1
|
Yang H, Zhou D, Zhou Z, Duan M, Yu H. Mechanistic Insight into the Mechanical Unfolding of the Integral Membrane Diacylglycerol Kinase. JACS AU 2024; 4:1422-1435. [PMID: 38665647 PMCID: PMC11040704 DOI: 10.1021/jacsau.3c00829] [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: 12/26/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/28/2024]
Abstract
The essential forces stabilizing membrane proteins and governing their folding and unfolding are difficult to decipher. Single-molecule atomic force spectroscopy mechanically unfolds individual membrane proteins and quantifies their dynamics and energetics. However, it remains challenging to structurally assign unfolding intermediates precisely and to deduce dominant interactions between specific residues that facilitate either the localized stabilization of these intermediates or the global assembly of membrane proteins. Here, we performed force spectroscopy experiments and multiscale molecular dynamics simulations to study the unfolding pathway of diacylglycerol kinase (DGK), a small trimeric multispan transmembrane enzyme. The remarkable agreement between experiments and simulations allowed precise structural assignment and interaction analysis of unfolding intermediates, bypassing existing limitations on structural mapping, and thus provided mechanistic explanations for the formation of these states. DGK unfolding was found to proceed with structural segments varying in size that do not correlate with its secondary structure. We identified intermolecular side-chain packing interactions as one of the major contributions to the stability of unfolding intermediates. Mutagenesis creating packing defects induced a dramatic decrease in the mechano-stability of corresponding intermediates and also in the thermo-stability of DGK trimer, in good agreement with predictions from simulations. Hence, the molecular determinants of the mechano- and thermo-stability of a membrane protein can be identified at residue resolution. The accurate structural assignment established and microscopic mechanism revealed in this work may substantially expand the scope of single-molecule studies of membrane proteins.
Collapse
Affiliation(s)
- Huiying Yang
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Daihong Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Zhangyi Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Mojie Duan
- Innovation
Academy for Precision Measurement Science and Technology, Chinese
Academy of Sciences, Wuhan 430071, China
| | - Hao Yu
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| |
Collapse
|
2
|
The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions. Catalysts 2022. [DOI: 10.3390/catal12111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.
Collapse
|
3
|
Li Q, Kang C. Dengue virus NS4B protein as a target for developing antivirals. Front Cell Infect Microbiol 2022; 12:959727. [PMID: 36017362 PMCID: PMC9398000 DOI: 10.3389/fcimb.2022.959727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Dengue virus is an important pathogen affecting global population while no specific treatment is available against this virus. Effort has been made to develop inhibitors through targeting viral nonstructural proteins such as NS3 and NS5 with enzymatic activities. No potent inhibitors entering clinical studies have been developed so far due to many challenges. The genome of dengue virus encodes four membrane-bound nonstructural proteins which do not possess any enzymatic activities. Studies have shown that the membrane protein-NS4B is a validated target for drug discovery and several NS4B inhibitors exhibited antiviral activities in various assays and entered preclinical studies.. Here, we summarize the recent studies on dengue NS4B protein. The structure and membrane topology of dengue NS4B derived from biochemical and biophysical studies are described. Function of NS4B through protein-protein interactions and some available NS4B inhibitors are summarized. Accumulated studies demonstrated that cell-based assays play important roles in developing NS4B inhibitors. Although the atomic structure of NS4B is not obtained, target-based drug discovery approach become feasible to develop NS4B inhibitors as recombinant NS4B protein is available.
Collapse
Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
| |
Collapse
|
4
|
Li Q, Huang Q, Kang C. Secondary Structures of the Transmembrane Domain of SARS-CoV-2 Spike Protein in Detergent Micelles. Int J Mol Sci 2022; 23:ijms23031040. [PMID: 35162961 PMCID: PMC8834715 DOI: 10.3390/ijms23031040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 01/11/2023] Open
Abstract
Spike protein of SARS-CoV-2 contains a single-span transmembrane (TM) domain and plays roles in receptor binding, viral attachment and viral entry to the host cells. The TM domain of spike protein is critical for viral infectivity. Herein, the TM domain of spike protein of SARS-CoV-2 was reconstituted in detergent micelles and subjected to structural analysis using solution NMR spectroscopy. The results demonstrate that the TM domain of the protein forms a helical structure in detergent micelles. An unstructured linker is identified between the TM helix and heptapeptide repeat 2 region. The linker is due to the proline residue at position 1213. Side chains of the three tryptophan residues preceding to and within the TM helix important for the function of S-protein might adopt multiple conformations which may be critical for their function. The side chain of W1212 was shown to be exposed to solvent and the side chains of residues W1214 and W1217 are buried in micelles. Relaxation study shows that the TM helix is rigid in solution while several residues have exchanges. The secondary structure and dynamics of the TM domain in this study provide insights into the function of the TM domain of spike protein.
Collapse
Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China;
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore 138670, Singapore;
| | - Congbao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore 138670, Singapore;
- Correspondence:
| |
Collapse
|
5
|
Dong XQ, Lin JY, Wang PF, Li Y, Wang J, Li B, Liao J, Lu JX. Solid-State NMR Studies of the Succinate-Acetate Permease from Citrobacter Koseri in Liposomes and Native Nanodiscs. Life (Basel) 2021; 11:life11090908. [PMID: 34575058 PMCID: PMC8471396 DOI: 10.3390/life11090908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022] Open
Abstract
The succinate-acetate permease (SatP) is an anion channel with six transmembrane domains. It forms different oligomers, especially hexamers in the detergent as well as in the membrane. Solid-state NMR studies of SatP were carried out successfully on SatP complexes by reconstructing the protein into liposomes or retaining the protein in the native membrane of E. coli., where it was expressed. The comparison of 13C-13C 2D correlation spectra between the two samples showed great similarity, opening the possibility to further study the acetate transport mechanism of SatP in its native membrane environment. Solid-state NMR studies also revealed small chemical shift differences of SatP in the two different membrane systems, indicating the importance of the lipid environment in determining the membrane protein structures and dynamics. Combining different 2D SSNMR spectra, chemical shift assignments were made on some sites, consistent with the helical structures in the transmembrane domains. In the end, we pointed out the limitation in the sensitivity for membrane proteins with such a size, and also indicated possible ways to overcome it.
Collapse
Affiliation(s)
- Xing-Qi Dong
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing-Yu Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Fei Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
| | - Bing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
| | - Jun Liao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
| | - Jun-Xia Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- Correspondence:
| |
Collapse
|
6
|
Combined Lipidomics and Network Pharmacology Study of Protective Effects of Salvia miltiorrhiza against Blood Stasis Syndrome. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:5526778. [PMID: 33790973 PMCID: PMC7997765 DOI: 10.1155/2021/5526778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
Blood stasis syndrome (BSS) is one of the most common symptoms of cardiovascular diseases (CVDs) in traditional Chinese medicine (TCM) theory. Previous studies have identified that Salvia miltiorrhiza (Danshen) has beneficial effects on BSS, but there is no relevant research from the perspective of lipidomics to study the mechanism of Danshen against BSS since hyperlipidemia has been the widely accepted risk factor of CVDs. In this study, lipidomics technology combined with network pharmacology was applied to investigate the pathological mechanism of BSS and the protective effects of Danshen. The lipidomics profiling based on the UPLC-QTOF-MS analysis method was applied to identify the differential metabolites in the plasma of blood stasis rats. The related pathway and potential targets involved in the anti-BSS effects of Danshen were predicted by pathway analysis and network pharmacology. The biochemical results showed that Danshen intervention significantly reduced whole blood viscosity (WBV) at all the shear rates and fibrinogen concentration (FIB) (p < 0.01) and increased activated partial thromboplastin time (APTT) effectively (p < 0.01). We also found that 52 lipid metabolites, including glycerophospholipid, sphingolipid, glycerolipid, plasmalogen, cholesterol ester, and testosterone, were associated with blood stasis. Moreover, Dgka, Hsd17b3, Hsd3b1, Inppl1, Lpl, Pik3ca, Pik3r1, Pla2g1b, Pla2g2a, Soat1, and Soat2 were predicted as potential targets, while glycerophospholipid metabolism, glycerolipid metabolism, steroid and steroid hormone biosynthesis, phosphatidylinositol signaling system, and ether lipid metabolism were involved as shared critical pathways of lipidomics analysis and network pharmacology. Collectively, this study offered a new understanding of the protection mechanism of Danshen against BSS, which provided new insight to explore the protective effects of Danshen.
Collapse
|
7
|
Dowhan W, Bogdanov M. Eugene P. Kennedy's Legacy: Defining Bacterial Phospholipid Pathways and Function. Front Mol Biosci 2021; 8:666203. [PMID: 33842554 PMCID: PMC8027125 DOI: 10.3389/fmolb.2021.666203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022] Open
Abstract
In the 1950's and 1960's Eugene P. Kennedy laid out the blueprint for phospholipid biosynthesis in somatic cells and Escherichia coli, which have been coined the Kennedy Pathways for phospholipid biosynthesis. His research group continued to make seminal contributions in the area of phospholipids until his retirement in the early 1990's. During these years he mentored many young scientists that continued to build on his early discoveries and who also mentored additional scientists that continue to make important contributions in areas related to phospholipids and membrane biogenesis. This review will focus on the initial E. coli Kennedy Pathways and how his early contributions have laid the foundation for our current understanding of bacterial phospholipid genetics, biochemistry and function as carried on by his scientific progeny and others who have been inspired to study microbial phospholipids.
Collapse
Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| |
Collapse
|
8
|
Structure of membrane diacylglycerol kinase in lipid bilayers. Commun Biol 2021; 4:282. [PMID: 33674677 PMCID: PMC7935881 DOI: 10.1038/s42003-021-01802-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/05/2021] [Indexed: 12/17/2022] Open
Abstract
Diacylglycerol kinase (DgkA) is a small integral membrane protein, responsible for the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. Its structures reported in previous studies, determined in detergent micelles by solution NMR and in monoolein cubic phase by X-ray crystallography, differ significantly. These differences point to the need to validate these detergent-based structures in phospholipid bilayers. Here, we present a well-defined homo-trimeric structure of DgkA in phospholipid bilayers determined by magic angle spinning solid-state NMR (ssNMR) spectroscopy, using an approach combining intra-, inter-molecular paramagnetic relaxation enhancement (PRE)-derived distance restraints and CS-Rosetta calculations. The DgkA structure determined in lipid bilayers is different from the solution NMR structure. In addition, although ssNMR structure of DgkA shows a global folding similar to that determined by X-ray, these two structures differ in monomeric symmetry and dynamics. A comparative analysis of DgkA structures determined in three different detergent/lipid environments provides a meaningful demonstration of the influence of membrane mimetic environments on the structure and dynamics of membrane proteins. Jianping Li et al. present the homo-trimeric structure of the small integral membrane protein diacylglycerol kinase (DgkA) in phospholipid bilayers determined by magic angle spinning solid-state NMR spectroscopy. They compare the structure with structures solved by solution NMR and X-ray crystallography and provide insights into the influence of membrane mimetic environments on membrane proteins.
Collapse
|
9
|
Yeh V, Goode A, Bonev BB. Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR. BIOLOGY 2020; 9:E396. [PMID: 33198410 PMCID: PMC7697852 DOI: 10.3390/biology9110396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022]
Abstract
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.
Collapse
Affiliation(s)
| | | | - Boyan B. Bonev
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (V.Y.); (A.G.)
| |
Collapse
|
10
|
Danmaliki GI, Hwang PM. Solution NMR spectroscopy of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183356. [PMID: 32416193 DOI: 10.1016/j.bbamem.2020.183356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/06/2023]
Abstract
Integral membrane proteins (IMPs) perform unique and indispensable functions in the cell, making them attractive targets for fundamental research and drug discovery. Developments in protein production, isotope labeling, sample preparation, and pulse sequences have extended the utility of solution NMR spectroscopy for studying IMPs with multiple transmembrane segments. Here we review some recent applications of solution NMR for studying structure, dynamics, and interactions of polytopic IMPs, emphasizing strategies used to overcome common technical challenges.
Collapse
Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| |
Collapse
|
11
|
Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
Collapse
|
12
|
Liao SM, Lu B, Liu XH, Lu ZL, Liang SJ, Chen D, Troy FA, Huang RB, Zhou GP. Molecular Interactions of the Polysialytransferase Domain (PSTD) in ST8Sia IV with CMP-Sialic Acid and Polysialic Acid Required for Polysialylation of the Neural Cell Adhesion Molecule Proteins: An NMR Study. Int J Mol Sci 2020; 21:ijms21051590. [PMID: 32111064 PMCID: PMC7084582 DOI: 10.3390/ijms21051590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 12/19/2022] Open
Abstract
Polysialic acid (polySia) is an unusual glycan that posttranslational modifies neural cell adhesion molecule (NCAM) proteins in mammalian cells. The up-regulated expression of polySia-NCAM is associated with tumor progression in many metastatic human cancers and in neurocognitive processes. Two members of the ST8Sia family of α2,8-polysialyltransferases (polySTs), ST8Sia II (STX) and ST8Sia IV (PST) both catalyze synthesis of polySia when activated cytidine monophosphate(CMP)-Sialic acid (CMP-Sia) is translocate into the lumen of the Golgi apparatus. Two key polybasic domains in the polySTs, the polybasic region (PBR) and the polysialyltransferase domain (PSTD) areessential forpolysialylation of the NCAM proteins. However, the precise molecular details to describe the interactions required for polysialylation remain unknown. In this study, we hypothesize that PSTD interacts with both CMP-Sia and polySia to catalyze polysialylation of the NCAM proteins. To test this hypothesis, we synthesized a 35-amino acid-PSTD peptide derived from the ST8Sia IV gene sequence and used it to study its interaction with CMP-Sia, and polySia. Our results showed for the PSTD-CMP-Sia interaction, the largest chemical-shift perturbations (CSP) were in amino acid residues V251 to A254 in the short H1 helix, located near the N-terminus of PSTD. However, larger CSP values for the PSTD-polySia interaction were observed in amino acid residues R259 to T270 in the long H2 helix. These differences suggest that CMP-Sia preferentially binds to the domain between the short H1 helix and the longer H2 helix. In contrast, polySia was principally bound to the long H2 helix of PSTD. For the PSTD-polySia interaction, a significant decrease in peak intensity was observed in the 20 amino acid residues located between the N-and C-termini of the long H2 helix in PSTD, suggesting a slower motion in these residues when polySia bound to PSTD. Specific features of the interactions between PSTD-CMP-Sia, and PSTD-polySia were further confirmed by comparing their 800 MHz-derived HSQC spectra with that of PSTD-Sia, PSTD-TriSia (DP 3) and PSTD-polySia. Based on the interactions between PSTD-CMP-Sia, PSTD-polySia, PBR-NCAM and PSTD-PBR, these findingsprovide a greater understanding of the molecular mechanisms underlying polySia-NCAM polysialylation, and thus provides a new perspective for translational pharmacological applications and development by targeting the two polysialyltransferases.
Collapse
Affiliation(s)
- Si-Ming Liao
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China; (S.-M.L.); (B.L.); (Z.-L.L.); (S.-J.L.); (D.C.)
| | - Bo Lu
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China; (S.-M.L.); (B.L.); (Z.-L.L.); (S.-J.L.); (D.C.)
| | - Xue-Hui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhi-Long Lu
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China; (S.-M.L.); (B.L.); (Z.-L.L.); (S.-J.L.); (D.C.)
| | - Shi-Jie Liang
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China; (S.-M.L.); (B.L.); (Z.-L.L.); (S.-J.L.); (D.C.)
| | - Dong Chen
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China; (S.-M.L.); (B.L.); (Z.-L.L.); (S.-J.L.); (D.C.)
| | - Frederic A. Troy
- Department of Biochemistry and Molecular Medicine, University of California School of Medicine, Davis, CA 95616-8635, USA
- Correspondence: (F.A.T.II); (R.-B.H.); (G.-P.Z.)
| | - Ri-Bo Huang
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China; (S.-M.L.); (B.L.); (Z.-L.L.); (S.-J.L.); (D.C.)
- College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
- Correspondence: (F.A.T.II); (R.-B.H.); (G.-P.Z.)
| | - Guo-Ping Zhou
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China; (S.-M.L.); (B.L.); (Z.-L.L.); (S.-J.L.); (D.C.)
- Gordon Life Science Institute, Rocky Mount, NC 27804, USA
- Correspondence: (F.A.T.II); (R.-B.H.); (G.-P.Z.)
| |
Collapse
|
13
|
Lu B, Liu XH, Liao SM, Lu ZL, Chen D, Troy Ii FA, Huang RB, Zhou GP. A Possible Modulation Mechanism of Intramolecular and Intermolecular Interactions for NCAM Polysialylation and Cell Migration. Curr Top Med Chem 2019; 19:2271-2282. [PMID: 31648641 DOI: 10.2174/1568026619666191018094805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/31/2022]
Abstract
Polysialic acid (polySia) is a novel glycan that posttranslationally modifies neural cell adhesion molecules (NCAMs) in mammalian cells. Up-regulation of polySia-NCAM expression or NCAM polysialylation is associated with tumor cell migration and progression in many metastatic cancers and neurocognition. It has been known that two highly homologous mammalian polysialyltransferases (polySTs), ST8Sia II (STX) and ST8Sia IV (PST), can catalyze polysialylation of NCAM, and two polybasic domains, polybasic region (PBR) and polysialyltransferase domain (PSTD) in polySTs play key roles in affecting polyST activity or NCAM polysialylation. However, the molecular mechanisms of NCAM polysialylation and cell migration are still not entirely clear. In this minireview, the recent research results about the intermolecular interactions between the PBR and NCAM, the PSTD and cytidine monophosphate-sialic acid (CMP-Sia), the PSTD and polySia, and as well as the intramolecular interaction between the PBR and the PSTD within the polyST, are summarized. Based on these cooperative interactions, we have built a novel model of NCAM polysialylation and cell migration mechanisms, which may be helpful to design and develop new polysialyltransferase inhibitors.
Collapse
Affiliation(s)
- Bo Lu
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Xue-Hui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Si-Ming Liao
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Zhi-Long Lu
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Dong Chen
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Frederic A Troy Ii
- Department of Biochemistry and Molecular Medicine, University of California School of Medicine, Davis, CA, 95817, United States
| | - Ri-Bo Huang
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China.,Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi 530004, China
| | - Guo-Ping Zhou
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| |
Collapse
|
14
|
Kang C. 19F-NMR in Target-based Drug Discovery. Curr Med Chem 2019; 26:4964-4983. [PMID: 31187703 DOI: 10.2174/0929867326666190610160534] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.
Collapse
Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| |
Collapse
|
15
|
Puthenveetil R, Vinogradova O. Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments. J Biol Chem 2019; 294:15914-15931. [PMID: 31551353 DOI: 10.1074/jbc.rev119.009178] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A third of the genes in prokaryotic and eukaryotic genomes encode membrane proteins that are either essential for signal transduction and solute transport or function as scaffold structures. Unlike many of their soluble counterparts, the overall structural and functional organization of membrane proteins is sparingly understood. Recent advances in X-ray crystallography, cryo-EM, and nuclear magnetic resonance (NMR) are closing this gap by enabling an in-depth view of these ever-elusive proteins at atomic resolution. Despite substantial technological advancements, however, the overall proportion of membrane protein entries in the Protein Data Bank (PDB) remains <4%. This paucity is mainly attributed to difficulties associated with their expression and purification, propensity to form large multisubunit complexes, and challenges pertinent to identification of an ideal detergent, lipid, or detergent/lipid mixture that closely mimic their native environment. NMR is a powerful technique to obtain atomic-resolution and dynamic details of a protein in solution. This is accomplished through an assortment of isotopic labeling schemes designed to acquire multiple spectra that facilitate deduction of the final protein structure. In this review, we discuss current approaches and technological developments in the determination of membrane protein structures by solution NMR and highlight recent structural and mechanistic insights gained with this technique. We also discuss strategies for overcoming size limitations in NMR applications, and we explore a plethora of membrane mimetics available for the structural and mechanistic understanding of these essential cellular proteins.
Collapse
Affiliation(s)
- Robbins Puthenveetil
- Department of Molecular and Cell Biology, college of liberal arts and sciences, University of Connecticut at Storrs, Storrs, Connecticut 06269
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut at Storrs, Storrs, Connecticut 06269
| |
Collapse
|
16
|
Solution NMR Spectroscopy for the Determination of Structures of Membrane Proteins in a Lipid Environment. Methods Mol Biol 2019. [PMID: 31218634 DOI: 10.1007/978-1-4939-9512-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
NMR spectroscopy has harnessed the recent technical advances to emerge as a competitive, elegant, and eminently viable technique for determining the solution structures of membrane proteins at the level of atomic resolution. Once a good level of cell-based or cell-free expression and purification of a suitably sized membrane protein has been achieved, then NMR offers a combination of several versatile strategies, for example choice of appropriate deuterated or nondeuterated detergents, temperature, and ionic strength; isotope labeling with 2H, 13C, 15N, with or without protonation of Ile (δ1), Leu, and Val methyl protons; combinatorial labeling or unlabeling of specific amino acids; TROSY based-, nonuniform sampling (NUS) based-, and other NMR experiments; measurement of residual dipolar couplings using stretched polyacrylamide gels or DNA nanotubes; spin labeling and paramagnetic relaxation enhancements (PRE). Strategic combinations of these advancements together with availability of highly sensitive cryogenically cooled-probes equipped high-field NMR spectrometers (up to 1 GHz 1H frequency) have allowed the perseverant investigator to successfully overcome several of the conventional pitfalls associated with the NMR technique and membrane proteins, viz., low sensitivity, poor sample stability, spectral crowding, and a limited number of NOEs and other constraints for structure calculations. This has resulted in an unprecedented growth in the number of successfully determined NMR structures of large and complex membrane proteins over the last two decades, and this technique now holds great promise for the structure determination of an ever larger body of membrane proteins.
Collapse
|
17
|
Global response of diacylglycerol kinase towards substrate binding observed by 2D and 3D MAS NMR. Sci Rep 2019; 9:3995. [PMID: 30850624 PMCID: PMC6408475 DOI: 10.1038/s41598-019-40264-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/11/2019] [Indexed: 01/01/2023] Open
Abstract
Escherichia coli diacylglycerol kinase (DGK) is an integral membrane protein, which catalyses the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatic acid (PA). It is a unique trimeric enzyme, which does not share sequence homology with typical kinases. It exhibits a notable complexity in structure and function despite of its small size. Here, chemical shift assignment of wild-type DGK within lipid bilayers was carried out based on 3D MAS NMR, utilizing manual and automatic analysis protocols. Upon nucleotide binding, extensive chemical shift perturbations could be observed. These data provide evidence for a symmetric DGK trimer with all of its three active sites concurrently occupied. Additionally, we could detect that the nucleotide substrate induces a substantial conformational change, most likely directing DGK into its catalytic active form. Furthermore, functionally relevant interprotomer interactions are identified by DNP-enhanced MAS NMR in combination with site-directed mutagenesis and functional assays.
Collapse
|
18
|
Mandala VS, Liao SY, Gelenter MD, Hong M. The Transmembrane Conformation of the Influenza B Virus M2 Protein in Lipid Bilayers. Sci Rep 2019; 9:3725. [PMID: 30842530 PMCID: PMC6403292 DOI: 10.1038/s41598-019-40217-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Influenza A and B viruses cause seasonal flu epidemics. The M2 protein of influenza B (BM2) is a membrane-embedded tetrameric proton channel that is essential for the viral lifecycle. BM2 is a functional analog of AM2 but shares only 24% sequence identity for the transmembrane (TM) domain. The structure and function of AM2, which is targeted by two antiviral drugs, have been well characterized. In comparison, much less is known about the structure of BM2 and no drug is so far available to inhibit this protein. Here we use solid-state NMR spectroscopy to investigate the conformation of BM2(1-51) in phospholipid bilayers at high pH, which corresponds to the closed state of the channel. Using 2D and 3D correlation NMR experiments, we resolved and assigned the 13C and 15N chemical shifts of 29 residues of the TM domain, which yielded backbone (φ, ψ) torsion angles. Residues 6-28 form a well-ordered α-helix, whereas residues 1-5 and 29-35 display chemical shifts that are indicative of random coil or β-sheet conformations. The length of the BM2-TM helix resembles that of AM2-TM, despite their markedly different amino acid sequences. In comparison, large 15N chemical shift differences are observed between bilayer-bound BM2 and micelle-bound BM2, indicating that the TM helix conformation and the backbone hydrogen bonding in lipid bilayers differ from the micelle-bound conformation. Moreover, HN chemical shifts of micelle-bound BM2 lack the periodic trend expected for coiled coil helices, which disagree with the presence of a coiled coil structure in micelles. These results establish the basis for determining the full three-dimensional structure of the tetrameric BM2 to elucidate its proton-conduction mechanism.
Collapse
Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Shu-Yu Liao
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.
| |
Collapse
|
19
|
Kawakami N, Fujisaki S. Undecaprenyl phosphate metabolism in Gram-negative and Gram-positive bacteria. Biosci Biotechnol Biochem 2018; 82:940-946. [DOI: 10.1080/09168451.2017.1401915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Undecaprenyl phosphate (UP) is essential for the biosynthesis of bacterial extracellular polysaccharides. UP is produced by the dephosphorylation of undecaprenyl diphosphate (UPP) via de novo synthetic and recycling pathways. Gram-positive bacteria contain remarkable amounts of undecaprenol (UOH), which is phosphorylated to UP, although UOH has not been found in Gram-negative bacteria. Here, current knowledge about UPP phosphatase and UOH kinase is reviewed. Dephosphorylation of UPP is catalyzed by a BacA homologue and a type-2 phosphatidic acid phosphatase (PAP2) homologue. The presence of one of these UPP phosphatases is essential for bacterial growth. The catalytic center of both types of enzyme is located outside the cytoplasmic membrane. In Gram-positive bacteria, an enzyme homologous to DgkA, which is the diacylglycerol kinase of Escherichia coli, catalyzes UOH phosphorylation. The possible role of UOH and the significance of systematic construction of Staphylococcus aureus mutants to determine UP metabolism are discussed.
Collapse
Affiliation(s)
- Naoki Kawakami
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Shingo Fujisaki
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
| |
Collapse
|
20
|
Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
Collapse
Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
| |
Collapse
|
21
|
Membrane properties that shape the evolution of membrane enzymes. Curr Opin Struct Biol 2018; 51:80-91. [PMID: 29597094 DOI: 10.1016/j.sbi.2018.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Spectacular recent progress in structural biology has led to determination of the structures of many integral membrane enzymes that catalyze reactions in which at least one substrate also is membrane bound. A pattern of results seems to be emerging in which the active site chemistry of these enzymes is usually found to be analogous to what is observed for water soluble enzymes catalyzing the same reaction types. However, in light of the chemical, structural, and physical complexity of cellular membranes plus the presence of transmembrane gradients and potentials, these enzymes may be subject to membrane-specific regulatory mechanisms that are only now beginning to be uncovered. We review the membrane-specific environmental traits that shape the evolution of membrane-embedded biocatalysts.
Collapse
|
22
|
Zhou S, Pettersson P, Brzezinski P, Ädelroth P, Mäler L. NMR Study of Rcf2 Reveals an Unusual Dimeric Topology in Detergent Micelles. Chembiochem 2018; 19:444-447. [PMID: 29240987 DOI: 10.1002/cbic.201700664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/09/2022]
Abstract
The Saccharomyces cerevisiae mitochondrial respiratory supercomplex factor 2 (Rcf2) plays a role in assembly of supercomplexes composed of cytochrome bc1 (complex III) and cytochrome c oxidase (complex IV). We expressed the Rcf2 protein in Escherichia coli, refolded it, and reconstituted it into dodecylphosphocholine (DPC) micelles. The structural properties of Rcf2 were studied by solution NMR, and near complete backbone assignment of Rcf2 was achieved. The secondary structure of Rcf2 contains seven helices, of which five are putative transmembrane (TM) helices, including, unexpectedly, a region formed by a charged 20-residue helix at the C terminus. Further studies demonstrated that Rcf2 forms a dimer, and the charged TM helix is involved in this dimer formation. Our results provide a basis for understanding the role of this assembly/regulatory factor in supercomplex formation and function.
Collapse
Affiliation(s)
- Shu Zhou
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691, Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691, Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691, Stockholm, Sweden
| |
Collapse
|
23
|
Koehler Leman J, D'Avino AR, Bhatnagar Y, Gray JJ. Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality. Proteins 2017; 86:57-74. [PMID: 29044728 DOI: 10.1002/prot.25402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/27/2017] [Accepted: 10/11/2017] [Indexed: 12/29/2022]
Abstract
Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is "which structure is most biologically relevant?" Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 Å in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo-chemical correctness, and are more tightly packed. After quantifying these differences, we used high-resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins.
Collapse
Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.,Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York
| | - Andrew R D'Avino
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.,Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Yash Bhatnagar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| |
Collapse
|
24
|
Hutchison JM, Lu Z, Li G, Travis B, Mittal R, Deatherage CL, Sanders CR. Dodecyl-β-melibioside Detergent Micelles as a Medium for Membrane Proteins. Biochemistry 2017; 56:5481-5484. [PMID: 28980804 PMCID: PMC5685800 DOI: 10.1021/acs.biochem.7b00810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There remains a need for new non-ionic detergents that are suitable for use in biochemical and biophysical studies of membrane proteins. Here we explore the properties of n-dodecyl-β-melibioside (β-DDMB) micelles as a medium for membrane proteins. Melibiose is d-galactose-α(1→6)-d-glucose. Light scattering showed the β-DDMB micelle to be roughly 30 kDa smaller than micelles formed by the commonly used n-dodecyl-β-maltoside (β-DDM). β-DDMB stabilized diacylglycerol kinase (DAGK) against thermal inactivation. Moreover, activity assays conducted using aliquots of DAGK purified into β-DDMB yielded activities that were 40% higher than those of DAGK purified into β-DDM. β-DDMB yielded similar or better TROSY-HSQC NMR spectra for two single-pass membrane proteins and the tetraspan membrane protein peripheral myelin protein 22. β-DDMB appears be a useful addition to the toolbox of non-ionic detergents available for membrane protein research.
Collapse
Affiliation(s)
- James M. Hutchison
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Geoffrey Li
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Ben Travis
- Anatrace, 434 W. Dussel Dr., Maumee, OH 43537
| | | | - Catherine L. Deatherage
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Charles R. Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| |
Collapse
|
25
|
Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
|
26
|
Huang LY, Wang SC, Cheng TJR, Wong CH. Undecaprenyl Phosphate Phosphatase Activity of Undecaprenol Kinase Regulates the Lipid Pool in Gram-Positive Bacteria. Biochemistry 2017; 56:5417-5427. [PMID: 28872301 DOI: 10.1021/acs.biochem.7b00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria cell walls contain many repeating glycan structures, such as peptidoglycans, lipopolysaccharides, teichoic acids, and capsular polysaccharides. Their synthesis starts in the cytosol, and they are constructed from a glycan lipid carrier, undecaprenyl phosphate (C55P), which is essential for cell growth and survival. The lipid derivative undecaprenol (C55OH) is predominant in many Gram-positive bacteria but has not been detected in Gram-negative bacteria; its origin and role have thus remained unknown. Recently, a homologue of diacylglycerol kinase (DgkA) in Escherichia coli (E. coli) was demonstrated to be an undecaprenol kinase (UK) in the Gram-positive bacterium Streptococcus mutans (S. mutans). In this study, we found that S. mutans UK was not only an undecaprenol kinase but also a Mg-ADP-dependent undecaprenyl phosphate phosphatase (UpP), catalyzing the hydrolysis of C55P to C55OH and a free inorganic phosphate. Furthermore, the naturally undetectable C55OH was observed in E. coli cells expressing S. mutans dgkA, supporting the phosphatase activity of UK/UpP in vivo. These two activities were indispensable to each other and utilized identical essential residues binding to their substrates, suggesting that both activities share the same active site and might involve a direct phosphoryl transfer mechanism. This study revealed a unique membrane enzyme displaying bifunctional activities determined by substrate binding and C55OH production. The reciprocal conversion of C55P and the undecaprenol pool efficiently regulate cell wall synthesis, especially in Gram-positive bacteria.
Collapse
Affiliation(s)
- Lin-Ya Huang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
| | - Shih-Chi Wang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
| | | | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
| |
Collapse
|
27
|
Sim DW, Lu Z, Won HS, Lee SN, Seo MD, Lee BJ, Kim JH. Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins. Molecules 2017; 22:molecules22081347. [PMID: 28809779 PMCID: PMC6152068 DOI: 10.3390/molecules22081347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 02/05/2023] Open
Abstract
A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology. Among these technologies, solution NMR is a powerful tool for studying protein-protein, protein-ligand interactions and protein dynamics at a wide range of time scales as well as structure determination of membrane proteins. This review provides general and useful guideline for membrane protein sample preparation and the choice of membrane-mimetic media, which are the key step for successful structural analysis. Furthermore, this review provides an opportunity to look at recent applications of solution NMR to structural studies on α-helical membrane proteins through some success stories.
Collapse
Affiliation(s)
- Dae-Won Sim
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37204, USA.
| | - Hyung-Sik Won
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Seu-Na Lee
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Min-Duk Seo
- Department of Molecular Science and Technology & College of Pharmacy, Ajou University, Suwon 16499, Korea.
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Korea.
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Chungbuk, Korea.
| |
Collapse
|
28
|
NMR as a tool to investigate the structure, dynamics and function of membrane proteins. Nat Struct Mol Biol 2017; 23:468-74. [PMID: 27273629 DOI: 10.1038/nsmb.3226] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/12/2016] [Indexed: 12/29/2022]
Abstract
Membrane-protein NMR occupies a unique niche for determining structures, assessing dynamics, examining folding, and studying the binding of lipids, ligands and drugs to membrane proteins. However, NMR analyses of membrane proteins also face special challenges that are not encountered with soluble proteins, including sample preparation, size limitation, spectral crowding and sparse data accumulation. This Perspective provides a snapshot of current achievements, future opportunities and possible limitations in this rapidly developing field.
Collapse
|
29
|
Expression, Purification, and Monitoring of Conformational Changes of hCB2 TMH67H8 in Different Membrane-Mimetic Lipid Mixtures Using Circular Dichroism and NMR Techniques. MEMBRANES 2017; 7:membranes7010010. [PMID: 28218648 PMCID: PMC5371971 DOI: 10.3390/membranes7010010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/26/2017] [Accepted: 02/06/2017] [Indexed: 12/13/2022]
Abstract
This work was intended to develop self-assembly lipids for incorporating G-protein coupled receptors (GPCRs) in order to improve the success rate for nuclear magnetic resonance spectroscopy (NMR) structural elucidation. We hereby report the expression and purification of uniformly 15N-labeled human cannabinoid receptor-2 domain in insect cell media. The domain was refolded by screening several membrane mimetic environments. Different q ratios of isotropic bicelles were screened for solubilizing transmembrane helix 6, 7 and 8 (TMH67H8). As the concentration of dimyristoylphosphocholine (DMPC) was increased such that the q ratio was between 0.16 and 0.42, there was less crowding in the cross peaks with increasing q ratio. In bicelles of q = 0.42, the maximum number of cross peaks were obtained and the cross peaks were uniformly dispersed. The receptor domain in bicelles beyond q = 0.42 resulted in peak crowding. These studies demonstrate that GPCRs folding especially in bicelles is protein-specific and requires the right mix of the longer chain and shorter chain lipids to provide the right environment for proper folding. These findings will allow further development of novel membrane mimetics to provide greater diversity of lipid mixtures than those currently being employed for GPCR stability and folding, which are critical for both X-ray and NMR studies of GPCRs.
Collapse
|
30
|
Dufrisne MB, Petrou VI, Clarke OB, Mancia F. Structural basis for catalysis at the membrane-water interface. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1368-1385. [PMID: 27913292 DOI: 10.1016/j.bbalip.2016.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 11/27/2022]
Abstract
The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
Collapse
Affiliation(s)
- Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Vasileios I Petrou
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Oliver B Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
31
|
Kroncke BM, Van Horn WD, Smith J, Kang C, Welch RC, Song Y, Nannemann DP, Taylor KC, Sisco NJ, George AL, Meiler J, Vanoye CG, Sanders CR. Structural basis for KCNE3 modulation of potassium recycling in epithelia. SCIENCE ADVANCES 2016; 2:e1501228. [PMID: 27626070 PMCID: PMC5017827 DOI: 10.1126/sciadv.1501228] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 08/10/2016] [Indexed: 05/25/2023]
Abstract
The single-span membrane protein KCNE3 modulates a variety of voltage-gated ion channels in diverse biological contexts. In epithelial cells, KCNE3 regulates the function of the KCNQ1 potassium ion (K(+)) channel to enable K(+) recycling coupled to transepithelial chloride ion (Cl(-)) secretion, a physiologically critical cellular transport process in various organs and whose malfunction causes diseases, such as cystic fibrosis (CF), cholera, and pulmonary edema. Structural, computational, biochemical, and electrophysiological studies lead to an atomically explicit integrative structural model of the KCNE3-KCNQ1 complex that explains how KCNE3 induces the constitutive activation of KCNQ1 channel activity, a crucial component in K(+) recycling. Central to this mechanism are direct interactions of KCNE3 residues at both ends of its transmembrane domain with residues on the intra- and extracellular ends of the KCNQ1 voltage-sensing domain S4 helix. These interactions appear to stabilize the activated "up" state configuration of S4, a prerequisite for full opening of the KCNQ1 channel gate. In addition, the integrative structural model was used to guide electrophysiological studies that illuminate the molecular basis for how estrogen exacerbates CF lung disease in female patients, a phenomenon known as the "CF gender gap."
Collapse
Affiliation(s)
- Brett M. Kroncke
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Center for Personalized Diagnostics, Arizona State University, Tempe, AZ 85287, USA
| | - Jarrod Smith
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - CongBao Kang
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Experimental Therapeutics Centre, Agency for Science Technology and Research, Singapore, Singapore
| | - Richard C. Welch
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Yuanli Song
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - David P. Nannemann
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Keenan C. Taylor
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Nicholas J. Sisco
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Center for Personalized Diagnostics, Arizona State University, Tempe, AZ 85287, USA
| | - Alfred L. George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Carlos G. Vanoye
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Charles R. Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| |
Collapse
|
32
|
Jiang Y, Tan H, Zheng J, Li X, Chen G, Jia Z. Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study. Phys Chem Chem Phys 2016; 17:25228-34. [PMID: 26352441 DOI: 10.1039/c5cp03342j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diacylglycerol kinase is an integral membrane protein which catalyzes phosphoryl transfer from ATP to diacylglycerol. As the smallest kinase known, it shares no sequence homology with conventional kinases and possesses a distinct trimer structure. Thus far, its catalytic mechanism remains elusive. Using molecular dynamics and quantum mechanics calculations, we investigated the co-factor and the substrate binding and phosphoryl transfer mechanism. Based on the analysis of density functional theory calculations, we reveal that the phosphorylation reaction of diacylglycerol kinase features the same phosphoryl transfer mechanism as other kinases, despite its unique structural properties. Our results further show that the active site is relatively open and able to accommodate ligands in multiple orientations, suggesting that the optimization of binding orientations and conformational changes would occur prior to actual phosphoryl transfer.
Collapse
Affiliation(s)
- Yafei Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | | | | | | | | | | |
Collapse
|
33
|
Oxenoid K, Dong Y, Cao C, Cui T, Sancak Y, Markhard AL, Grabarek Z, Kong L, Liu Z, Ouyang B, Cong Y, Mootha VK, Chou JJ. Architecture of the mitochondrial calcium uniporter. Nature 2016; 533:269-73. [PMID: 27135929 PMCID: PMC4874835 DOI: 10.1038/nature17656] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/08/2016] [Indexed: 01/12/2023]
Abstract
Mitochondria from multiple, eukaryotic clades uptake and buffer large amounts of calcium (Ca2+) via an inner membrane transporter called the uniporter. Early studies demonstrated that this transport requires a mitochondrial membrane potential and that the uniporter is itself Ca2+ activated, and blocked by ruthenium red or Ru3601. Later, electrophysiological studies demonstrated that the uniporter is an ion channel with remarkably high conductance and selectivity2. Ca2+ entry into mitochondria is also known to activate the TCA cycle and appears to be critical for matching ATP production in mitochondria with its cytosolic demand3. MCU (mitochondrial calcium uniporter) is the pore forming and Ca2+ conducting subunit of the uniporter, but its primary sequence does not resemble any calcium channel known to date. Here, we report the structure of the core region of MCU, determined using nuclear magnetic resonance (NMR) and electron microscopy (EM). MCU is a homo-oligomer with the second transmembrane helix forming a hydrophilic pore across the membrane. The channel assembly represents a new solution of ion channel architecture and is stabilized by a coiled coil motif protruding in the mitochondrial matrix. The critical DxxE motif forms the pore entrance featuring two carboxylate rings, which appear to be the selectivity filter based on the ring dimensions and functional mutagenesis. To our knowledge, this is one of the largest structures characterized by NMR, which provides a structural blueprint for understanding the function of this channel.
Collapse
Affiliation(s)
- Kirill Oxenoid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ying Dong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chan Cao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,State Key Laboratory of Elemento-Organic Chemistry and College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tanxing Cui
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yasemin Sancak
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Andrew L Markhard
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Zenon Grabarek
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Liangliang Kong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhijun Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo Ouyang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 200031, China
| | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
34
|
Oxenoid K, Chou JJ. A functional NMR for membrane proteins: dynamics, ligand binding, and allosteric modulation. Protein Sci 2016; 25:959-73. [PMID: 26928605 DOI: 10.1002/pro.2910] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 02/25/2016] [Accepted: 02/25/2016] [Indexed: 01/13/2023]
Abstract
By nature of conducting ions, transporting substrates and transducing signals, membrane channels, transporters and receptors are expected to exhibit intrinsic conformational dynamics. It is therefore of great interest and importance to understand the various properties of conformational dynamics acquired by these proteins, for example, the relative population of states, exchange rate, conformations of multiple states, and how small molecule ligands modulate the conformational exchange. Because small molecule binding to membrane proteins can be weak and/or dynamic, structural characterization of these effects is very challenging. This review describes several NMR studies of membrane protein dynamics, ligand-induced conformational rearrangements, and the effect of ligand binding on the equilibrium of conformational exchange. The functional significance of the observed phenomena is discussed.
Collapse
Affiliation(s)
- Kirill Oxenoid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, 02115
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, 02115
| |
Collapse
|
35
|
Hiruma-Shimizu K, Shimizu H, Thompson GS, Kalverda AP, Patching SG. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications. Mol Membr Biol 2016; 32:139-55. [DOI: 10.3109/09687688.2015.1125536] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Hiroki Shimizu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan,
| | - Gary S. Thompson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | - Arnout P. Kalverda
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | | |
Collapse
|
36
|
Li Y, Liew LSY, Li Q, Kang C. Structure of the transmembrane domain of human nicastrin-a component of γ-secretase. Sci Rep 2016; 6:19522. [PMID: 26776682 PMCID: PMC4726005 DOI: 10.1038/srep19522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/09/2015] [Indexed: 02/04/2023] Open
Abstract
Nicastrin is the largest component of γ-secretase that is an intramembrane protease important in the development of Alzheimer's disease. Nicastrin contains a large extracellular domain, a single transmembrane (TM) domain, and a short C-terminus. Its TM domain is important for the γ-secretase complex formation. Here we report nuclear magnetic resonance (NMR) studies of the TM and C-terminal regions of human nicastrin in both sodium dodecyl sulfate (SDS) and dodecylphosphocholine (DPC) micelles. Structural study and dynamic analysis reveal that the TM domain is largely helical and stable under both SDS and DPC micelles with its N-terminal region undergoing intermediate time scale motion. The TM helix contains a hydrophilic patch that is important for TM-TM interactions. The short C-terminus is not structured in solution and a region formed by residues V697-A702 interacts with the membrane, suggesting that these residues may play a role in the γ-secretase complex formation. Our study provides structural insight into the function of the nicastrin TM domain and the C-terminus in γ-secretase complex.
Collapse
Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Lynette Sin Yee Liew
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Qingxin Li
- Institute of Chemical &Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| |
Collapse
|
37
|
NMR of Membrane Proteins: Beyond Crystals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:29-42. [DOI: 10.1007/978-3-319-35072-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
38
|
Sahoo A, Khare S, Devanarayanan S, Jain PC, Varadarajan R. Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis. eLife 2015; 4. [PMID: 26716404 PMCID: PMC4758949 DOI: 10.7554/elife.09532] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/29/2015] [Indexed: 12/16/2022] Open
Abstract
Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the X-ray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists. DOI:http://dx.doi.org/10.7554/eLife.09532.001 Common techniques to determine the three-dimensional structures of proteins can help researchers to understand these molecules’ activities, but are often time-consuming and do not work for all proteins. Proteins are made of chains of amino acids. When a protein chain folds, some of these amino acids interact with other amino acids and these contacts dictate the overall shape of the protein. This means that identifying the pairs of contacting amino acids could make it possible to predict the protein’s structure. Interactions between pairs of contacting amino acids tend to remain conserved throughout evolution, and if a mutation alters one of the amino acids in a pair then a 'compensatory' change often occurs to alter the second amino acid as well. Compensatory mutations can suggest that two amino acids are close to each other in the three-dimensional shape of a protein, but the computational methods used to identify such amino acid pairs can sometimes be inaccurate. In 2012, researchers generated mutants of a bacterial protein called CcdB with changes to single amino acids that caused the protein to fail to fold correctly. Now, Sahoo et al. – who include two of the researchers involved in the 2012 work – have developed an experimental method to identify contacting amino acids and use the CcdB protein as a test case. The approach involved searching for additional mutations that could restore the activity of five of the original mutant proteins when the proteins were produced in yeast cells. The rationale was that any secondary mutations that restored the activity must have corrected the folding defect caused by the original mutation. Sahoo et al. then predicted how close the amino acids affected by the secondary mutations were to the amino acids altered by the original mutations. This information was used to select reliable three-dimensional models of CcdB from a large set of possible structures that had been generated previously using computer models. Next, the technique was applied to a protein called diacylglycerol kinase A. The structure of this protein had previously been inferred using techniques such as X-ray crystallography and nuclear magnetic resonance, but there was a mismatch between the two methods. Sahoo et al. found that the amino acid contacts derived from their experimental method matched those found in the crystal structure, suggesting that the functional protein structure in living cells is similar to the crystal structure. In the future, the experimental approach developed in this work could be combined with existing methods to reliably guide protein structure prediction. DOI:http://dx.doi.org/10.7554/eLife.09532.002
Collapse
Affiliation(s)
- Anusmita Sahoo
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Pankaj C Jain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| |
Collapse
|
39
|
Sim DW, Lee YS, Seo MD, Won HS, Kim JH. A simple guide to the structural study on membrane proteins in detergents using solution NMR. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2015. [DOI: 10.6564/jkmrs.2015.19.3.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
40
|
Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Nat Commun 2015; 6:10140. [PMID: 26673816 PMCID: PMC4703834 DOI: 10.1038/ncomms10140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 11/09/2015] [Indexed: 11/24/2022] Open
Abstract
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution. Diacylglycerol kinase is a small bacterial membrane-bound trimer that catalyses diacylglycerol conversion to phosphatidic acid. Here, the authors solve the crystal structure of the kinase bound to a lipid substrate and an ATP analogue, and show that the active site arose through convergent evolution.
Collapse
|
41
|
Structure and multistate function of the transmembrane electron transporter CcdA. Nat Struct Mol Biol 2015; 22:809-14. [PMID: 26389738 DOI: 10.1038/nsmb.3099] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/27/2015] [Indexed: 01/23/2023]
Abstract
The mechanism by which transmembrane reductases use a single pair of cysteine residues to relay electrons between protein substrates across biological membranes is a long-standing mystery in thiol-redox biochemistry. Here we show the NMR structure of a reduced-state mimic of archaeal CcdA, a protein that transfers electrons across the inner membrane, by using a redox-active NMR sample. The two cysteine positions in CcdA are separated by 20 Å. Whereas one is accessible to the cytoplasm, the other resides in the protein core, thus implying that conformational exchange is required for periplasmic accessibility. In vivo mixed disulfide-trapping experiments validated the functional positioning of the cysteines, and in vitro accessibility results confirmed conformational exchange. Our NMR and functional data together show the existence of multiple conformational states and suggest a four-state model for relaying electrons from cytosolic to periplasmic redox substrates.
Collapse
|
42
|
Molecular properties of diacylglycerol kinase-epsilon in relation to function. Chem Phys Lipids 2015; 192:100-108. [PMID: 26134136 DOI: 10.1016/j.chemphyslip.2015.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/21/2015] [Indexed: 01/12/2023]
Abstract
The epsilon isoform of mammalian diacylglycerol kinase (DGKϵ) is an enzyme that associates strongly with membranes and acts on a lipid substrate, diacylglycerol. The protein has one segment that is predicted to be a transmembrane helix, but appears to interconvert between a transmembrane helix and a re-entrant helix. Despite the hydrophobicity of this segment and the fact that the lipid substrate is also hydrophobic, removal of this hydrophobic segment by truncating the protein at the amino terminus has no effect on its enzymatic activity. The amino acid sequence of the catalytic segment of DGKϵ is highly homologous to that of a bacterial DGK, DgkB. This has allowed us to predict a conformation of DGKϵ based on the known crystal structure of DgkB. An important property of DGKϵ is that it is specific for diacylglycerol species containing an arachidonoyl group. The region of DGKϵ that interacts with this group is found within the accessory domain of the protein and not in the active site nor in the hydrophobic amino terminus. The nature of the acyl chain specificity of the enzyme indicates that DGKϵ is associated with the synthesis of phosphatidylinositol. Defects or deletion of the enzyme give rise to several disease states.
Collapse
|
43
|
Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
Collapse
Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| |
Collapse
|
44
|
Solution NMR Structure Determination of Polytopic α-Helical Membrane Proteins: A Guide to Spin Label Paramagnetic Relaxation Enhancement Restraints. Methods Enzymol 2015; 557:329-48. [PMID: 25950972 DOI: 10.1016/bs.mie.2014.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solution nuclear magnetic resonance structures of polytopic α-helical membrane proteins require additional restraints beyond the traditional Nuclear Overhauser Effect (NOE) restraints. Several methods have been developed and this review focuses on paramagnetic relaxation enhancement (PRE). Important aspects of spin labeling, PRE measurements, structure calculations, and structural quality are discussed.
Collapse
|
45
|
Martin JW, Zhou P, Donald BR. Systematic solution to homo-oligomeric structures determined by NMR. Proteins 2015; 83:651-61. [PMID: 25620116 DOI: 10.1002/prot.24768] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 12/12/2014] [Accepted: 01/12/2015] [Indexed: 11/07/2022]
Abstract
Protein structure determination by NMR has predominantly relied on simulated annealing-based conformational search for a converged fold using primarily distance constraints, including constraints derived from nuclear Overhauser effects, paramagnetic relaxation enhancement, and cysteine crosslinkings. Although there is no guarantee that the converged fold represents the global minimum of the conformational space, it is generally accepted that good convergence is synonymous to the global minimum. Here, we show such a criterion breaks down in the presence of large numbers of ambiguous constraints from NMR experiments on homo-oligomeric protein complexes. A systematic evaluation of the conformational solutions that satisfy the NMR constraints of a trimeric membrane protein, DAGK, reveals 9 distinct folds, including the reported NMR and crystal structures. This result highlights the fundamental limitation of global fold determination for homo-oligomeric proteins using ambiguous distance constraints and provides a systematic solution for exhaustive enumeration of all satisfying solutions.
Collapse
Affiliation(s)
- Jeffrey W Martin
- Department of Computer Science, Duke University, Durham, North Carolina, 27708
| | | | | |
Collapse
|
46
|
Furuita K, Kataoka S, Sugiki T, Hattori Y, Kobayashi N, Ikegami T, Shiozaki K, Fujiwara T, Kojima C. Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints. JOURNAL OF BIOMOLECULAR NMR 2015; 61:55-64. [PMID: 25428765 DOI: 10.1007/s10858-014-9882-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
NMR structure determination of soluble proteins depends in large part on distance restraints derived from NOE. In this study, we examined the impact of paramagnetic relaxation enhancement (PRE)-derived distance restraints on protein structure determination. A high-resolution structure of the loop-rich soluble protein Sin1 could not be determined by conventional NOE-based procedures due to an insufficient number of NOE restraints. By using the 867 PRE-derived distance restraints obtained from the NOE-based structure determination procedure, a high-resolution structure of Sin1 could be successfully determined. The convergence and accuracy of the determined structure were improved by increasing the number of PRE-derived distance restraints. This study demonstrates that PRE-derived distance restraints are useful in the determination of a high-resolution structure of a soluble protein when the number of NOE constraints is insufficient.
Collapse
Affiliation(s)
- Kyoko Furuita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
Collapse
Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
48
|
Li D, Pye VE, Caffrey M. Experimental phasing for structure determination using membrane-protein crystals grown by the lipid cubic phase method. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:104-22. [PMID: 25615865 PMCID: PMC4304691 DOI: 10.1107/s1399004714010360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/07/2014] [Indexed: 03/02/2023]
Abstract
Despite the marked increase in the number of membrane-protein structures solved using crystals grown by the lipid cubic phase or in meso method, only ten have been determined by SAD/MAD. This is likely to be a consequence of the technical difficulties associated with handling proteins and crystals in the sticky and viscous hosting mesophase that is usually incubated in glass sandwich plates for the purposes of crystallization. Here, a four-year campaign aimed at phasing the in meso structure of the integral membrane diacylglycerol kinase (DgkA) from Escherichia coli is reported. Heavy-atom labelling of this small hydrophobic enzyme was attempted by pre-labelling, co-crystallization, soaking, site-specific mercury binding to genetically engineered single-cysteine mutants and selenomethionine incorporation. Strategies and techniques for special handling are reported, as well as the typical results and the lessons learned for each of these approaches. In addition, an assay to assess the accessibility of cysteine residues in membrane proteins for mercury labelling is introduced. The various techniques and strategies described will provide a valuable reference for future experimental phasing of membrane proteins where crystals are grown by the lipid cubic phase method.
Collapse
Affiliation(s)
- Dianfan Li
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Valerie E. Pye
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
49
|
Murray DT, Li C, Gao FP, Qin H, Cross TA. Membrane protein structural validation by oriented sample solid-state NMR: diacylglycerol kinase. Biophys J 2014; 106:1559-69. [PMID: 24739155 DOI: 10.1016/j.bpj.2014.02.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/29/2014] [Accepted: 02/12/2014] [Indexed: 12/28/2022] Open
Abstract
The validation of protein structures through functional assays has been the norm for many years. Functional assays perform this validation for water-soluble proteins very well, but they need to be performed in the same environment as that used for the structural analysis. This is difficult for membrane proteins that are often structurally characterized in detergent environments, although functional assays for these proteins are most frequently performed in lipid bilayers. Because the structure of membrane proteins is known to be sensitive to the membrane mimetic environment, such functional assays are appropriate for validating the protein construct, but not the membrane protein structure. Here, we compare oriented sample solid-state NMR spectral data of diacylglycerol kinase previously published with predictions of such data from recent structures of this protein. A solution NMR structure of diacylglycerol kinase has been obtained in detergent micelles and three crystal structures have been obtained in a monoolein cubic phase. All of the structures are trimeric with each monomer having three transmembrane and one amphipathic helices. However, the solution NMR structure shows typical perturbations induced by a micelle environment that is reflected in the predicted solid-state NMR resonances from the structural coordinates. The crystal structures show few such perturbations, especially for the wild-type structure and especially for the monomers that do not have significant crystal contacts. For these monomers the predicted and observed data are nearly identical. The thermostabilized constructs do show more perturbations, especially the A41C mutation that introduces a hydrophilic residue into what would be the middle of the lipid bilayer inducing additional hydrogen bonding between trimers. These results demonstrate a general technique for validating membrane protein structures with minimal data obtained from membrane proteins in liquid crystalline lipid bilayers by oriented sample solid-state NMR.
Collapse
Affiliation(s)
- Dylan T Murray
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Molecular and Atomic Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, PR China
| | - F Philip Gao
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas
| | - Huajun Qin
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida
| | - Timothy A Cross
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida.
| |
Collapse
|
50
|
Eichmann C, Orts J, Tzitzilonis C, Vögeli B, Smrt S, Lorieau J, Riek R. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes. J Phys Chem B 2014; 118:14288-301. [PMID: 25419869 DOI: 10.1021/jp509137q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.
Collapse
Affiliation(s)
- Cédric Eichmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , CH-8093 Zürich, Switzerland
| | | | | | | | | | | | | |
Collapse
|