1
|
Fridolf S, Hamid MK, Svenningsson L, Skepö M, Sparr E, Topgaard D. Molecular dynamics simulations and solid-state nuclear magnetic resonance spectroscopy measurements of C-H bond order parameters and effective correlation times in a POPC-GM3 bilayer. Phys Chem Chem Phys 2022; 24:25588-25601. [PMID: 36254685 DOI: 10.1039/d2cp02860c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Glycolipids such as gangliosides affect the properties of lipid membranes and in extension the interactions between membranes and other biomolecules like proteins. To better understand how the properties of individual lipid molecules can contribute to shape the functional aspects of a membrane, the spatial restriction and dynamics of C-H bond segments can be measured using nuclear magnetic resonance (NMR) spectroscopy. We combine solid-state NMR spectroscopy with all-atom molecular dynamics (MD) simulations to investigate how ganglioside GM3 affects the bilayer structure and dynamics of C-H bond segments. These two methods yield reorientational correlation functions, molecular profiles of C-H bond order parameters |SCH| and effective correlation times τe, which we compare for lipids in POPC bilayers with and without 30 mol% GM3. Our results revealed that all C-H segments of POPC reorient slower in the presence of GM3 and that the defining features of the GM3-POPC bilayer lie in the GM3 headgroup; it gives the bilayer an extended headgroup layer with high order (|SCH| up to 0.3-0.4) and slow dynamics (τe up to 100 ns), a character that may be mechanistically important in ganglioside interactions with other biomolecules.
Collapse
Affiliation(s)
- Simon Fridolf
- Division of Physical Chemistry, Lund University, Lund, Sweden.
| | - Mona Koder Hamid
- Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | | | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Lund University, Lund, Sweden.
| | - Daniel Topgaard
- Division of Physical Chemistry, Lund University, Lund, Sweden.
| |
Collapse
|
2
|
Banerjee P, Silva DV, Lipowsky R, Santer M. The importance of side branches of glycosylphosphatidylinositol anchors: a molecular dynamics perspective. Glycobiology 2022; 32:933-948. [PMID: 36197124 PMCID: PMC9620968 DOI: 10.1093/glycob/cwac037] [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: 05/06/2021] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
Many proteins are anchored to the cell surface of eukaryotes using a unique family of glycolipids called glycosylphosphatidylinositol (GPI) anchors. These glycolipids also exist without a covalently bound protein, in particular on the cell surfaces of protozoan parasites where they are densely populated. GPIs and GPI-anchored proteins participate in multiple cellular processes such as signal transduction, cell adhesion, protein trafficking and pathogenesis of Malaria, Toxoplasmosis, Trypanosomiasis and prion diseases, among others. All GPIs share a common conserved glycan core modified in a cell-dependent manner with additional side glycans or phosphoethanolamine residues. Here, we use atomistic molecular dynamic simulations and perform a systematic study to evaluate the structural properties of GPIs with different side chains inserted in lipid bilayers. Our results show a flop-down orientation of GPIs with respect to the membrane surface and the presentation of the side chain residues to the solvent. This finding agrees well with experiments showing the role of the side residues as active epitopes for recognition of GPIs by macrophages and induction of GPI-glycan-specific immune responses. Protein-GPI interactions were investigated by attaching parasitic GPIs to Green Fluorescent Protein. GPIs are observed to recline on the membrane surface and pull down the attached protein close to the membrane facilitating mutual contacts between protein, GPI and the lipid bilayer. This model is efficient in evaluating the interaction of GPIs and GPI-anchored proteins with membranes and can be extended to study other parasitic GPIs and proteins and develop GPI-based immunoprophylaxis to treat infectious diseases.
Collapse
Affiliation(s)
- Pallavi Banerjee
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.,Mathematisch-Naturwissenschaftlichen Fakultät, University of Potsdam, Potsdam 14476, Germany
| | - Daniel Varon Silva
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Reinhard Lipowsky
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.,Mathematisch-Naturwissenschaftlichen Fakultät, University of Potsdam, Potsdam 14476, Germany
| | - Mark Santer
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| |
Collapse
|
3
|
Oligosaccharide Presentation Modulates the Molecular Recognition of Glycolipids by Galectins on Membrane Surfaces. Pharmaceuticals (Basel) 2022; 15:ph15020145. [PMID: 35215258 PMCID: PMC8878398 DOI: 10.3390/ph15020145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Galectins are a family of glycan binding proteins that stand out for the wide range of biological phenomena in which they are involved. Most galectin functions are associated with their glycan binding capacities, which are generally well characterized at the oligosaccharide level, but not at the glycoprotein or glycolipid level. Glycolipids form the part of cell membranes where they can act as galectin cellular receptors. In this scenario, glycan presentation as well as the membrane chemical and structural features are expected to have a strong impact in these molecular association processes. Herein, liposomes were used as membrane mimicking scaffolds for the presentation of glycosphingolipids (GSLs) and to investigate their interaction with Galectin-3 and the N-domain of Galectin-8 (Gal8N). The binding towards GM3 and GM1 and their non-silaylated GSLs was compared to the binding to the free glycans, devoid of lipid. The analysis was carried out using a combination of NMR methods, membrane perturbation studies, and molecular modeling. Our results showed a different tendency of the two galectins in their binding capacities towards the glycans, depending on whether they were free oligosaccharides or as part of GSL inserted into a lipid bilayer, highlighting the significance of GSL glycan presentation on membranes in lectin binding.
Collapse
|
4
|
Kozak F, Kurzbach D. How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2097-2105. [PMID: 33995905 PMCID: PMC8085671 DOI: 10.1016/j.csbj.2021.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
We review recent advances in modeling structural ensembles of transcription factors from nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopic data, integrated with molecular dynamics (MD) simulations. We focus on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. This combination enables the deduction of functional and structural protein models even if nuclear Overhauser effects (NOEs) are too scarce for conventional structure determination. We highlight recent insights into the folding-upon-DNA binding transitions of intrinsically disordered transcription factors that could be assessed using such integrative approaches.
Collapse
Affiliation(s)
- Fanny Kozak
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| |
Collapse
|
5
|
Grigolato F, Arosio P. The role of surfaces on amyloid formation. Biophys Chem 2021; 270:106533. [PMID: 33529995 DOI: 10.1016/j.bpc.2020.106533] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 01/02/2023]
Abstract
Interfaces can strongly accelerate or inhibit protein aggregation, destabilizing proteins that are stable in solution or, conversely, stabilizing proteins that are aggregation-prone. Although this behaviour is well-known, our understanding of the molecular mechanisms underlying surface-induced protein aggregation is still largely incomplete. A major challenge is represented by the high number of physico-chemical parameters involved, which are highly specific to the considered combination of protein, surface properties, and solution conditions. The key aspect determining the role of interfaces is the relative propensity of the protein to aggregate at the surface with respect to bulk. In this review, we discuss the multiple molecular determinants that regulate this balance. We summarize current experimental techniques aimed at characterizing protein aggregation at interfaces, and highlight the need to complement experimental analysis with theoretical modelling. In particular, we illustrate how chemical kinetic analysis can be combined with experimental methods to provide insights into the molecular mechanisms underlying surface-induced protein aggregation, under both stagnant and agitation conditions. We summarize recent progress in the study of important amyloids systems, focusing on selected relevant interfaces.
Collapse
Affiliation(s)
- Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland.
| |
Collapse
|
6
|
Jiang X, Chen Y, Yuan Y, Zheng L. Thermal Response in Cellulose I β Based on Molecular Dynamics. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2019. [DOI: 10.1515/cmb-2019-0007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The structural details of cellulose I β were discussed according to molecular dynamics simulations with the GLYCAM-06 force field. The simulation outcomes were in agreement with previous experimental data, including structural parameters and hydrogen bond pattern at 298 K. We found a new conformation of cellulose Iβ existed at the intermediate temperature that is between the low and high temperatures. Partial chain rotations along the backbone direction were found and conformations of hydroxymethyl groups that alternated from tg to either gt or gg were observed when the temperature increased from 298 K to 400 K. In addition, the gg conformation is preferred than gt. For the structure adopted at high temperature of 500 K, major chains were twisted and two chains detached from each plain. In contrast to the observation under intermediate temperature, the population of hydroxymethyl groups in gt exceeded that in gg conformation at high temperature. In addition, three patterns of hydrogen bonding were identified at low, intermediate and high temperatures in the simulations. The provided structural information indicated the transitions occurred around 350 K and 450 K, considered as the transitional temperatures of cellulose Iβ in this work.
Collapse
Affiliation(s)
- Xuewei Jiang
- Wuhan Textile and Apparel Digital Engineering Technology Research Center , Wuhan Textile University , Wuhan 430073 , Hubei, China ; Hubei Key Laboratory of Biomass Fibers and Eco-dyeing & Finishing , Wuhan Textile University , Wuhan 430073 , China
| | - Yu Chen
- Wuhan Textile and Apparel Digital Engineering Technology Research Center , Wuhan Textile University , Wuhan 430073 , Hubei, China
| | - Yue Yuan
- Department of Textile Engineering, Chemistry and Science , North Carolina State University , USA 27067
| | - Lu Zheng
- Wuhan Textile and Apparel Digital Engineering Technology Research Center , Wuhan Textile University , Wuhan 430073 , Hubei, China
| |
Collapse
|
7
|
Owen MC, Karner A, Šachl R, Preiner J, Amaro M, Vácha R. Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments. J Phys Chem B 2019; 123:7504-7517. [PMID: 31397569 DOI: 10.1021/acs.jpcb.9b05095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The great physiological relevance of glycolipids is being increasingly recognized, and glycolipid interactions have been shown to be central to cell-cell recognition, neuronal plasticity, protein-ligand recognition, and other important processes. However, detailed molecular-level understanding of these processes remains to be fully resolved. Molecular dynamics simulations could reveal the details of the glycolipid interactions, but the results may be influenced by the choice of the employed force field. Here, we have compared the behavior and properties of GM1, a common, biologically important glycolipid, using the CHARMM36, OPLS, GROMOS, and Amber99-GLYCAM06 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids and compared the results to atomic force microscopy and fluorescence resonance energy transfer experiments. We found discrepancies within the GM1 behavior displayed between the investigated force fields. Based on a direct comparison with complementary experimental results derived from fluorescence and AFM measurements, we recommend using the Amber99-GLYCAM force field in bilayers comprising LIPID14 or SLIPIDS lipids followed by CHARMM36 and OPLS force fields in simulations. The GROMOS force field is not recommended for reproducing the properties of the GM1 head group.
Collapse
Affiliation(s)
- Michael C Owen
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Andreas Karner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Radek Šachl
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the C.A.S., v.v.i., Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Mariana Amaro
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the C.A.S., v.v.i., Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| |
Collapse
|
8
|
Srivastava AK, Pittman JM, Zerweck J, Venkata BS, Moore PC, Sachleben JR, Meredith SC. β-Amyloid aggregation and heterogeneous nucleation. Protein Sci 2019; 28:1567-1581. [PMID: 31276610 PMCID: PMC6699094 DOI: 10.1002/pro.3674] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 01/09/2023]
Abstract
In this article, we consider the role of heterogeneous nucleation in β-amyloid aggregation. Heterogeneous nucleation is more common and occurs at lower levels of supersaturation than homogeneous nucleation. The nucleation period is also the stage at which most of the polymorphism of amyloids arises, this being one of the defining features of amyloids. We focus on several well-known heterogeneous nucleators of β-amyloid, including lipid surfaces, especially those enriched in gangliosides and cholesterol, and divalent metal ions. These two broad classes of nucleators affect β-amyloid particularly in light of the amphiphilicity of these peptides: the N-terminal region, which is largely polar and charged, contains the metal binding site, whereas the C-terminal region is aliphatic and is important in lipid binding. Notably, these two classes of nucleators can interact cooperatively, aggregation begetting greater aggregation.
Collapse
Affiliation(s)
- Atul K. Srivastava
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | - Jay M. Pittman
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | - Jonathan Zerweck
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | - Bharat S. Venkata
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | | | | | - Stephen C. Meredith
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| |
Collapse
|
9
|
Lee J, Patel DS, Ståhle J, Park SJ, Kern NR, Kim S, Lee J, Cheng X, Valvano MA, Holst O, Knirel YA, Qi Y, Jo S, Klauda JB, Widmalm G, Im W. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. J Chem Theory Comput 2018; 15:775-786. [PMID: 30525595 DOI: 10.1021/acs.jctc.8b01066] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Glycolipids (such as glycoglycerolipids, glycosphingolipids, and glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS), lipooligosaccharides (LOS), mycobacterial lipoarabinomannan, and mycoplasma lipoglycans) are typically found on the surface of cell membranes and play crucial roles in various cellular functions. Characterizing their structure and dynamics at the molecular level is essential to understand their biological roles, but systematic generation of glycolipid and lipoglycan structures is challenging because of great variations in lipid structures and glycan sequences (i.e., carbohydrate types and their linkages). To facilitate the generation of all-atom glycolipid/LPS/LOS structures, we have developed Glycolipid Modeler and LPS Modeler in CHARMM-GUI ( http://www.charmm-gui.org ), a web-based interface that simplifies building of complex biological simulation systems. In addition, we have incorporated these modules into Membrane Builder so that users can readily build a complex symmetric or asymmetric biological membrane system with various glycolipids and LPS/LOS. These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolipid-/LPS-/LOS-containing biological membrane systems.
Collapse
Affiliation(s)
- Jumin Lee
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Dhilon S Patel
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Sang-Jun Park
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Nathan R Kern
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Seonghoon Kim
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Joonseong Lee
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Xi Cheng
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine , Queen's University Belfast BT9 7BL , United Kingdom
| | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel , Airway Research Center North, Member of the German Center for Lung Research (DZL) , D-23845 Borstel , Germany
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry , Russian Academy of Sciences , 119991 Moscow , Russia
| | - Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
| | - Sunhwan Jo
- Leadership Computing Facility , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| |
Collapse
|
10
|
Hunter CD, Guo T, Daskhan G, Richards MR, Cairo CW. Synthetic Strategies for Modified Glycosphingolipids and Their Design as Probes. Chem Rev 2018; 118:8188-8241. [DOI: 10.1021/acs.chemrev.8b00070] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Carmanah D. Hunter
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tianlin Guo
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gour Daskhan
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Michele R. Richards
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
11
|
Alibay I, Burusco KK, Bruce NJ, Bryce RA. Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics. J Phys Chem B 2018; 122:2462-2474. [PMID: 29419301 DOI: 10.1021/acs.jpcb.7b09841] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4C1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.
Collapse
Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Kepa K Burusco
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Neil J Bruce
- Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , Heidelberg 69118 , Germany
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| |
Collapse
|
12
|
Matsuzaki K, Kato K, Yanagisawa K. Ganglioside-Mediated Assembly of Amyloid β-Protein: Roles in Alzheimer's Disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 156:413-434. [PMID: 29747822 DOI: 10.1016/bs.pmbts.2017.10.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Assembly and deposition of amyloid β-protein (Aβ) is an early and invariable pathological event of Alzheimer's disease (AD), a chronic neurodegenerative disease affecting the neurons in the brain of aging population. Thus, clarification of the molecular mechanism underlying Aβ assembly is crucial not only for understanding the pathogenesis of AD, but also for developing disease-modifying remedies. In 1995, ganglioside-bound Aβ (GAβ), with unique molecular characteristics, including its altered immunoreactivity and its conspicuous ability to accelerate Aβ assembly, was discovered in an autopsied brain showing early pathological changes of AD. Based on these findings, it was hypothesized that GAβ is an endogenous seed for amyloid fibril formation in the AD brain. A body of evidence that supports the GAβ hypothesis has been growing for over 20years as follows. First, the conformational changes of Aβ from a random coil to an α-helix, and then to a β-sheet in the presence of ganglioside were validated by several techniques. Second, the seed activity of GAβ to accelerate the assembly of soluble Aβ into amyloid fibrils was confirmed by various in vitro and in vivo experiments. Third, it was found that the Aβ binding to ganglioside to form GAβ occurs under limited conditions, which were provided by the lipid environment surrounding ganglioside. Fourth, the region-specific Aβ deposition in the brain appeared to be dependent on the presence of the lipid environment that was in favor of GAβ generation. In this chapter, further progress of the study of ganglioside-mediated Aβ assembly, especially from the aspects of physicochemistry, structural biology, and neuropathology, is reviewed.
Collapse
Affiliation(s)
| | - Koichi Kato
- Nagoya City University, Nagoya, Japan; Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Katsuhiko Yanagisawa
- Center for Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Japan.
| |
Collapse
|
13
|
Kobayashi C, Jung J, Matsunaga Y, Mori T, Ando T, Tamura K, Kamiya M, Sugita Y. GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. J Comput Chem 2017; 38:2193-2206. [PMID: 28718930 DOI: 10.1002/jcc.24874] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 01/09/2023]
Abstract
GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan.,Theoretical Molecular Science Laboratory, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yasuhiro Matsunaga
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan.,JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tadashi Ando
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center Computational Biology Research Core, 1-6-5 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan.,Department of Applied Electronics, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan.,Water Frontier Science and Technology Research Center, Research Institute for Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan.,Research Division of Multiscale Interfacial Thermofluid Dynamics, Research Institute for Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Koichi Tamura
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Motoshi Kamiya
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan.,Theoretical Molecular Science Laboratory, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center Computational Biology Research Core, 1-6-5 Minatojima-minamachi, Chuo-ku, Kobe, 650-0047, Japan
| |
Collapse
|
14
|
Patel DS, Park S, Wu EL, Yeom MS, Widmalm G, Klauda JB, Im W. Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature. Biophys J 2017; 111:1987-1999. [PMID: 27806280 DOI: 10.1016/j.bpj.2016.09.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/18/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022] Open
Abstract
Gangliosides are a class of glycosphingolipids (GSLs) with amphiphilic character that are found at the outer leaflet of the cell membranes, where their ability to organize into special domains makes them vital cell membrane components. However, a molecular understanding of GSL-rich membranes in terms of their clustered organization, stability, and dynamics is still elusive. To gain molecular insight into the organization and dynamics of GSL-rich membranes, we performed all-atom molecular-dynamics simulations of bicomponent ganglioside GM1 in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers with varying concentrations of GM1 (10%, 20%, and 30%). Overall, the simulations show very good agreement with available experimental data, including x-ray electron density profiles along the membrane normal, NMR carbohydrate proton-proton distances, and x-ray crystal structures. This validates the quality of our model systems for investigating GM1 clustering through an ordered-lipid-cluster analysis. The increase in GM1 concentration induces tighter lipid packing, driven mainly by inter-GM1 carbohydrate-carbohydrate interactions, leading to a greater preference for the positive curvature of GM1-containing membranes and larger cluster sizes of ordered-lipid clusters (with a composite of GM1 and POPC). These clusters tend to segregate and form a large percolated cluster at a 30% GM1 concentration at 293 K. At a higher temperature of 330 K, however, the segregation is not maintained.
Collapse
Affiliation(s)
- Dhilon S Patel
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Soohyung Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Emilia L Wu
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information, Daejeon, Korea
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland; Biophysics Program, University of Maryland, College Park, Maryland.
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.
| |
Collapse
|
15
|
Pilla KB, Gaalswyk K, MacCallum JL. Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28648524 DOI: 10.1016/j.bbapap.2017.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modeling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures. In this review, we discuss various types of paramagnetic NMR/computational hybrid modeling techniques that can be applied to successful modeling of not only the atomic structure of proteins but also their interacting partners. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
Collapse
Affiliation(s)
| | - Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | | |
Collapse
|
16
|
Nasir W, Frank M, Kunze A, Bally M, Parra F, Nyholm PG, Höök F, Larson G. Histo-Blood Group Antigen Presentation Is Critical for Binding of Norovirus VLP to Glycosphingolipids in Model Membranes. ACS Chem Biol 2017; 12:1288-1296. [PMID: 28294600 DOI: 10.1021/acschembio.7b00152] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Virus entry depends on biomolecular recognition at the surface of cell membranes. In the case of glycolipid receptors, these events are expected to be influenced by how the glycan epitope close to the membrane is presented to the virus. This presentation of membrane-associated glycans is more restricted than that of glycans in solution, particularly because of orientational constraints imposed on the glycolipid through its lateral interactions with other membrane lipids and proteins. We have developed and employed a total internal reflection fluorescence microscopy-based binding assay and a scheme for molecular dynamics (MD) membrane simulations to investigate the consequences of various glycan presentation effects. The system studied was histo-blood group antigen (HBGA) epitopes of membrane-bound glycosphingolipids (GSLs) derived from small intestinal epithelium of humans (type 1 chain) and dogs (type 2 chain) interacting with GII.4 norovirus-like particles. Our experimental results showed strong binding to all lipid-linked type 1 chain HBGAs but no or only weak binding to the corresponding type 2 chain HBGAs. This is in contrast to results derived from STD experiments with free HBGAs in solution where binding was observed for Lewis x. The MD data suggest that the strong binding to type 1 chain glycolipids was due to the well-exposed (1,2)-linked α-l-Fucp and (1,4)-linked α-l-Fucp residues, while the weaker binding or lack of binding to type 2 chain HBGAs was due to the very restricted accessibility of the (1,3)-linked α-l-Fucp residue when the glycolipid is embedded in a phospholipid membrane. Our results not only contribute to a general understanding of protein-carbohydrate interactions on model membrane surfaces, particularly in the context of virus binding, but also suggest a possible role of human intestinal GSLs as potential receptors for norovirus uptake.
Collapse
Affiliation(s)
- Waqas Nasir
- Department
of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Martin Frank
- Biognos AB, Generatorsgatan 1, P.O. Box 8963, 40274 Gothenburg, Sweden
| | - Angelika Kunze
- Department
of Applied Physics, Chalmers University of Technology, S-412 96 Gothenburg, Sweden
| | - Marta Bally
- Department
of Applied Physics, Chalmers University of Technology, S-412 96 Gothenburg, Sweden
| | - Francisco Parra
- Instituto
Universitario de Biotecnología de Asturias, Departamento de
Bioquimíca y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Per-Georg Nyholm
- Biognos AB, Generatorsgatan 1, P.O. Box 8963, 40274 Gothenburg, Sweden
- Department
of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Höök
- Department
of Applied Physics, Chalmers University of Technology, S-412 96 Gothenburg, Sweden
| | - Göran Larson
- Department
of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
17
|
Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
Collapse
Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| |
Collapse
|
18
|
Lee J, Gregory SM, Nelson EA, White JM, Tamm LK. The Roles of Histidines and Charged Residues as Potential Triggers of a Conformational Change in the Fusion Loop of Ebola Virus Glycoprotein. PLoS One 2016; 11:e0152527. [PMID: 27023721 PMCID: PMC4811418 DOI: 10.1371/journal.pone.0152527] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/15/2016] [Indexed: 11/23/2022] Open
Abstract
Ebola virus (EBOV) enters cells from late endosomes/lysosomes under mildly acidic conditions. Entry by fusion with the endosomal membrane requires the fusion loop (FL, residues 507–560) of the EBOV surface glycoprotein to undergo a pH-dependent conformational change. To find the pH trigger for this reaction we mutated multiple conserved histidines and charged and uncharged hydrophilic residues in the FL and measured their activity by liposome fusion and cell entry of virus-like particles. The FL location in the membrane was assessed by NMR using soluble and lipid-bound paramagnetic relaxation agents. While we could not identify a single residue to be alone responsible for pH triggering, we propose that a distributed pH effect over multiple residues induces the conformational change that enhances membrane insertion and triggers the fusion activity of the EBOV FL.
Collapse
Affiliation(s)
- Jinwoo Lee
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Sonia M Gregory
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Elizabeth A Nelson
- Department Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Judith M White
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States of America
| |
Collapse
|
19
|
Blaum BS, Frank M, Walker RC, Neu U, Stehle T. Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations. Glycobiology 2015; 26:532-9. [PMID: 26715202 DOI: 10.1093/glycob/cwv170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
Mammalian cell surfaces are decorated with a variety of glycan chains that orchestrate development and defense and are exploited by pathogens for cellular attachment and entry. While glycosidic linkages are, in principle, flexible, the conformational space that a given glycan can sample is subject to spatial and electrostatic restrictions imposed by its overall chemical structure. Here, we show how the glycan moiety of the GM1 ganglioside, a branched, monosialylated pentasaccharide that serves as a ligand for various proteins, undergoes differential conformational selection in its interactions with different lectins. Using STD NMR and X-ray crystallography, we found that the innate immune regulator complement Factor H (FH) binds a previously not reported GM1 conformation that is not compatible with the GM1-binding sites of other structurally characterized GM1-binding lectins such as the Simian Virus 40 (SV40) capsid. Molecular dynamics simulations of the free glycan in explicit solvent on the 10 μs timescale reveal that the FH-bound conformation nevertheless corresponds to a minimum in the Gibbs free energy plot. In contrast to the GM1 conformation recognized by SV40, the FH-bound GM1 conformation is associated with poor NOE restraints, explaining how it escaped(1)H-(1)H NOE-restrained modeling in the past and highlighting the necessity for ensemble representations of glycan structures.
Collapse
Affiliation(s)
- Bärbel S Blaum
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | - Martin Frank
- Biognos AB, Generatorsgatan 1, Gothenburg 41705, Sweden
| | - Ross C Walker
- San Diego Supercomputer Center and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ursula Neu
- Max-Planck-Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37212, USA
| |
Collapse
|
20
|
Kato K, Yamaguchi T. Paramagnetic NMR probes for characterization of the dynamic conformations and interactions of oligosaccharides. Glycoconj J 2015; 32:505-13. [PMID: 26050258 DOI: 10.1007/s10719-015-9599-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 12/21/2022]
Abstract
Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques have recently been applied to a wide variety of biomolecular systems, using sophisticated immobilization methods to attach paramagnetic probes, such as spin labels and lanthanide-chelating groups, at specific sites of the target biomolecules. This is also true in the field of carbohydrate NMR spectroscopy. NMR analysis of oligosaccharides is often precluded by peak overlap resulting from the lack of variability of local chemical structures, by the insufficiency of conformational restraints from nuclear Overhauser effect (NOE) data due to low proton density, and moreover, by the inherently flexible nature of carbohydrate chains. Paramagnetic probes attached to the reducing ends of oligosaccharides cause paramagnetic relaxation enhancements (PREs) and/or pseudocontact shifts (PCSs) resolve the peak overlap problem. These spectral perturbations can be sources of long-range atomic distance information, which complements the local conformational information derived from J couplings and NOEs. Furthermore, paramagnetic NMR approaches, in conjunction with computational methods, have opened up possibilities for the description of dynamic conformational ensembles of oligosaccharides in solution. Several applications of paramagnetic NMR techniques are presented to demonstrate their utility for characterizing the conformational dynamics of oligosaccharides and for probing the carbohydrate-recognition modes of proteins. These techniques can be applied to the characterization of transient, non-stoichiometric interactions and will contribute to the visualization of dynamic biomolecular processes involving sugar chains.
Collapse
Affiliation(s)
- Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tababe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
- The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tababe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| |
Collapse
|
21
|
Yagi-Utsumi M, Kato K. Structural and dynamic views of GM1 ganglioside. Glycoconj J 2015; 32:105-12. [DOI: 10.1007/s10719-015-9587-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/30/2015] [Indexed: 11/29/2022]
|
22
|
Ryabov Y. Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra. Proteins 2015; 83:1571-81. [PMID: 25900685 DOI: 10.1002/prot.24814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/23/2015] [Accepted: 04/05/2015] [Indexed: 11/08/2022]
Abstract
In this work, we formulate a closed-form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high-frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571-1581. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Yaroslav Ryabov
- BC Portal Inc., 260 Congressional Ln. #204, Rockville, Maryland, 20852
| |
Collapse
|
23
|
The Greater Affinity of JC Polyomavirus Capsid for α2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity. J Virol 2015; 89:6364-75. [PMID: 25855729 DOI: 10.1128/jvi.00489-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/30/2015] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED The human JC polyomavirus (JCPyV) establishes an asymptomatic, persistent infection in the kidneys of the majority of the population and is the causative agent of the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) in immunosuppressed individuals. The Mad-1 strain of JCPyV, a brain isolate, was shown earlier to require α2,6-linked sialic acid on the lactoseries tetrasaccharide c (LSTc) glycan for attachment to host cells. In contrast, a JCPyV kidney isolate type 3 strain, WT3, has been reported to interact with sialic acid-containing gangliosides, but the role of these glycans in JCPyV infection has remained unclear. To help rationalize these findings and probe the effects of strain-specific differences on receptor binding, we performed a comprehensive analysis of the glycan receptor specificities of these two representative JCPyV strains using high-resolution X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, and correlated these data with the results of infectivity assays. We show here that capsid proteins of Mad-1 and WT3 JCPyV can both engage LSTc as well as multiple sialylated gangliosides. However, the binding affinities exhibit subtle differences, with the highest affinity observed for LSTc. Engagement of LSTc is a prerequisite for functional receptor engagement, while the more weakly binding gangliosides are not required for productive infection. Our findings highlight the complexity of virus-carbohydrate interactions and demonstrate that subtle differences in binding affinities, rather than the binding event alone, help determine tissue tropism and viral pathogenesis. IMPORTANCE Viral infection is initiated by attachment to receptors on host cells, and this event plays an important role in viral disease. We investigated the receptor-binding properties of human JC polyomavirus (JCPyV), a virus that resides in the kidneys of the majority of the population and can cause the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) in the brains of immunosuppressed individuals. JCPyV has been reported to interact with multiple carbohydrate receptors, and we sought to clarify how the interactions between JCPyV and cellular carbohydrate receptors influenced infection. Here we demonstrate that JCPyV can engage numerous sialylated carbohydrate receptors. However, the virus displays preferential binding to LSTc, and only LSTc mediates a productive infection. Our findings demonstrate that subtle differences in binding affinity, rather than receptor engagement alone, are a key determinant of viral infection.
Collapse
|
24
|
Computerized Models of Carbohydrates. POLYSACCHARIDES 2015. [DOI: 10.1007/978-3-319-16298-0_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
25
|
DeMarco ML. Molecular dynamics simulations of membrane- and protein-bound glycolipids using GLYCAM. Methods Mol Biol 2015; 1273:379-390. [PMID: 25753721 DOI: 10.1007/978-1-4939-2343-4_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This chapter outlines protocols for the preparation, execution, and analysis of molecular dynamics (MD) simulations of glycolipids in biologically relevant environments, i.e., imbedded in lipid bilayers or bound to proteins, with the goal of generating biologically relevant structural and dynamic information. Also included is a description of ensemble average (EA) charge set development consistent with the GLYCAM06 force field and its implementation using the AMBER molecular dynamics software suite.
Collapse
Affiliation(s)
- Mari L DeMarco
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, University of British Columbia, 1081 Burrard St, Vancouver, BC, Canada, V6Z 1Y6,
| |
Collapse
|
26
|
Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
Collapse
Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
27
|
|
28
|
Yamaguchi T, Sakae Y, Zhang Y, Yamamoto S, Okamoto Y, Kato K. Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation. Angew Chem Int Ed Engl 2014; 53:10941-4. [PMID: 25196214 DOI: 10.1002/anie.201406145] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Indexed: 12/11/2022]
Abstract
Exploration of the conformational spaces of flexible biomacromolecules is essential for quantitatively understanding the energetics of their molecular recognition processes. We employed stable isotope- and lanthanide-assisted NMR approaches in conjunction with replica-exchange molecular dynamics (REMD) simulations to obtain atomic descriptions of the conformational dynamics of high-mannose-type oligosaccharides, which harbor intracellular glycoprotein-fate determinants in their triantennary structures. The experimentally validated REMD simulation provided quantitative views of the dynamic conformational ensembles of the complicated, branched oligosaccharides, and indicated significant expansion of the conformational space upon removal of a terminal mannose residue during the functional glycan-processing pathway.
Collapse
Affiliation(s)
- Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan); Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603 (Japan); School of Physical Sciences, The Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan)
| | | | | | | | | | | |
Collapse
|
29
|
Yamaguchi T, Sakae Y, Zhang Y, Yamamoto S, Okamoto Y, Kato K. Exploration of Conformational Spaces of High-Mannose-Type Oligosaccharides by an NMR-Validated Simulation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
30
|
The challenges of understanding glycolipid functions: An open outlook based on molecular simulations. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1130-45. [DOI: 10.1016/j.bbalip.2013.12.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/20/2022]
|
31
|
Molecular dynamics study of GM1 ganglioside complex with amyloid β peptide (Aβ42) in lipid membrane. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.01.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
32
|
Zhang Y, Yamaguchi T, Kato K. New NMR Tools for Characterizing the Dynamic Conformations and Interactions of Oligosaccharides. CHEM LETT 2013. [DOI: 10.1246/cl.130789] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ying Zhang
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- The Glycoscience Institute, Ochanomizu University
| |
Collapse
|
33
|
Neu U, Khan ZM, Schuch B, Palma AS, Liu Y, Pawlita M, Feizi T, Stehle T. Structures of B-lymphotropic polyomavirus VP1 in complex with oligosaccharide ligands. PLoS Pathog 2013; 9:e1003714. [PMID: 24204265 PMCID: PMC3814675 DOI: 10.1371/journal.ppat.1003714] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/03/2013] [Indexed: 12/04/2022] Open
Abstract
B-Lymphotropic Polyomavirus (LPyV) serves as a paradigm of virus receptor binding and tropism, and is the closest relative of the recently discovered Human Polyomavirus 9 (HPyV9). LPyV infection depends on sialic acid on host cells, but the molecular interactions underlying LPyV-receptor binding were unknown. We find by glycan array screening that LPyV specifically recognizes a linear carbohydrate motif that contains α2,3-linked sialic acid. High-resolution crystal structures of the LPyV capsid protein VP1 alone and in complex with the trisaccharide ligands 3′-sialyllactose and 3′-sialyl-N-acetyl-lactosamine (3SL and 3SLN, respectively) show essentially identical interactions. Most contacts are contributed by the sialic acid moiety, which is almost entirely buried in a narrow, preformed cleft at the outer surface of the capsid. The recessed nature of the binding site on VP1 and the nature of the observed glycan interactions differ from those of related polyomaviruses and most other sialic acid-binding viruses, which bind sialic acid in shallow, more exposed grooves. Despite their different modes for recognition, the sialic acid binding sites of LPyV and SV40 are half-conserved, hinting at an evolutionary strategy for diversification of binding sites. Our analysis provides a structural basis for the observed specificity of LPyV for linear glycan motifs terminating in α2,3-linked sialic acid, and links the different tropisms of known LPyV strains to the receptor binding site. It also serves as a useful template for understanding the ligand-binding properties and serological crossreactivity of HPyV9. Viruses must engage specific receptors on host cells in order to initiate infection. The type of receptor and its concentration on cells determine viral spread and tropism, but for many viruses, the receptor and the mode of recognition by the virus are not known. We have characterized the structural requirements for receptor binding of B-lymphotropic polyomavirus (LPyV). This virus was originally isolated from African Green Monkey lymph node cultures and attracted interest because of its narrow tropism for a human tumor cell line. LPyV is also the closest relative of the recently discovered Human Polyomavirus 9 (HPyV9). We screened the LPyV coat protein VP1 on an carbohydrate microarray and found that it specifically recognizes a linear sugar motif that terminates in α2,3-linked sialic acid. We then determined the structures LPyV VP1 bound to these carbohydrates. The protein has a preformed, deeply recessed binding site for sialic acid. The binding site differs in both architecture and mode of recognition from the binding sites of other viruses. LPyV only binds linear carbohydrates that are able to penetrate into the binding slot.
Collapse
Affiliation(s)
- Ursula Neu
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Zaigham Mahmood Khan
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Benjamin Schuch
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Angelina S. Palma
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London, United Kingdom
| | - Yan Liu
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London, United Kingdom
| | - Michael Pawlita
- Department of Genome Modificati and Carcinogenesis (F020), German Cancer Research Center, Heidelberg, Germany
| | - Ten Feizi
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London, United Kingdom
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
| |
Collapse
|
34
|
Yamaguchi T, Kamiya Y, Choo YM, Yamamoto S, Kato K. Terminal Spin Labeling of a High-mannose-type Oligosaccharide for Quantitative NMR Analysis of Its Dynamic Conformation. CHEM LETT 2013. [DOI: 10.1246/cl.130040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takumi Yamaguchi
- Institute for Molecular Science, National Institutes of Natural Sciences
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Yukiko Kamiya
- Institute for Molecular Science, National Institutes of Natural Sciences
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Yeun-Mun Choo
- Institute for Molecular Science, National Institutes of Natural Sciences
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Chemistry, University of Malaya
| | - Sayoko Yamamoto
- Institute for Molecular Science, National Institutes of Natural Sciences
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Koichi Kato
- Institute for Molecular Science, National Institutes of Natural Sciences
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- The Glycoscience Institute, Ochanomizu University
- GLYENCE Co., Ltd
| |
Collapse
|
35
|
López CA, Sovova Z, van Eerden FJ, de Vries AH, Marrink SJ. Martini Force Field Parameters for Glycolipids. J Chem Theory Comput 2013; 9:1694-708. [DOI: 10.1021/ct3009655] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- César A. López
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Zofie Sovova
- Faculty
of Science, University
of South Bohemia, Czech Republic, and Institute of Nanobiology and
Structural Biology GCRC ASCR, v.v.i. Nove Hrady, Czech Republic
| | - Floris J. van Eerden
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Alex H. de Vries
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| |
Collapse
|
36
|
Dürr UH, Soong R, Ramamoorthy A. When detergent meets bilayer: birth and coming of age of lipid bicelles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:1-22. [PMID: 23465641 PMCID: PMC3741677 DOI: 10.1016/j.pnmrs.2013.01.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/30/2012] [Indexed: 05/12/2023]
|
37
|
Kamiya Y, Yanagi K, Kitajima T, Yamaguchi T, Chiba Y, Kato K. Application of Metabolic 13C Labeling in Conjunction with High-Field Nuclear Magnetic Resonance Spectroscopy for Comparative Conformational Analysis of High Mannose-Type Oligosaccharides. Biomolecules 2013; 3:108-23. [PMID: 24970159 PMCID: PMC4030882 DOI: 10.3390/biom3010108] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
High mannose-type oligosaccharides are enzymatically trimmed in the endoplasmic reticulum, resulting in various processing intermediates with exposed glycotopes that are recognized by a series of lectins involved in glycoprotein fate determination in cells. Although recent crystallographic data have provided the structural basis for the carbohydrate recognition of intracellular lectins, atomic information of dynamic oligosaccharide conformations is essential for a quantitative understanding of the energetics of carbohydrate–lectin interactions. Carbohydrate NMR spectroscopy is useful for characterizing such conformational dynamics, but often hampered by poor spectral resolution and lack of recombinant techniques required to produce homogeneous glycoforms. To overcome these difficulties, we have recently developed a methodology for the preparation of a homogeneous high mannose-type oligosaccharide with 13C labeling using a genetically engineered yeast strain. We herein successfully extended this method to result in the overexpression of 13C-labeled Man9GlcNAc2 (M9) with a newly engineered yeast strain with the deletion of four genes involved in N-glycan processing. This enabled high-field NMR analyses of 13C-labeled M9 in comparison with its processing product lacking the terminal mannose residue ManD2. Long-range NOE data indicated that the outer branches interact with the core in both glycoforms, and such foldback conformations are enhanced upon the removal of ManD2. The observed conformational variabilities might be significantly associated with lectins and glycan-trimming enzymes.
Collapse
Affiliation(s)
- Yukiko Kamiya
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
| | - Kotaro Yanagi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
| | - Toshihiko Kitajima
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
| | - Yasunori Chiba
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaiji, Okazaki 444-8787, Japan.
| |
Collapse
|
38
|
Yamaguchi T, Uno T, Uekusa Y, Yagi-Utsumi M, Kato K. Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins. Chem Commun (Camb) 2013; 49:1235-7. [DOI: 10.1039/c2cc38016a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
39
|
DeMarco ML. Three-Dimensional Structure of Glycolipids in Biological Membranes. Biochemistry 2012; 51:5725-32. [DOI: 10.1021/bi3003633] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mari L. DeMarco
- Division of Laboratory
and Genomic Medicine, Washington University School of Medicine, 660 South
Euclid Avenue, St. Louis, Missouri 63110, United States
| |
Collapse
|
40
|
Lütteke T. The use of glycoinformatics in glycochemistry. Beilstein J Org Chem 2012; 8:915-29. [PMID: 23015842 PMCID: PMC3388882 DOI: 10.3762/bjoc.8.104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/29/2012] [Indexed: 01/10/2023] Open
Abstract
Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to glycochemistry: Databases can provide information on candidate glycan structures for synthesis, or on glyco-enzymes that can be used to synthesize carbohydrates. Statistical analyses of glycan databases help to plan glycan synthesis experiments. 3D-Structural data of protein-carbohydrate complexes are used in targeted drug design, and tools to support glycan structure analysis aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed.
Collapse
Affiliation(s)
- Thomas Lütteke
- Justus-Liebig-University Gießen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392 Gießen, Germany
| |
Collapse
|
41
|
Zhang Y, Yamamoto S, Yamaguchi T, Kato K. Application of paramagnetic NMR-validated molecular dynamics simulation to the analysis of a conformational ensemble of a branched oligosaccharide. Molecules 2012; 17:6658-71. [PMID: 22728360 PMCID: PMC6268797 DOI: 10.3390/molecules17066658] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/29/2012] [Accepted: 05/29/2012] [Indexed: 02/05/2023] Open
Abstract
Oligosaccharides of biological importance often exhibit branched covalent structures and dynamic conformational multiplicities. Here we report the application of a method that we developed, which combined molecular dynamics (MD) simulations and lanthanide-assisted paramagnetic NMR spectroscopy, to evaluate the dynamic conformational ensemble of a branched oligosaccharide. A lanthanide-chelating tag was attached to the reducing end of the branched tetrasaccharide of GM2 ganglioside to observe pseudocontact shifts as the source of long distance information for validating the conformational ensemble derived from MD simulations. By inspecting the results, the conformational space of the GM2 tetrasaccharide was compared with that of its nonbranched derivative, the GM3 trisaccharide.
Collapse
Affiliation(s)
- Ying Zhang
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Department of Functional Molecular Science, the Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Sayoko Yamamoto
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Department of Functional Molecular Science, the Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Department of Functional Molecular Science, the Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
- The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
- GLYENCE Co., Ltd., 2-22-8 Chikusa, Chikusa-ku, Nagoya 464-0858, Japan
- Author to whom correspondence should be addressed; ; Tel.: +81-564-59-5225; Fax: +81-564-59-5224
| |
Collapse
|
42
|
Su Y, Hu F, Hong M. Paramagnetic Cu(II) for probing membrane protein structure and function: inhibition mechanism of the influenza M2 proton channel. J Am Chem Soc 2012; 134:8693-702. [PMID: 22519936 DOI: 10.1021/ja3026328] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paramagnetic Cu(II) ions enhance nuclear spin relaxation in a distance-dependent fashion and can be used as a structural probe of proteins. Cu(II) can also serve as a functionally important ligand in proteins. Here we investigate the structural basis of Cu(II) inhibition of the influenza M2 proton channel through Cu(II)-induced paramagnetic relaxation enhancement (PRE). (13)C T(1) relaxation rates of the central residues of the transmembrane (TM) domain of M2 are significantly enhanced by Cu(II), and pronounced spectral broadening is observed for the proton-selective residue, His37. These data yielded quantitative distances of (13)C spins to the Cu(II) center and identified the Cu(II) binding site to be Nε2 of His37. This binding site is surrounded by four imidazole rings from the top and four indole rings of Trp41 from the bottom, thus explaining the high affinity of Cu(II) binding. Bound at this location, Cu(II) can inhibit proton currents by perturbing histidine-water proton exchange, preventing histidine conformational dynamics, and interfering with His-Trp cation-π interaction. The Cu(II) binding site is distinct from the binding site of the hydrophobic drug amantadine, which is about 10 Å N-terminal to His37. Consistently, Cu(II) and amantadine induce distinct conformational changes at several key residues, suggesting the possibility of designing new drugs that target the His37 site to inhibit amantadine-resistant mutant M2 proteins. In addition to the high-affinity His37 binding site, we also examined the weaker and nonspecific binding of Cu(II) to membrane-surface lipid phosphates and the extent of the resulting PRE to surface-proximal protein residues. This study demonstrates the feasibility of NMR studies of paramagnetic-ion-complexed membrane proteins, where the ion serves as both a functional ligand and a distance probe.
Collapse
Affiliation(s)
- Yongchao Su
- Department of Chemistry, Iowa State University, Ames, 50011, United States
| | | | | |
Collapse
|
43
|
Mori K, Mahmood MI, Neya S, Matsuzaki K, Hoshino T. Formation of GM1 ganglioside clusters on the lipid membrane containing sphingomyeline and cholesterol. J Phys Chem B 2012; 116:5111-21. [PMID: 22494278 DOI: 10.1021/jp207881k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
GM1 gangliosides form a microdomain with sphingomyeline (SM) and cholesterol (Chol) and are deeply involved in the aggregation of amyloid beta (Aβ) peptides on neural membranes. We performed molecular dynamics simulations on two kinds of lipid bilayers containing GM1 ganglioside: GM1/SM/Chol and GM1/POPC. Both 10 and 100 ns simulations and another set of 10 ns simulations with different initial lipid arrangement essentially showed the same computational results. GM1 molecules in the GM1/SM/Chol membrane were condensed, whereas those in GM1/POPC membrane scattered. That is, the formation of GM1 cluster was observed only on the GM1/SM/Chol mixed membrane. There appeared numerous hydrogen bonds among glycan portions of the GM1 clusters due to the condensation. A comparison in distribution of lipid molecules between the two kinds of membranes suggested that cholesterol had important roles to prevent the membrane from interdigitation and to stabilize other lipids for interacting with each other. This property of cholesterol promotes the formation of GM1 clusters.
Collapse
Affiliation(s)
- Kenichi Mori
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba, Japan
| | | | | | | | | |
Collapse
|
44
|
Kasson PM. Receptor binding by influenza virus: using computational techniques to extend structural data. Biochemistry 2012; 51:2359-65. [PMID: 22409249 DOI: 10.1021/bi201684v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Influenza attaches to host cells via hemagglutinin binding of cell-surface glycans. These relatively low-affinity interactions involving flexible ligands are critical in determining tissue and host specificity, but their dynamic nature complicates structural characterization of hemagglutinin-receptor complexes. Molecular simulation can assist in analyzing glycan and protein flexibility in crystallized complexes, assessing how binding might change under mutation or altered glycosylation patterns, and evaluating how soluble ligands may relate to physiological presentation on the plasma membrane. Molecular dynamics simulation also has the potential to help integrate structural and dynamic data sources. Here we review recent progress from analysis of molecular dynamics simulation and outline challenges for the future.
Collapse
Affiliation(s)
- Peter M Kasson
- Department of Molecular Physiology and Biological Physics and Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, United States.
| |
Collapse
|
45
|
Yamamoto K, Vivekanandan S, Ramamoorthy A. Fast NMR data acquisition from bicelles containing a membrane-associated peptide at natural-abundance. J Phys Chem B 2011; 115:12448-55. [PMID: 21939237 DOI: 10.1021/jp2076098] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In spite of recent technological advances in NMR spectroscopy, its low sensitivity continues to be a major limitation particularly for the structural studies of membrane proteins. The need for a large quantity of a membrane protein and acquisition of NMR data for a long duration are not desirable. Therefore, there is considerable interest in the development of methods to speed up the NMR data acquisition from model membrane samples. In this study, we demonstrate the feasibility of acquiring two-dimensional spectra of an antimicrobial peptide (MSI-78; also known as pexiganan) embedded in isotropic bicelles using natural-abundance (15)N nuclei. A copper-chelated lipid embedded in bicelles is used to speed-up the spin-lattice relaxation of protons without affecting the spectral resolution and thus enabling fast data acquisition. Our results suggest that even a 2D SOFAST-HMQC spectrum can be obtained four times faster using a very small amount (∼3 mM) of a copper-chelated lipid. These results demonstrate that this approach will be useful in the structural studies of membrane-associated peptides and proteins without the need for isotopic enrichment for solution NMR studies.
Collapse
Affiliation(s)
- Kazutoshi Yamamoto
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | | | | |
Collapse
|
46
|
Optimal mutation sites for PRE data collection and membrane protein structure prediction. Structure 2011; 19:484-95. [PMID: 21481772 DOI: 10.1016/j.str.2011.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 02/11/2011] [Accepted: 02/11/2011] [Indexed: 01/16/2023]
Abstract
Nuclear magnetic resonance paramagnetic relaxation enhancement (PRE) measures long-range distances to isotopically labeled residues, providing useful constraints for protein structure prediction. The method usually requires labor-intensive conjugation of nitroxide labels to multiple locations on the protein, one at a time. Here a computational procedure, based on protein sequence and simple secondary structure models, is presented to facilitate optimal placement of a minimum number of labels needed to determine the correct topology of a helical transmembrane protein. Tests on DsbB (four helices) using just one label lead to correct topology predictions in four of five cases, with the predicted structures <6 Å to the native structure. Benchmark results using simulated PRE data show that we can generally predict the correct topology for five and six to seven helices using two and three labels, respectively, with an average success rate of 76% and structures of similar precision. The results show promise in facilitating experimentally constrained structure prediction of membrane proteins.
Collapse
|
47
|
Roldós V, Cañada FJ, Jiménez-Barbero J. Carbohydrate-Protein Interactions: A 3D View by NMR. Chembiochem 2011; 12:990-1005. [DOI: 10.1002/cbic.201000705] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Indexed: 12/29/2022]
|
48
|
Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations. ACTA ACUST UNITED AC 2011. [DOI: 10.1155/2011/950256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.
Collapse
|
49
|
Gayen A, Goswami SK, Mukhopadhyay C. NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:127-39. [DOI: 10.1016/j.bbamem.2010.09.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 08/24/2010] [Accepted: 09/22/2010] [Indexed: 01/30/2023]
|
50
|
Calle LP, Cañada FJ, Jiménez-Barbero J. Application of NMR methods to the study of the interaction of natural products with biomolecular receptors. Nat Prod Rep 2011; 28:1118-25. [DOI: 10.1039/c0np00071j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|