order of milliseconds. Hence, understanding how these channels can be activated by a nsPEF would be an important step in order to conciliate fundamental biophysical knowledge with improved nsPEF applications. To get insights on both the kinetics and thermodynamics of ion channel gating induced by nsPEF, in this work, we simulated the Voltage Sensing Domain (VSD) of a voltage-gated Ca2+ channel, inserted in phospholipidic membranes with different concentrations of cholesterol. We studied the conformational changes of the VSD under a nsPEF mimicked by the application of a continuous electric field lasting 50 ns with different intensities as an approach to reveal novel mechanisms leading to ion channel gating in such short timescales. Our results show that using a membrane with high cholesterol content, under an nsPEF of 50 ns and E→ = 0.2 V/nm, the VSD undergoes major conformational changes. As a whole, our work supports the notion that membrane composition may act as an allosteric regulator, specifically cholesterol content, which is fundamental for the response of the VSD to an external electric field. Moreover, changes on the VSD structure suggest that the gating of voltage-gated Ca2+ channels by a nsPEF may be due to major conformational changes elicited in response to the external electric field. Finally, the VSD/cholesterol-bilayer under an nsPEF of 50 ns and E→ = 0.2 V/nm elicits a pore formation across the VSD suggesting a new non-reported effect of nsPEF into cells, which can be called a “protein mediated electroporation”.
Collapse
|
13
|
Işbilir A, Serfling R, Möller J, Thomas R, De Faveri C, Zabel U, Scarselli M, Beck-Sickinger AG, Bock A, Coin I, Lohse MJ, Annibale P. Determination of G-protein-coupled receptor oligomerization by molecular brightness analyses in single cells. Nat Protoc 2021; 16:1419-1451. [PMID: 33514946 DOI: 10.1038/s41596-020-00458-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
Oligomerization of membrane proteins has received intense research interest because of their importance in cellular signaling and the large pharmacological and clinical potential this offers. Fluorescence imaging methods are emerging as a valid tool to quantify membrane protein oligomerization at high spatial and temporal resolution. Here, we provide a detailed protocol for an image-based method to determine the number and oligomerization state of fluorescently labeled prototypical G-protein-coupled receptors (GPCRs) on the basis of small out-of-equilibrium fluctuations in fluorescence (i.e., molecular brightness) in single cells. The protocol provides a step-by-step procedure that includes instructions for (i) a flexible labeling strategy for the protein of interest (using fluorescent proteins, small self-labeling tags or bio-orthogonal labeling) and the appropriate controls, (ii) performing temporal and spatial brightness image acquisition on a confocal microscope and (iii) analyzing and interpreting the data, excluding clusters and intensity hot-spots commonly observed in receptor distributions. Although specifically tailored for GPCRs, this protocol can be applied to diverse classes of membrane proteins of interest. The complete protocol can be implemented in 1 month.
Collapse
Affiliation(s)
- Ali Işbilir
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Jan Möller
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Romy Thomas
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Chiara De Faveri
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Marco Scarselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Andreas Bock
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany. .,ISAR Bioscience Institute, Munich, Germany.
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
| |
Collapse
|
14
|
Sample Preparation and Data Collection for Electron Crystallographic Studies on Membrane Protein Structures and Lipid-Protein Interaction. Methods Mol Biol 2020. [PMID: 33368007 DOI: 10.1007/978-1-0716-0966-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Electron crystallography is a unique tool to study membrane protein structures and lipid-protein interactions in their native-like environments. Two-dimensional (2D) protein crystallization enables the lipids immobilized by the proteins, and the generated high-resolution density map allows us to model the atomic coordinates of the surrounding lipids to study lipid-protein interaction. This protocol describes the sample preparation for electron crystallographic studies, including back-injection method and carbon sandwich method. The protocols of data collection for electron crystallography, including electron imaging and diffraction, of the 2D membrane crystal will be followed.
Collapse
|
15
|
Guérin A, Sulaeman S, Coquet L, Ménard A, Barloy-Hubler F, Dé E, Tresse O. Membrane Proteocomplexome of Campylobacter jejuni Using 2-D Blue Native/SDS-PAGE Combined to Bioinformatics Analysis. Front Microbiol 2020; 11:530906. [PMID: 33329413 PMCID: PMC7717971 DOI: 10.3389/fmicb.2020.530906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/14/2020] [Indexed: 12/27/2022] Open
Abstract
Campylobacter is the leading cause of the human bacterial foodborne infections in the developed countries. The perception cues from biotic or abiotic environments by the bacteria are often related to bacterial surface and membrane proteins that mediate the cellular response for the adaptation of Campylobacter jejuni to the environment. These proteins function rarely as a unique entity, they are often organized in functional complexes. In C. jejuni, these complexes are not fully identified and some of them remain unknown. To identify putative functional multi-subunit entities at the membrane subproteome level of C. jejuni, a holistic non a priori method was addressed using two-dimensional blue native/Sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) in strain C. jejuni 81-176. Couples of acrylamide gradient/migration-time, membrane detergent concentration and hand-made strips were optimized to obtain reproducible extraction and separation of intact membrane protein complexes (MPCs). The MPCs were subsequently denatured using SDS-PAGE and each spot from each MPCs was identified by mass spectrometry. Altogether, 21 MPCs could be detected including multi homo-oligomeric and multi hetero-oligomeric complexes distributed in both inner and outer membranes. The function, the conservation and the regulation of the MPCs across C. jejuni strains were inspected by functional and genomic comparison analyses. In this study, relatedness between subunits of two efflux pumps, CmeABC and MacABputC was observed. In addition, a consensus sequence CosR-binding box in promoter regions of MacABputC was present in C. jejuni but not in Campylobacter coli. The MPCs identified in C. jejuni 81-176 membrane are involved in protein folding, molecule trafficking, oxidative phosphorylation, membrane structuration, peptidoglycan biosynthesis, motility and chemotaxis, stress signaling, efflux pumps and virulence.
Collapse
Affiliation(s)
| | | | - Laurent Coquet
- UMR 6270 Laboratoire Polymères Biopolymères Surfaces, UNIROUEN, INSA Rouen, CNRS, Normandie Université, Rouen, France
- UNIROUEN, Plateforme PISSARO, IRIB, Normandie Université, Mont-Saint-Aignan, France
| | - Armelle Ménard
- INSERM, UMR 1053 Bordeaux Research in Translational Oncology, BaRITOn, Bordeaux, France
| | - Frédérique Barloy-Hubler
- UMR 6290, CNRS, Institut de Génétique et Développement de Rennes, University of Rennes, Rennes, France
| | - Emmanuelle Dé
- UMR 6270 Laboratoire Polymères Biopolymères Surfaces, UNIROUEN, INSA Rouen, CNRS, Normandie Université, Rouen, France
| | | |
Collapse
|
16
|
Nwamba OC. Membranes as the third genetic code. Mol Biol Rep 2020; 47:4093-4097. [PMID: 32279211 DOI: 10.1007/s11033-020-05437-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
Biological membranes and their compositions influence cellular function, age and disease states of organisms. They achieve this by effecting the outcome of bound enzymes/proteins and carbohydrate moieties. While the membrane-bound carbohydrates give rise to antigenicity, membranes impact the eventual outcome of protein structures that would function even outside their enclosure. This is achieved by membrane modulation of translational and post-translational protein folding. Thus, the eventual 3D structures and functions of proteins might not be solely dependent on their primary amino acid sequences and surrounding environments. The 3D protein structures would also depend on enclosing membrane properties such as fluidity, other intrinsic and extrinsic proteins and carbohydrate functionalities. Also, membranes moderate DNA activities with consequences on gene activation-inactivation mechanisms. Consequently, membranes are almost indispensable to the functioning of other cell compositions and serve to modulate these other components. Besides, membrane lipid compositions are also moderated by nutrition and diets and the converse is true. Thus, it could be argued that membranes are the third genetic codes. Suggestively, membranes are at the center of the interplay between nature and nurture in health and disease states.
Collapse
|
17
|
Sahu ID, Dixit G, Reynolds WD, Kaplevatsky R, Harding BD, Jaycox CK, McCarrick RM, Lorigan GA. Characterization of the Human KCNQ1 Voltage Sensing Domain (VSD) in Lipodisq Nanoparticles for Electron Paramagnetic Resonance (EPR) Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2020; 124:2331-2342. [PMID: 32130007 DOI: 10.1021/acs.jpcb.9b11506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane proteins are responsible for conducting essential biological functions that are necessary for the survival of living organisms. In spite of their physiological importance, limited structural information is currently available as a result of challenges in applying biophysical techniques for studying these protein systems. Electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study the structural and dynamic properties of membrane proteins. However, the application of EPR spectroscopy to membrane proteins in a native membrane-bound state is extremely challenging due to the complexity observed in inhomogeneity sample preparation and the dynamic motion of the spin label. Detergent micelles are very popular membrane mimetics for membrane proteins due to their smaller size and homogeneity, providing high-resolution structure analysis by solution NMR spectroscopy. However, it is important to test whether the protein structure in a micelle environment is the same as that of its membrane-bound state. Lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have been introduced as a potentially good membrane-mimetic system for structural studies of membrane proteins. Recently, we reported on the EPR characterization of the KCNE1 membrane protein having a single transmembrane incorporated into lipodisq nanoparticles. In this work, lipodisq nanoparticles were used as a membrane mimic system for probing the structural and dynamic properties of the more complicated membrane protein system human KCNQ1 voltage sensing domain (Q1-VSD) having four transmembrane helices using site-directed spin-labeling EPR spectroscopy. Characterization of spin-labeled Q1-VSD incorporated into lipodisq nanoparticles was carried out using CW-EPR spectral line shape analysis and pulsed EPR double-electron electron resonance (DEER) measurements. The CW-EPR spectra indicate an increase in spectral line broadening with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated a superior quality of distance measurement with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles when compared to proteoliposomes. These results are consistent with the solution NMR structural studies on the Q1-VSD. This study will be beneficial for researchers working on investigating the structural and dynamic properties of more complicated membrane protein systems using lipodisq nanoparticles.
Collapse
Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
| | - Gunjan Dixit
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Warren D Reynolds
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ryan Kaplevatsky
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Colleen K Jaycox
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| |
Collapse
|
18
|
Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. Methods Mol Biol 2020. [PMID: 31218616 DOI: 10.1007/978-1-4939-9512-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.
Collapse
|
19
|
Burridge KM, Harding BD, Sahu ID, Kearns MM, Stowe RB, Dolan MT, Edelmann RE, Dabney-Smith C, Page RC, Konkolewicz D, Lorigan GA. Simple Derivatization of RAFT-Synthesized Styrene-Maleic Anhydride Copolymers for Lipid Disk Formulations. Biomacromolecules 2020; 21:1274-1284. [PMID: 31961664 DOI: 10.1021/acs.biomac.0c00041] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Styrene-maleic acid copolymers have received significant attention because of their ability to interact with lipid bilayers and form styrene-maleic acid copolymer lipid nanoparticles (SMALPs). However, these SMALPs are limited in their chemical diversity, with only phenyl and carboxylic acid functional groups, resulting in limitations because of sensitivity to low pH and high concentrations of divalent metals. To address this limitation, various nucleophiles were reacted with the anhydride unit of well-defined styrene-maleic anhydride copolymers in order to assess the potential for a new lipid disk nanoparticle-forming species. These styrene-maleic anhydride copolymer derivatives (SMADs) can form styrene-maleic acid derivative lipid nanoparticles (SMADLPs) when they interact with lipid molecules. Polymers were synthesized, purified, characterized by Fourier-transform infrared spectroscopy, gel permeation chromatography, and nuclear magnetic resonance and then used to make disk-like SMADLPs, whose sizes were measured by dynamic light scattering (DLS). The SMADs form lipid nanoparticles, observable by DLS and transmission electron microscopy, and were used to reconstitute a spin-labeled transmembrane protein, KCNE1. The polymer method reported here is facile and scalable and results in functional and robust polymers capable of forming lipid nanodisks that are stable against a wide pH range and 100 mM magnesium.
Collapse
Affiliation(s)
- Kevin M Burridge
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, KY 42718, United States
| | - Madison M Kearns
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Rebecca B Stowe
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Madison T Dolan
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Richard E Edelmann
- Center for Advanced Microscopy & Imaging, Miami University, Oxford, Ohio 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University of Oxford Ohio, Oxford, Ohio 45056, United States
| |
Collapse
|
20
|
Bali AP, Sahu ID, Craig AF, Clark EE, Burridge KM, Dolan MT, Dabney-Smith C, Konkolewicz D, Lorigan GA. Structural characterization of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using EPR spectroscopy. Chem Phys Lipids 2019; 220:6-13. [PMID: 30796886 DOI: 10.1016/j.chemphyslip.2019.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/29/2019] [Accepted: 02/18/2019] [Indexed: 12/31/2022]
Abstract
Spectroscopic studies of membrane proteins (MPs) are challenging due to difficulties in preparing homogenous and functional lipid membrane mimetic systems into which membrane proteins can properly fold and function. It has recently been shown that styrene-maleic acid (SMA) copolymers act as a macromolecular surfactant and therefore facilitate the formation of disk-shaped lipid bilayer nanoparticles (styrene-maleic acid copolymer-lipid nanoparticles (SMALPs)) that retain structural characteristics of native lipid membranes. We have previously reported controlled synthesis of SMA block copolymers using reversible addition-fragmentation chain transfer (RAFT) polymerization, and that alteration of the weight ratio of styrene to maleic acid affects nanoparticle size. RAFT-synthesis offers superior control over SMA polymer architecture compared to conventional radical polymerization techniques used for commercially available SMA. However, the interactions between the lipid bilayer and the solubilized RAFT-synthesized SMA polymer are currently not fully understood. In this study, EPR spectroscopy was used to detect the perturbation on the acyl chain upon introduction of the RAFT-synthesized SMA polymer by attaching PC-based nitroxide spin labels to the 5th, 12th, and 16th positions along the acyl chain of the lipid bilayer. EPR spectra showed high rigidity at the 12th position compared to the other two regions, displaying similar qualities to commercially available polymers synthesized via conventional methods. In addition, central EPR linewidths and correlation time data were obtained that are consistent with previous findings.
Collapse
Affiliation(s)
- Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Emily E Clark
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Kevin M Burridge
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Madison T Dolan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
| |
Collapse
|
21
|
Bioinformatics Analysis and Functional Prediction of Transmembrane Proteins in Entamoeba histolytica. Genes (Basel) 2018; 9:genes9100499. [PMID: 30332795 PMCID: PMC6209943 DOI: 10.3390/genes9100499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/09/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022] Open
Abstract
Entamoeba histolytica is an invasive, pathogenic parasite causing amoebiasis. Given that proteins involved in transmembrane (TM) transport are crucial for the adherence, invasion, and nutrition of the parasite, we conducted a genome-wide bioinformatics analysis of encoding proteins to functionally classify and characterize all the TM proteins in E. histolytica. In the present study, 692 TM proteins have been identified, of which 546 are TM transporters. For the first time, we report a set of 141 uncharacterized proteins predicted as TM transporters. The percentage of TM proteins was found to be lower in comparison to the free-living eukaryotes, due to the extracellular nature and functional diversification of the TM proteins. The number of multi-pass proteins is larger than the single-pass proteins; though both have their own significance in parasitism, multi-pass proteins are more extensively required as these are involved in acquiring nutrition and for ion transport, while single-pass proteins are only required at the time of inciting infection. Overall, this intestinal parasite implements multiple mechanisms for establishing infection, obtaining nutrition, and adapting itself to the new host environment. A classification of the repertoire of TM transporters in the present study augments several hints on potential methods of targeting the parasite for therapeutic benefits.
Collapse
|
22
|
Ereño-Orbea J, Sicard T, Cui H, Akula I, Julien JP. Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques. J Vis Exp 2018. [PMID: 30035760 PMCID: PMC6124603 DOI: 10.3791/57750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Glycoproteins on the surface of cells play critical roles in cellular function, including signalling, adhesion and transport. On leukocytes, several of these glycoproteins possess immunoglobulin (Ig) folds and are central to immune recognition and regulation. Here, we present a platform for the design, expression and biophysical characterization of the extracellular domain of human B cell receptor CD22. We propose that these approaches are broadly applicable to the characterization of mammalian glycoprotein ectodomains containing Ig domains. Two suspension human embryonic kidney (HEK) cell lines, HEK293F and HEK293S, are used to express glycoproteins harbouring complex and high-mannose glycans, respectively. These recombinant glycoproteins with different glycoforms allow investigating the effect of glycan size and composition on ligand binding. We discuss protocols for studying the kinetics and thermodynamics of glycoprotein binding to biologically relevant ligands and therapeutic antibody candidates. Recombinant glycoproteins produced in HEK293S cells are amenable to crystallization due to glycan homogeneity, reduced flexibility and susceptibility to endoglycosidase H treatment. We present methods for soaking glycoprotein crystals with heavy atoms and small molecules for phase determination and analysis of ligand binding, respectively. The experimental protocols discussed here hold promise for the characterization of mammalian glycoproteins to give insight into their function and investigate the mechanism of action of therapeutics.
Collapse
Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Indira Akula
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto; Department of Immunology, University of Toronto;
| |
Collapse
|
23
|
Liao C, Zhao X, Liu J, Schneebeli ST, Shelley JC, Li J. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models. Phys Chem Chem Phys 2018; 19:9181-9188. [PMID: 28317993 DOI: 10.1039/c7cp00200a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.
Collapse
Affiliation(s)
- Chenyi Liao
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
| | - Xiaochuan Zhao
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
| | - Jiyuan Liu
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
| | | | - John C Shelley
- Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, OR 97204, USA
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
| |
Collapse
|
24
|
Huang X, He J, Zhang HT, Sun K, Yang J, Wang H, Zhang H, Guo Z, Zha ZG, Zhou C. Effect of dacarbazine on CD44 in live melanoma cells as measured by atomic force microscopy-based nanoscopy. Int J Nanomedicine 2017; 12:8867-8886. [PMID: 29296081 PMCID: PMC5739545 DOI: 10.2147/ijn.s149107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
CD44 ligand-receptor interactions are known to be involved in regulating cell migration and tumor cell metastasis. High expression levels of CD44 correlate with a poor prognosis of melanoma patients. In order to understand not only the mechanistic basis for dacarbazine (DTIC)-based melanoma treatment but also the reason for the poor prognosis of melanoma patients treated with DTIC, dynamic force spectroscopy was used to structurally map single native CD44-coupled receptors on the surface of melanoma cells. The effect of DTIC treatment was quantified by the dynamic binding strength and the ligand-binding free-energy landscape. The results demonstrated no obvious effect of DTIC on the unbinding force between CD44 ligand and its receptor, even when the CD44 nanodomains were reduced significantly. However, DTIC did perturb the kinetic and thermodynamic interactions of the CD44 ligand-receptor, with a resultant greater dissociation rate, lower affinity, lower binding free energy, and a narrower energy valley for the free-energy landscape. For cells treated with 25 and 75 μg/mL DTIC for 24 hours, the dissociation constant for CD44 increased 9- and 70-fold, respectively. The CD44 ligand binding free energy decreased from 9.94 for untreated cells to 8.65 and 7.39 kcal/mol for DTIC-treated cells, which indicated that the CD44 ligand-receptor complexes on DTIC-treated melanoma cells were less stable than on untreated cells. However, affinity remained in the micromolar range, rather than the millimolar range associated with nonaffinity ligands. Hence, the CD44 receptor could still be activated, resulting in intracellular signaling that could trigger a cellular response. These results demonstrate DTIC perturbs, but not completely inhibits, the binding of CD44 ligand to membrane receptors, suggesting a basis for the poor prognosis associated with DTIC treatment of melanoma. Overall, atomic force microscopy-based nanoscopic methods offer thermodynamic and kinetic insight into the effect of DTIC on the CD44 ligand-binding process.
Collapse
Affiliation(s)
- Xun Huang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University
- Department of Materials Science and Engineering, Jinan University
| | - Jiexiang He
- Department of Materials Science and Engineering, Jinan University
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education, Guangzhou, China
| | - Huan-tian Zhang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University
| | - Kai Sun
- Department of Materials Science and Engineering, Jinan University
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education, Guangzhou, China
| | - Jie Yang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University
| | - Huajun Wang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University
| | - Hongxin Zhang
- Department of Materials Science and Engineering, Jinan University
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education, Guangzhou, China
| | - Zhenzhao Guo
- Department of Materials Science and Engineering, Jinan University
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education, Guangzhou, China
| | - Zhen-gang Zha
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University
| | - Changren Zhou
- Department of Materials Science and Engineering, Jinan University
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education, Guangzhou, China
| |
Collapse
|
25
|
Affiliation(s)
- Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
- Department of Physics, University of Arizona, Tucson, Arizona 85721
| |
Collapse
|
26
|
Pfreundschuh M, Harder D, Ucurum Z, Fotiadis D, Müller DJ. Detecting Ligand-Binding Events and Free Energy Landscape while Imaging Membrane Receptors at Subnanometer Resolution. NANO LETTERS 2017; 17:3261-3269. [PMID: 28361535 DOI: 10.1021/acs.nanolett.7b00941] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Force-distance curve-based atomic force microscopy has emerged into a sophisticated technique for imaging cellular membranes and for detecting specific ligand-binding events of native membrane receptors. However, so far the resolution achieved has been insufficient to structurally map ligand-binding sites onto membrane proteins. Here, we introduce experimental and theoretical approaches for overcoming this limitation. To establish a structurally and functionally well-defined reference sample, we engineer a ligand-binding site to the light-driven proton pump bacteriorhodopsin of purple membrane. Functionalizing the AFM stylus with an appropriate linker-system tethering the ligand and optimizing the AFM conditions allows for imaging the engineered bacteriorhodopsin at subnanometer resolution while structurally mapping the specific ligand-receptor binding events. Improved data analysis allows reconstructing the ligand-binding free energy landscape from the experimental data, thus providing thermodynamic and kinetic insight into the ligand-binding process. The nanoscopic method introduced is generally applicable for imaging receptors in native membranes at subnanometer resolution and for systematically mapping and quantifying the free energy landscape of ligand binding.
Collapse
Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
| |
Collapse
|
27
|
Bhattarai N, Gc JB, Gerstman BS, Stahelin RV, Chapagain PP. Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer. RSC Adv 2017; 7:22741-22748. [PMID: 28580138 PMCID: PMC5436087 DOI: 10.1039/c7ra02940c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 04/19/2017] [Indexed: 11/21/2022] Open
Abstract
The membrane binding interface of the Marburg virus protein mVP40 dimer differs from that of the Ebola virus eVP40 dimer but membrane binding allows conformational changes in mVP40 that makes it structurally similar to the eVP40 dimer.
Filovirus infections cause hemorrhagic fever in humans and non-human primates that often results in high fatality rates. The Marburg virus is a lipid-enveloped virus from the Filoviridae family and is closely related to the Ebola virus. The viral matrix layer underneath the lipid envelope is formed by the matrix protein VP40 (VP40), which is also involved in other functions during the viral life-cycle. As in the Ebola virus VP40 (eVP40), the recently determined X-ray crystal structure of the Marburg virus VP40 (mVP40) features loops containing cationic residues that form a lipid binding basic patch. However, the mVP40 basic patch is significantly flatter with a more extended surface than in eVP40, suggesting the possibility of differences in the plasma membrane interactions and phospholipid specificity between the VP40 dimers. In this paper, we report on molecular dynamics simulations that investigate the roles of various residues and lipid types in PM association as well as the conformational changes of the mVP40 dimer facilitated by membrane association. We compared the structural changes of the mVP40 dimer with the mVP40 dimer in both lipid free and membrane associated conditions. Despite the significant structural differences in the crystal structure, the Marburg VP40 dimer is found to adopt a configuration very similar to the Ebola VP40 dimer after associating with the membrane. This conformational rearrangement upon lipid binding allows Marburg VP40 to localize and stabilize at the membrane surface in a manner similar to the Ebola VP40 dimer. Consideration of the structural information in its lipid-interacting condition may be important in targeting mVP40 for novel drugs to inhibit viral budding from the plasma membrane.
Collapse
Affiliation(s)
- Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL 33199, USA.
| | - Jeevan B Gc
- Department of Physics, Florida International University, Miami, FL 33199, USA.
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA. .,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Robert V Stahelin
- Department of Chemistry and Biochemistry, The Eck Institute for Global Health, The Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA. .,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
28
|
Hughes AV, Ciesielski F, Kalli AC, Clifton LA, Charlton TR, Sansom MSP, Webster JRP. On the interpretation of reflectivity data from lipid bilayers in terms of molecular-dynamics models. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1227-1240. [PMID: 27917824 DOI: 10.1107/s2059798316016235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/12/2016] [Indexed: 02/08/2023]
Abstract
Neutron and X-ray reflectivity of model membranes is increasingly used as a tool for the study of membrane structures and dynamics. As the systems under study become more complex, and as long, all-atom molecular-dynamics (MD) simulations of membranes become more available, there is increasing interest in the use of MD simulations in the analysis of reflectometry data from membranes. In order to perform this, it is necessary to produce a model of the complete interface, including not only the MD-derived structure of the membrane, but also the supporting substrate and any other interfacial layers that may be present. Here, it is shown that this is best performed by first producing a model of the occupied volume across the entire interface, and then converting this into a scattering length density (SLD) profile, rather than by splicing together the separate SLD profiles from the substrate layers and the membrane, since the latter approach can lead to discontinuities in the SLD profile and subsequent artefacts in the reflectivity calculation. It is also shown how the MD-derived membrane structure should be corrected to account for lower than optimal coverage and out-of-plane membrane fluctuations. Finally, the method of including the entire membrane structure in the reflectivity calculation is compared with an alternative approach in which the membrane components are approximated by functional forms, with only the component volumes being extracted from the simulation. It is shown that using only the fragment volumes is insufficient for a typical neutron data set of a single deuteration measured at several water contrasts, and that either weighting the model by including more structural information from the fit, or a larger data set involving a range of deuterations, are required to satisfactorily define the problem.
Collapse
Affiliation(s)
- Arwel V Hughes
- ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Harwell OX11 0QX, England
| | - Fillip Ciesielski
- ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Harwell OX11 0QX, England
| | - Antreas C Kalli
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England
| | - Luke A Clifton
- ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Harwell OX11 0QX, England
| | - Timothy R Charlton
- ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Harwell OX11 0QX, England
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England
| | - John R P Webster
- ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Harwell OX11 0QX, England
| |
Collapse
|
29
|
Varshney GK, Kintali SR, Gupta PK, Das K. Effect of Bilayer Partitioning of Curcumin on the Adsorption and Transport of a Cationic Dye Across POPG Liposomes Probed by Second-Harmonic Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10415-10421. [PMID: 27636651 DOI: 10.1021/acs.langmuir.6b02797] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The effect of Curcumin partitioning into the bilayer during the adsorption and transport of a cationic dye, LDS, across a negatively charged POPG bilayer was investigated by the interface-selective second-harmonic (SH) spectroscopic technique. The intensity of SH electric field (E2ω) arising due to LDS adsorbed on the outer bilayer of the POPG liposome was observed to increase instantaneously (<1 s) following the addition of Curcumin. The fractional increase in the SH electric field (Ef2ω) and the bilayer transport rates (kT) of LDS were studied with respect to the pH of the solution and also with the Curcumin content in the lipid bilayer. Results obtained indicate that compared with the anionic form of the drug, its neutral form is more conducive of increasing the Ef2ω of LDS. With increasing Curcumin content in the lipid bilayer, two distinct regimes could be observed in terms of Ef2ω and kT values of LDS. For Curcumin:Lipid (C/L) ratio ≤0.02, the Ef2ω of LDS increases rapidly, while kT remains unchanged; and for C/L ratio ≥0.02, the Ef2ω values remains more or less constant, while there is a significant (∼40 times) increase followed by a modest increase in the kT values of LDS. The observed results support an earlier two-state binding model of Curcumin with the POPG bilayer. In addition, it is further proposed that at low C/L ratio Curcumin binds to the surface of the bilayer replacing the counterions (Na+) bound to the lipid head groups, which changes the bilayer surface charge density, thereby causing more LDS cations to adsorb on the bilayer surface. At high C/L ratio, Curcumin intercalates within the hydrophobic domain of the bilayer, altering its hydrophobicity and inducing enhanced transport of the LDS cation. Results presented in this work provide further insights into how Curcumin alters bilayer properties when it partitions from the aqueous to the bilayer phase.
Collapse
Affiliation(s)
- G K Varshney
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - S R Kintali
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - P K Gupta
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - K Das
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| |
Collapse
|
30
|
Craig AF, Clark EE, Sahu ID, Zhang R, Frantz ND, Al-Abdul-Wahid MS, Dabney-Smith C, Konkolewicz D, Lorigan GA. Tuning the size of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using RAFT polymerization for biophysical studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2931-2939. [PMID: 27539205 DOI: 10.1016/j.bbamem.2016.08.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/15/2016] [Accepted: 08/07/2016] [Indexed: 11/29/2022]
Abstract
Characterization of membrane proteins is challenging due to the difficulty in mimicking the native lipid bilayer with properly folded and functional membrane proteins. Recently, styrene-maleic acid (StMA) copolymers have been shown to facilitate the formation of disc-like lipid bilayer mimetics that maintain the structural and dynamic integrity of membrane proteins. Here we report the controlled synthesis and characterization of StMA containing block copolymers. StMA polymers with different compositions and molecular weights were synthesized and characterized by size exclusion chromatography (SEC). These polymers act as macromolecular surfactants for 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol (POPG) lipids, forming disc like structures of the lipids with the polymer wrapping around the hydrophobic lipid edge. A combination of dynamic light scattering (DLS), solid-state nuclear magnetic resonance (SSNMR) spectroscopy, and transmission electron microscopy (TEM) was used to characterize the size of the nanoparticles created using these StMA polymers. At a weight ratio of 1.25:1 StMA to lipid, the nanoparticle size created is 28+1nm for a 2:1 ratio, 10+1nm for a 3:1 StMA ratio and 32+1nm for a 4:1 StMA ratio independent of the molecular weight of the polymer. Due to the polymer acting as a surfactant that forms disc like nanoparticles, we term these StMA based block copolymers "RAFT SMALPs". RAFT SMALPs show promise as a new membrane mimetic with different nanoscale sizes, which can be used for a wide variety of biophysical studies of membrane proteins.
Collapse
Affiliation(s)
- Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Emily E Clark
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Nick D Frantz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - M Sameer Al-Abdul-Wahid
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States.
| |
Collapse
|
31
|
Lipids modulate the conformational dynamics of a secondary multidrug transporter. Nat Struct Mol Biol 2016; 23:744-51. [PMID: 27399258 DOI: 10.1038/nsmb.3262] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/16/2016] [Indexed: 02/06/2023]
Abstract
Direct interactions with lipids have emerged as key determinants of the folding, structure and function of membrane proteins, but an understanding of how lipids modulate protein dynamics is still lacking. Here, we systematically explored the effects of lipids on the conformational dynamics of the proton-powered multidrug transporter LmrP from Lactococcus lactis, using the pattern of distances between spin-label pairs previously shown to report on alternating access of the protein. We uncovered, at the molecular level, how the lipid headgroups shape the conformational-energy landscape of the transporter. The model emerging from our data suggests a direct interaction between lipid headgroups and a conserved motif of charged residues that control the conformational equilibrium through an interplay of electrostatic interactions within the protein. Together, our data lay the foundation for a comprehensive model of secondary multidrug transport in lipid bilayers.
Collapse
|
32
|
Kumar B, Sheetal S, Mantha AK, Kumar V. Recent developments on the structure–activity relationship studies of MAO inhibitors and their role in different neurological disorders. RSC Adv 2016. [DOI: 10.1039/c6ra00302h] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Development of MAO inhibitors as effective drug candidates for the management and/or treatment of different neurological disorders.
Collapse
Affiliation(s)
- Bhupinder Kumar
- Laboratory of Organic and Medicinal Chemistry
- Centre for Pharmaceutical Sciences and Natural Products
- Central University of Punjab
- Bathinda
- India-151001
| | - Sheetal Sheetal
- Laboratory of Organic and Medicinal Chemistry
- Centre for Pharmaceutical Sciences and Natural Products
- Central University of Punjab
- Bathinda
- India-151001
| | - Anil K. Mantha
- Centre for Animal Sciences
- School of Basic and Applied Sciences
- Central University of Punjab
- Bathinda
- India
| | - Vinod Kumar
- Laboratory of Organic and Medicinal Chemistry
- Centre for Pharmaceutical Sciences and Natural Products
- Central University of Punjab
- Bathinda
- India-151001
| |
Collapse
|
33
|
Zhang R, Sahu ID, Gibson KR, Muhammad NB, Bali AP, Comer RG, Liu L, Craig AF, Mccarrick RM, Dabney-Smith C, Sanders CR, Lorigan GA. Development of electron spin echo envelope modulation spectroscopy to probe the secondary structure of recombinant membrane proteins in a lipid bilayer. Protein Sci 2015; 24:1707-13. [PMID: 26355804 DOI: 10.1002/pro.2795] [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] [Received: 07/22/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 12/19/2022]
Abstract
Membrane proteins conduct many important biological functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is very difficult to obtain structural information on membrane-bound proteins using traditional biophysical techniques. We are developing a new approach to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. This method has been successfully applied to model peptides made synthetically. However, in order for this ESEEM technique to be widely applicable to larger membrane protein systems with no size limitations, protein samples with deuterated residues need to be prepared via protein expression methods. For the first time, this study shows that the ESEEM approach can be used to probe the local secondary structure of a (2) H-labeled d8 -Val overexpressed membrane protein in a membrane mimetic environment. The membrane-bound human KCNE1 protein was used with a known solution NMR structure to demonstrate the applicability of this methodology. Three different α-helical regions of KCNE1 were probed: the extracellular domain (Val21), transmembrane domain (Val50), and cytoplasmic domain (Val95). These results indicated α-helical structures in all three segments, consistent with the micelle structure of KCNE1. Furthermore, KCNE1 was incorporated into a lipid bilayer and the secondary structure of the transmembrane domain (Val50) was shown to be α-helical in a more native-like environment. This study extends the application of this ESEEM approach to much larger membrane protein systems that are difficult to study with X-ray crystallography and/or NMR spectroscopy.
Collapse
Affiliation(s)
- Rongfu Zhang
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Kaylee R Gibson
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Nefertiti B Muhammad
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Raven G Comer
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Robert M Mccarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Carole Dabney-Smith
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Gary A Lorigan
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| |
Collapse
|
34
|
Ashkar R, Nagao M, Butler PD, Woodka AC, Sen MK, Koga T. Tuning membrane thickness fluctuations in model lipid bilayers. Biophys J 2015; 109:106-12. [PMID: 26153707 PMCID: PMC4571027 DOI: 10.1016/j.bpj.2015.05.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 11/21/2022] Open
Abstract
Membrane thickness fluctuations have been associated with a variety of critical membrane phenomena, such as cellular exchange, pore formation, and protein binding, which are intimately related to cell functionality and effective pharmaceuticals. Therefore, understanding how these fluctuations are controlled can remarkably impact medical applications involving selective macromolecule binding and efficient cellular drug intake. Interestingly, previous reports on single-component bilayers show almost identical thickness fluctuation patterns for all investigated lipid tail-lengths, with similar temperature-independent membrane thickness fluctuation amplitude in the fluid phase and a rapid suppression of fluctuations upon transition to the gel phase. Presumably, in vivo functions require a tunability of these parameters, suggesting that more complex model systems are necessary. In this study, we explore lipid tail-length mismatch as a regulator for membrane fluctuations. Unilamellar vesicles of an equimolar mixture of dimyristoylphosphatidylcholine and distearoylphosphatidylcholine molecules, with different tail-lengths and melting transition temperatures, are used as a model system for this next level of complexity. Indeed, this binary system exhibits a significant response of membrane dynamics to thermal variations. The system also suggests a decoupling of the amplitude and the relaxation time of the membrane thickness fluctuations, implying a potential for independent control of these two key parameters.
Collapse
Affiliation(s)
- Rana Ashkar
- National Institute of Standards and Technology (NIST) Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland; Department of Material Science and Engineering, University of Maryland, College Park, Maryland
| | - Michihiro Nagao
- National Institute of Standards and Technology (NIST) Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland; Center for Exploration of Energy and Matter, Indiana University, Bloomington, Indiana.
| | - Paul D Butler
- National Institute of Standards and Technology (NIST) Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland; Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware
| | - Andrea C Woodka
- Department of Chemistry & Life Science, United States Military Academy, West Point, New York
| | - Mani K Sen
- Department of Materials Science and Engineering, Stony Brook University, Stony Brook, New York
| | - Tadanori Koga
- Department of Materials Science and Engineering, Stony Brook University, Stony Brook, New York; Chemical and Molecular Engineering Program, Stony Brook University, Stony Brook, New York
| |
Collapse
|
35
|
Jun MH, Jun YW, Kim KH, Lee JA, Jang DJ. Characterization of the cellular localization of C4orf34 as a novel endoplasmic reticulum resident protein. BMB Rep 2015; 47:563-8. [PMID: 24499674 PMCID: PMC4261514 DOI: 10.5483/bmbrep.2014.47.10.252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Indexed: 01/09/2023] Open
Abstract
Human genome projects have enabled whole genome mapping and improved our understanding of the genes in humans. However, many unknown genes remain to be functionally characterized. In this study, we characterized human chromosome 4 open reading frame 34 gene (hC4orf34). hC4orf34 was highly conserved from invertebrate to mammalian cells and ubiquitously expressed in the organs of mice, including the heart and brain. Interestingly, hC4orf34 is a novel ER-resident, type I transmembrane protein. Mutant analysis showed that the transmembrane domain (TMD) of hC4orf34 was involved in ER retention. Overall, our results indicate that hC4orf34 is an ER-resident type I transmembrane protein, and might play a role in ER functions including Ca2+ homeostasis and ER stress. [BMB Reports 2014; 47(10): 563-568]
Collapse
Affiliation(s)
- Mi-Hee Jun
- Department of Biotechnology, College of Life Science and Nano Technology, Hannam University, Daejeon 305-811, Korea
| | - Young-Wu Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju 742-711, Korea
| | - Kun-Hyung Kim
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju 742-711, Korea
| | - Jin-A Lee
- Department of Biotechnology, College of Life Science and Nano Technology, Hannam University, Daejeon 305-811, Korea
| | - Deok-Jin Jang
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju 742-711, Korea
| |
Collapse
|
36
|
Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
|
37
|
Sun B. Proteomics and glycoproteomics of pluripotent stem-cell surface proteins. Proteomics 2014; 15:1152-63. [DOI: 10.1002/pmic.201400300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/07/2014] [Accepted: 09/08/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Bingyun Sun
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University; Burnaby British Columbia Canada
| |
Collapse
|
38
|
Muir A, Ramachandran S, Roelants FM, Timmons G, Thorner J. TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids. eLife 2014; 3. [PMID: 25279700 PMCID: PMC4217029 DOI: 10.7554/elife.03779] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/02/2014] [Indexed: 12/14/2022] Open
Abstract
Plasma membrane lipid composition must be maintained during growth and under environmental insult. In yeast, signaling mediated by TOR Complex 2 (TORC2)-dependent protein kinase Ypk1 controls lipid abundance and distribution in response to membrane stress. Ypk1, among other actions, alleviates negative regulation of L-serine:palmitoyl-CoA acyltransferase, upregulating production of long-chain base precursors to sphingolipids. To explore other roles for TORC2-Ypk1 signaling in membrane homeostasis, we devised a three-tiered genome-wide screen to identify additional Ypk1 substrates, which pinpointed both catalytic subunits of the ceramide synthase complex. Ypk1-dependent phosphorylation of both proteins increased upon either sphingolipid depletion or heat shock and was important for cell survival. Sphingolipidomics, other biochemical measurements and genetic analysis demonstrated that these modifications of ceramide synthase increased its specific activity and stimulated channeling of long-chain base precursors into sphingolipid end-products. Control at this branch point also prevents accumulation of intermediates that could compromise cell growth by stimulating autophagy. DOI:http://dx.doi.org/10.7554/eLife.03779.001 Cells are enclosed by a plasma membrane that separates and protects each cell from its environment. These membranes are made of a variety of proteins and fatty molecules called lipids, which are carefully organized throughout the membrane. When cells experience stresses such as heat or excessive pressure, the plasma membrane changes to help protect the cell. In particular, more of a group of lipids called sphingolipids are incorporated into the membrane under stress conditions. In yeast cells, a protein called Ypk1 plays an important role in protecting the cell from stress. Ypk1 controls the activity of a number of proteins that are responsible for balancing the amounts of different types of lipids in cell membranes. The combined action of these Ypk1-dependent proteins leads to the remodelling of the cell membrane to protect against stress. While several proteins that work with Ypk1 are known, some of the changes that serve to protect the plasma membrane cannot be explained by the action of these proteins alone. To provide a more comprehensive picture of how Ypk1 helps cells to respond to changes in the environment, Muir et al. developed a new approach that combines biochemical, genetic and bioinformatics techniques to survey the yeast genome for proteins that could be Ypk1 targets. Muir et al. first produced a list of potential candidate proteins by searching for proteins with features similar to known Ypk1 targets, and then considered those that are known to be involved in processes that also involve Ypk1. To filter the potential targets further, Muir et al. performed experiments in yeast cells to see which proteins prevented normal cell growth if they were over-produced. Further experiments investigating which of these proteins interact with Ypk1 when purified identified 12 new proteins that are most likely targets of the Ypk1 protein. Two of these newly identified Ypk1 target proteins form part of an enzyme complex called ceramide synthase, which produces a family of waxy lipid molecules from which more complex sphingolipids are built. Muir et al. discovered that during stress, Ypk1 enhances the activity of the ceramide synthase enzyme, which increases lipid production and the amount of sphingolipid deposited in the cell membrane. If this process is interrupted at any stage, cells struggle to survive under stress conditions. The other candidate proteins identified by Muir et al. remain to be validated and characterized as Ypk1 targets. Nevertheless, the techniques used have conclusively identified some new Ypk1 targets and could also be applied to similar searches for proteins targeted in other biological processes. DOI:http://dx.doi.org/10.7554/eLife.03779.002
Collapse
Affiliation(s)
- Alexander Muir
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Subramaniam Ramachandran
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Françoise M Roelants
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Garrett Timmons
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
39
|
The structural and functional coordination of glycolytic enzymes in muscle: evidence of a metabolon? BIOLOGY 2014; 3:623-44. [PMID: 25247275 PMCID: PMC4192631 DOI: 10.3390/biology3030623] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/05/2014] [Accepted: 09/08/2014] [Indexed: 12/22/2022]
Abstract
Metabolism sustains life through enzyme-catalyzed chemical reactions within the cells of all organisms. The coupling of catalytic function to the structural organization of enzymes contributes to the kinetic optimization important to tissue-specific and whole-body function. This coupling is of paramount importance in the role that muscle plays in the success of Animalia. The structure and function of glycolytic enzyme complexes in anaerobic metabolism have long been regarded as a major regulatory element necessary for muscle activity and whole-body homeostasis. While the details of this complex remain to be elucidated through in vivo studies, this review will touch on recent studies that suggest the existence of such a complex and its structure. A potential model for glycolytic complexes and related subcomplexes is introduced.
Collapse
|
40
|
Tonnesen A, Christensen SM, Tkach V, Stamou D. Geometrical membrane curvature as an allosteric regulator of membrane protein structure and function. Biophys J 2014; 106:201-9. [PMID: 24411252 DOI: 10.1016/j.bpj.2013.11.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 11/07/2013] [Accepted: 11/12/2013] [Indexed: 10/25/2022] Open
Abstract
Transmembrane proteins are embedded in cellular membranes of varied lipid composition and geometrical curvature. Here, we studied for the first time the allosteric effect of geometrical membrane curvature on transmembrane protein structure and function. We used single-channel optical analysis of the prototypic transmembrane β-barrel α-hemolysin (α-HL) reconstituted on immobilized single small unilamellar liposomes of different diameter and therefore curvature. Our data demonstrate that physiologically abundant geometrical membrane curvatures can enforce a dramatic allosteric regulation (1000-fold inhibition) of α-HL permeability. High membrane curvatures (1/diameter ~1/40 nm(-1)) compressed the effective pore diameter of α-HL from 14.2 ± 0.8 Å to 11.4 ± 0.6 Å. This reduction in effective pore area (~40%) when combined with the area compressibility of α-HL revealed an effective membrane tension of ~50 mN/m and a curvature-imposed protein deformation energy of ~7 kBT. Such substantial energies have been shown to conformationally activate, or unfold, β-barrel and α-helical transmembrane proteins, suggesting that membrane curvature could likely regulate allosterically the structure and function of transmembrane proteins in general.
Collapse
Affiliation(s)
- Asger Tonnesen
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark; Nano-Science Center, University of Copenhagen, Copenhagen, Denmark; Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Sune M Christensen
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark; Nano-Science Center, University of Copenhagen, Copenhagen, Denmark; Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Vadym Tkach
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark; Nano-Science Center, University of Copenhagen, Copenhagen, Denmark; Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Dimitrios Stamou
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark; Nano-Science Center, University of Copenhagen, Copenhagen, Denmark; Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
41
|
Kar P, Gopal SM, Cheng YM, Panahi A, Feig M. Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association. J Chem Theory Comput 2014; 10:3459-3472. [PMID: 25136271 PMCID: PMC4132866 DOI: 10.1021/ct500443v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 12/03/2022]
Abstract
![]()
An
extension of the recently developed PRIMO coarse-grained force
field to membrane environments, PRIMO-M, is described. The membrane
environment is modeled with the heterogeneous dielectric generalized
Born (HDGB) methodology that simply replaces the standard generalized
Born model in PRIMO without further parametrization. The resulting
model was validated by comparing amino acid insertion free energy
profiles and application in molecular dynamics simulations of membrane
proteins and membrane-interacting peptides. Membrane proteins with
148–661 amino acids show stable root-mean-squared-deviations
(RMSD) between 2 and 4 Å for most systems. Transmembrane helical
peptides maintain helical shape and exhibit tilt angles in good agreement
with experimental or other simulation data. The association of two
glycophorin A (GpA) helices was simulated using replica exchange molecular
dynamics simulations yielding the correct dimer structure with a crossing
angle in agreement with previous studies. Finally, conformational
sampling of the influenza fusion peptide also generates structures
in agreement with previous studies. Overall, these findings suggest
that PRIMO-M can be used to study membrane bound peptides and proteins
and validates the transferable nature of the PRIMO coarse-grained
force field.
Collapse
Affiliation(s)
- Parimal Kar
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Srinivasa Murthy Gopal
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Yi-Ming Cheng
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Afra Panahi
- Departments of Chemistry and Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States ; Department of Biochemistry and Molecular Biology and Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| |
Collapse
|
42
|
Characterizing the structure of lipodisq nanoparticles for membrane protein spectroscopic studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:329-33. [PMID: 24853657 DOI: 10.1016/j.bbamem.2014.05.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/28/2014] [Accepted: 05/04/2014] [Indexed: 11/21/2022]
Abstract
Membrane protein spectroscopic studies are challenging due to the difficulty introduced in preparing homogenous and functional hydrophobic proteins incorporated into a lipid bilayer system. Traditional membrane mimics such as micelles or liposomes have proved to be powerful in solubilizing membrane proteins for biophysical studies, however, several drawbacks have limited their applications. Recently, a nanosized complex termed lipodisq nanoparticles was utilized as an alternative membrane mimic to overcome these caveats by providing a homogeneous lipid bilayer environment. Despite all the benefits that lipodisq nanoparticles could provide to enhance the biophysical studies of membrane proteins, structural characterization in different lipid compositions that closely mimic the native membrane environment is still lacking. In this study, the formation of lipodisq nanoparticles using different weight ratios of POPC/POPG lipids to SMA polymers was characterized via solid-state nuclear magnetic resonance (SSNMR) spectroscopy and dynamic light scattering (DLS). A critical weight ratio of (1/1.25) for the complete solubilization of POPC/POPG vesicles has been observed and POPC/POPG vesicles turned clear instantaneously upon the addition of the SMA polymer. The size of lipodisq nanoparticles formed from POPC/POPG lipids at this weight ratio of (1/1.25) was found to be about 30 nm in radius. We also showed that upon the complete solubilization of POPC/POPG vesicles by SMA polymers, the average size of the lipodisq nanoparticles is weight ratio dependent, when more SMA polymers were introduced, smaller lipodisq nanoparticles were obtained. The results of this study will be helpful for a variety of biophysical experiments when specific size of lipid disc is required. Further, this study will provide a proper path for researchers working on membrane proteins to obtain pertinent structure and dynamic information in a physiologically relevant membrane mimetic environment.
Collapse
|
43
|
Bilayer surface association of the pHLIP peptide promotes extensive backbone desolvation and helically-constrained structures. Biophys Chem 2014; 187-188:1-6. [DOI: 10.1016/j.bpc.2013.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/15/2013] [Accepted: 12/15/2013] [Indexed: 01/23/2023]
|
44
|
Balasubramanian PK, Balupuri A, Kothandan G, Cho SJ. In silico study of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanones derivatives as CCR1 antagonist: homology modeling, docking and 3D-QSAR approach. Bioorg Med Chem Lett 2013; 24:928-33. [PMID: 24424131 DOI: 10.1016/j.bmcl.2013.12.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 12/04/2013] [Accepted: 12/17/2013] [Indexed: 11/30/2022]
Abstract
C-C chemokine receptor type 1 (CCR1) is a chemokine receptor with seven transmembrane helices and it belongs to the G-Protein Coupled receptor (GPCR) family. It plays an important role in rheumatoid arthritis, organ transplant rejection, Alzheimer's disease and also causes inflammation. Because of its role in disease processes, CCR1 is considered to be an important drug target. In the present study, we have performed three dimensional Quantitative Structure activity relationship (3D-QSAR) studies on a series of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanone derivatives targeting CCR1. Homology modeling of CCR1 was performed based on a template structure (4EA3) which has a high sequence identity and resolution. The highest active molecule was docked into this model. Ligand-based and Receptor-based quantitative structure-activity relationship (QSAR) study was performed and CoMFA models with reasonable statistics was developed for both ligand-based (q(2)=0.606; r(2)=0.968) and receptor-guided (q(2)=0.640; r(2)=0.932) alignment methods. Contour map analyses identified favorable regions for high affinity binding. The docking results highlighted the important active site residues. Tyr113 was found to interact with the ligand through hydrogen bonding. This residue has been considered responsible for anchoring ligands inside the active site. Our results could also be helpful to understand the inhibitory mechanism of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanone derivatives thereby to design more effective ligands in the future.
Collapse
Affiliation(s)
- Pavithra K Balasubramanian
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju 501-759, Republic of Korea
| | - Anand Balupuri
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju 501-759, Republic of Korea
| | - Gugan Kothandan
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju 501-759, Republic of Korea
| | - Seung Joo Cho
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju 501-759, Republic of Korea; Department of Cellular Molecular Medicine, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju 501-759, Republic of Korea.
| |
Collapse
|
45
|
Chao L, Richards MJ, Hsia CY, Daniel S. Two-Dimensional Continuous Extraction in Multiphase Lipid Bilayers To Separate, Enrich, and Sort Membrane-Bound Species. Anal Chem 2013; 85:6696-702. [DOI: 10.1021/ac4006952] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ling Chao
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
| | - Mark J. Richards
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
| | - Chih-Yun Hsia
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
| | - Susan Daniel
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
| |
Collapse
|
46
|
Sapra KT. Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers. Methods Mol Biol 2013; 974:73-110. [PMID: 23404273 DOI: 10.1007/978-1-62703-275-9_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.
Collapse
Affiliation(s)
- K Tanuj Sapra
- Department of Chemistry, University of Oxford, Oxford, UK.
| |
Collapse
|
47
|
Ohkubo YZ, Pogorelov TV, Arcario MJ, Christensen GA, Tajkhorshid E. Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. Biophys J 2012; 102:2130-9. [PMID: 22824277 DOI: 10.1016/j.bpj.2012.03.015] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/21/2012] [Accepted: 03/06/2012] [Indexed: 11/26/2022] Open
Abstract
Characterizing atomic details of membrane binding of peripheral membrane proteins by molecular dynamics (MD) has been significantly hindered by the slow dynamics of membrane reorganization associated with the phenomena. To expedite lateral diffusion of lipid molecules without sacrificing the atomic details of such interactions, we have developed a novel membrane representation, to our knowledge, termed the highly mobile membrane-mimetic (HMMM) model to study binding and insertion of various molecular species into the membrane. The HMMM model takes advantage of an organic solvent layer to represent the hydrophobic core of the membrane and short-tailed phospholipids for the headgroup region. We demonstrate that using these components, bilayer structures are formed spontaneously and rapidly, regardless of the initial position and orientation of the lipids. In the HMMM membrane, lipid molecules exhibit one to two orders of magnitude enhancement in lateral diffusion. At the same time, the membrane atomic density profile of the headgroup region produced by the HMMM model is essentially identical to those obtained for full-membrane models, indicating the faithful representation of the membrane surface by the model. We demonstrate the efficiency of the model in capturing spontaneous binding and insertion of peripheral proteins by using the membrane anchor (γ-carboxyglutamic-acid-rich domain; GLA domain) of human coagulation factor VII as a test model. Achieving full insertion of the GLA domain consistently in 10 independent unbiased simulations within short simulation times clearly indicates the robustness of the HMMM model in capturing membrane association of peripheral proteins very efficiently and reproducibly. The HMMM model will provide significant improvements to the current all-atom models by accelerating lipid dynamics to examine protein-membrane interactions more efficiently.
Collapse
Affiliation(s)
- Y Zenmei Ohkubo
- Department of Biochemistry, Beckman Institute for Advanced Science and Technology, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | | | | |
Collapse
|
48
|
Abstract
Membrane biochemists are becoming increasingly aware of the role of lipid-protein interactions in diverse cellular functions. This review describes how conformational changes in membrane proteins, involving folding, stability, and membrane shape transitions, potentially involve elastic remodeling of the lipid bilayer. Evidence suggests that membrane lipids affect proteins through interactions of a relatively long-range nature, extending beyond a single annulus of next-neighbor boundary lipids. It is assumed the distance scale of the forces is large compared to the molecular range of action. Application of the theory of elasticity to flexible soft surfaces derives from classical physics and explains the polymorphism of both detergents and membrane phospholipids. A flexible surface model (FSM) describes the balance of curvature and hydrophobic forces in lipid-protein interactions. Chemically nonspecific properties of the lipid bilayer modulate the conformational energetics of membrane proteins. The new biomembrane model challenges the standard model (the fluid mosaic model) found in biochemistry texts. The idea of a curvature force field based on data first introduced for rhodopsin gives a bridge between theory and experiment. Influences of bilayer thickness, nonlamellar-forming lipids, detergents, and osmotic stress are all explained by the FSM. An increased awareness of curvature forces suggests that research will accelerate as structural biology becomes more closely entwined with the physical chemistry of lipids in explaining membrane structure and function.
Collapse
Affiliation(s)
- Michael F Brown
- Department of Chemistry and Biochemistry and Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
| |
Collapse
|
49
|
Lin Q, London E. Altering hydrophobic sequence lengths shows that hydrophobic mismatch controls affinity for ordered lipid domains (rafts) in the multitransmembrane strand protein perfringolysin O. J Biol Chem 2012; 288:1340-52. [PMID: 23150664 DOI: 10.1074/jbc.m112.415596] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The hypothesis that mismatch between transmembrane (TM) length and bilayer width controls TM protein affinity for ordered lipid domains (rafts) was tested using perfringolysin O (PFO), a pore-forming cholesterol-dependent cytolysin. PFO forms a multimeric barrel with many TM segments. The properties of PFO mutants with lengthened or shortened TM segments were compared with that of PFO with wild type TM sequences. Both mutant and wild type length PFO exhibited cholesterol-dependent membrane insertion. Maximal PFO-induced pore formation occurred in vesicles with wider bilayers for lengthened TM segments and in thinner bilayers for shortened TM segments. In diC(18:0) phosphatidylcholine (PC)/diC(14:1) PC/cholesterol vesicles, which form ordered domains with a relatively thick bilayer and disordered domains with a relatively thin bilayer, affinity for ordered domains was greatest with lengthened TM segments and least with shortened TM segments as judged by FRET. Similar results were observed by microscopy in giant vesicles containing sphingomyelin in place of diC(18:0) PC. In contrast, in diC(16:0) PC/diC(14:0) PC/diC(20:1) PC/cholesterol vesicles, which should form ordered domains with a relatively thin bilayer and disordered domains with a relatively thick bilayer, relative affinity for ordered domains was greatest with shortened TM segments and least with lengthened TM segments. The inability of multi-TM segment proteins (unlike single TM segment proteins) to adapt to mismatch by tilting may explain the sensitivity of raft affinity to mismatch. The difference in width sensitivity for single and multi-TM helix proteins may link raft affinity to multimeric state and thus control the assembly of multimeric TM complexes in rafts.
Collapse
Affiliation(s)
- Qingqing Lin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
| | | |
Collapse
|
50
|
Micheletti C. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys Life Rev 2012. [PMID: 23199577 DOI: 10.1016/j.plrev.2012.10.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship.
Collapse
Affiliation(s)
- Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, Italy.
| |
Collapse
|