Multiple Conformational States Contribute to the 3D Structure of a

Article pubs.acs.org/JPCB

Cite This: J. Phys. Chem. B 2018, 122, 1169−1175

Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study Sunhwan Jo,† Daniel Myatt,‡ Yifei Qi,§ James Doutch,‡ Luke A. Clifton,‡ Wonpil Im,∥ and Göran Widmalm*,⊥ †

Leadership Computing Facility, Argonne National Laboratory, 9700 Cass Avenue, Argonne 60439, Illinois, United States ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Oxfordshire OX11 OQX, U.K. § College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China ∥ Department of Biological Sciences and Bioengineering, Lehigh University, Bethlehem 18015, Pennsylvania, United States ⊥ Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden ‡

S Supporting Information *

ABSTRACT: The inherent flexibility of carbohydrates is dependent on stereochemical arrangements, and characterization of their influence and importance will give insight into the three-dimensional structure and dynamics. In this study, a β-(1→4)/β-(1→3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (Rg) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated Rg values from the MD simulation reveal that in addition to syn-conformers the presence of anti-ψ conformational states is required to reproduce experimental scattering data, unveiling inherent glycosidic linkage flexibility. The CHARMM36 force field for carbohydrates thus describes the conformational flexibility of the decasaccharide very well and captures the conceptual importance that anti-conformers are to be anticipated at glycosidic linkages of carbohydrates.

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INTRODUCTION Carbohydrates are found as structural components in the plant kingdom in the form of cellulose and hemicellulose;1 whereas the former is made of β-(1→4)-linked glucosyl residues, the latter can include several different monosaccharides.2 In contrast, as a source of stored energy, the glucosyl residues are α-linked in its two constituent polysaccharides amylose and amylopectin. The glycans in mammals and invertebrates form highly complex glycoconjugates from a limited number of different sugar residues, whereas in bacteria, the number of various sugars is 2 orders of magnitude larger, facilitating an immense structural variety.3 The combinatorial nature of these structures thus poses an intricate problem, and if the threedimensional structure is added to the permutation aspects of glycans, the challenges become even more formidable. The properties of carbohydrates are governed by their primary structure, shape, charge, flexibility, and dynamics, which can be determined by various biophysical methods. For glycans in solution, NMR spectroscopy is of utmost importance,4 but other techniques such as size exclusion chromatography with multiangle laser light scattering and viscometry,5 circular dichroism spectroscopy,6 and Raman optical activity and infrared spectroscopy7 contribute to the © 2017 American Chemical Society

characterization of their structures and properties. Small-angle scattering utilizing X-rays (SAXS) or neutrons8 in combination with techniques such as analytical ultracentrifugation,9 dynamic light scattering, or size exclusion chromatography10 have been used to elucidate the size and shape of proteins; application of all-atom modeling in combination with SAXS data of glycoproteins facilitates generation of models that are in excellent agreement with scattering data and consequently the spatial distribution of glycan chains can be deduced for this class of glycoconjugates.11 The major degrees of freedom of oligo- or polysaccharides giving rise to their flexibility and dynamics over time are torsion angles ϕ and ψ at the glycosidic linkage.12 The flexibility of the ω torsion angle for hydroxymethyl groups in hexopyranoses such as glucose or similar exocyclic torsions in higher-carbon sugars such as sialic acid with (2→8)- and (2→9)-linkages is also of importance,13 together with inherent ring-flexibility in the monosaccharide per se, e.g., α-L-iduronic acids present in heparin or xylose and their derivatives.14,15 The ϕ torsion angle Received: November 9, 2017 Revised: December 18, 2017 Published: December 22, 2017 1169

DOI: 10.1021/acs.jpcb.7b11085 J. Phys. Chem. B 2018, 122, 1169−1175

Article

The Journal of Physical Chemistry B

Figure 1. Schematic of decasaccharide 1 with glycosidic torsion angles annotated.

examined for the presence of radiation-induced sample damage, where it was found that the frames were not reduced and further processed. The detector was at 3.9 m from the sample position, yielding a Q-range of 0.012 Å−1 < 0.4 Å−1. Q = 4π sin θ/λ, where 2θ is the scattering angle and λ is the wavelength, which in this case was 1 Å. Two-dimensional data reduction consisted of normalization for beam current and sample transmission, radial sector integration, and background buffer subtraction and averaging. Further data analyses, such as scaling, merging, and Guinier analysis, were performed in PRIMUS.26 Molecular Dynamics Simulations. We have used the Glycan Fragment Database (GFDB; http://www. glycanstructure.org/fragment-db)27 to model the glycan conformation for MD simulation. Employing the GFDB, PDB entries that contain the sequences of β-D-Glcp-(1→3)β-D-Glcp and β-D-Glcp-(1→4)-β-D-Glcp and whose resolution is less than 3 Å were searched. The filtering options provided by the GFDB were used to remove distorted residues and redundant entries. The major glycosidic linkage torsion angle populations were selected, and the initial model was generated using the IC EDIT facility in CHARMM simulation software.28 Glycan Reader29 and Quick MD Simulator in CHARMMGUI30 were used to build a solvated MD simulation system. The system size was determined so that the resulting systems have a water layer of at least 12.5 Å in x, y, and z directions. The solvated simulation systems were minimized while the positional harmonic restraints were applied to the nonhydrogen atoms of the decasaccharide using CHARMM simulation software,28 followed by a 4 ns equilibration simulation at 288 K using the NPT (constant particle number, pressure, and temperature) ensemble and NAMD simulation software.31,32 All simulations were performed using the recently updated CHARMM36 carbohydrate force field33,34 and TIP3P water model.35 The van der Waals interactions were smoothly switched off between 10 and 12 Å by a force-based switching function.36 Long-range electrostatic interactions were calculated using the particle-mesh Ewald (PME) method. 37 An interpolation order of 6 and a direct space tolerance of 10−6 were used for the PME method. A time step of 2 fs was used with the SHAKE algorithm.38 For the NAMD simulations, Langevin dynamics was used to maintain constant temperatures for each system, whereas the Nosé−Hoover Langevin-piston algorithm39,40 was used to maintain constant pressure at 1 bar. The equilibrated simulation system was used as an initial configuration for a replica-exchange simulation (REMD). A variant of REMD, namely, replica-exchange solute tempering (REST2),41,42 was used to accelerate the sampling of glycosidic linkage conformations. In the REST2 algorithm, the simulation system is decomposed into solute and solvent components, and the solute−solute and solute−solvent interaction energies are scaled, which mimics the effect of increasing temperature of the solute. A recently implemented REST2 module for the NAMD simulation package was used.43 A total of 16 replicas were used to cover the effective temperature range from 288 to 650 K, and the simulations were performed for 60 ns at 1.01325 bar using the NPT ensemble.

mainly populates the exo-anomeric conformation, but non-exoanomeric conformations may be present to some extent. The ψ torsion angle is populating conformational states close to ψH ≈ 0°, where ψH is defined by C1′−Ox−Cx−Hx and x refers to the linkage position, leading to syn-conformations, but anti-ψ conformations (ψH ≈ 180°) can also be populated. For the ω torsion angle O5−C5−C6−O6, conformational states referred to as gauche-trans, gauche-gauche and trans-gauche with respect to O5 and C4, respectively, may be populated, the specific one favored being dependent on the monosaccharide, i.e., whether it has the gluco- or galacto-configuration.16 To a large extent, NMR spectroscopy has been utilized to obtain this kind of conformational information in conjunction with molecular modeling and molecular dynamics (MD) simulations. The extent to which anti-conformers17,18 are present in solution has been discussed on the basis of NMR spectroscopy measurements.19,20 We have previously studied decasaccharide β-D-Glcp-(1→4)-β-D-Glcp-(1→3)-β-D-Glcp(1→4)-β-D-Glcp-(1→3)-β-D-Glcp-(1→4)-β-D-Glcp-(1→3)-βD -Glcp-(1→4)-β- D -Glcp-(1→3)-β- D -Glcp-(1→4)-β- D -GlcpOMe (1) (Figure 1) by NMR residual dipolar couplings and one-dimensional 1H,1H NOESY experiments in conjunction with molecular modeling21 with focus on the conformational preference(s) of the central β-(1→4)-linkage using a highly deuterated isotopologue of the decasaccharide.22 It was shown that the major conformational state at this linkage can be described by a syn-conformation with the ϕ torsion in the exoanomeric conformation. In this study, we obtain information on glycosidic linkage flexibility by acquiring SAXS data of 1 and analyze and interpret the experimental results aided by MD simulations.

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MATERIALS AND METHODS

General Considerations. The synthesis of decasaccharide β-D-Glcp-(1→4)-β-D-Glcp-(1→3)-β-D-Glcp-(1→4)-β-D-Glcp(1→3)-β-D-Glcp-(1→4)-β-D-Glcp-(1→3)-β-D-Glcp-(1→4)-βD-Glcp-(1→3)-β-D-Glcp-(1→4)-β-D-Glcp-OMe was reported previously.22 For the SAXS experiments, the d67-deuterated isotopologue was used. The glycosidic torsion angles are defined as follows: ϕ = H1(n) − C1(n) − Ox(n + 1) − Cx(n + 1) and ψ = C1(n) − Ox(n + 1) − Cx(n + 1) − Hx(n + 1), where x is the linkage position and n denotes the glucosyl residue in the decasaccharide, numbered from the terminal nonreducing end. Small-Angle X-ray Scattering Experiments. SAXS data sets from the saccharide sample were obtained at the B21 beamline at the Diamond Light Source (Harwell, U.K.).23−25 The decasaccharide sample and buffer solution were exposed to the beam in a 1.6 mm diameter quartz capillary, which was loaded using an Arinax (Grenoble, France) BioSAXS automated sample changer robot. The exposure unit temperature was set to 15 °C. The sample capillary was held in vacuum and cleaned between each measurement. Samples were stored in 96-well plates at 5 °C. SAXS data was collected on a Pilatus 2 M two-dimensional detector. A total of 180 frame exposures of 1 s from the sample and the corresponding buffer were summed to produce each data set. Each frame was 1170


Article

The Journal of Physical Chemistry B Coarse-Graining of Conformational States Using Glycosidic Torsion Angles. The torsion angle distribution from the target temperature replica (288 K) in the REST2 simulation was used to identify a set of conformational basins, as described by Jo et al.44 The decasaccharide conformation can be described with a 9-letter notation (states A−D), starting from residue 1 (terminal end) in Figure 1. For example, “AAAAAAAAA” indicates that all glycosidic (ϕ, ψ) torsion angles adopt a conformation corresponding to the largest basin. SAXS Profile from the Simulation Trajectory. The representative structures for each coarse-grained conformational state were generated by assigning the corresponding central glycosidic (ϕ, ψ) torsion angles using the IC EDIT facility in the CHARMM software package.28 The SAXS profile was then computed for each representative structure using the CRYSOL program45 with the explicit hydrogen and constant subtraction options. The experimental SAXS curve was then fitted against the theoretical computation. In addition, the REMD simulation trajectory snapshot from the simulation was saved for every 10 ps and subjected to the CRYSOL program for computing the SAXS profile, after deleting all other molecules except the decasaccharide molecule.

Figure 2. Experimental SAXS data and a fit using the “AAAAAACAA” conformation of 1 resulting in an Rg = 13.1 Å.

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RESULTS AND DISCUSSION The canonical conformation of D-glucose-containing decasaccharide 1 (Figure 1) is a highly extended rodlike structure due to the exo (ϕ) and syn (ψ) conformations46 at the glycosidic linkages. The alternating (1→4)- and (1→3)-linkages of the 10 sugar residues result in highly degenerate NMR chemical shifts beyond the disaccharide level, and to study the conformational preference of the central β-(1→4)-linkage, a highly deuterated analogue was used.22 1H,1H NOESY and 1H,13C-RDC NMR experiments revealed that the exo−syn conformation with ϕ ≈ 30° and ψ ≈ 10° prevailed at this linkage,21 which is referred to as linkage number 5 in this study. However, the negative sign of the trans-glycosidic dipolar coupling between H1 in residue 5 and H4 in residue 6 confirmed that this interaction was close to parallel to the principal axis of the decasaccharide, although it did not disclose any detailed information about the overall shape of the molecule. To obtain further information on conformational preferences, we therefore employed an experimental technique that is rarely used in the study of oligosaccharide structure, viz., SAXS, although it was used to study an amylose fragment (maltoheptaose)47 and the solution structure of heparin oligosaccharide conformation in conjunction with ultracentrifugation and constrained molecular modeling.48 Acquiring SAXS data on the decasaccharide as a function of scattering angle facilitates the scattering intensity I(Q) to be analyzed as a function of scattering vector Q, as shown in Figure 2. The interpretation of the experimental SAXS results calls for a molecular description, and to this end, we carried out an REMD simulation of decasaccharide 1 with explicit water as the solvent. Similar conformational states can be identified for both the (1→4)- and (1→3)-linkages (Figure 3), viz., the exo−syn conformation (A), non-exo (B), anti-ψ (C), and anti-ϕ (D) regions. Conformational state A is the major one for both types of glycosidic linkages but is more prominent for the β-(1→3)linkage than for the β-(1→4)-linkage (Table 1). Conformational region B is also populated to a significant extent, although for this conformational state, it is the β-(1→4)-linkage that is present to a larger degree compared to the β-(1→3)linkage. Anti-ψ state C is populated to a larger extent than anti-

Figure 3. Probability density plots of the β-(1→4)-linkages (a) and the β-(1→3)-linkages (b) from MD simulation of decasaccharide 1 where the blue color indicates high probability and the white color corresponds to low probability. Conformational states are labeled A− D.

ϕ state D for both of the glycosidic linkages. Thus, for the conformational regions, the populations are present as A > B > C > D (Table 1). The glycosidic torsion angles and their fluctuations are compiled in Table 2, and information on each glycosidic linkage 1171


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The Journal of Physical Chemistry B Table 1. Conformational State Populations (%) of Decasaccharide 1 P (χ2 < 0.007)

Pall state

β-(1→4)

β-(1→3)

combined

β-(1→4)

β-(1→3)

combined

A B C D

69.6 26.0 4.1 0.2

86.9 11.6 1.3 0.1

77.3 19.6 2.9 0.2

69.9 23.6 6.4 0.1

90.7 7.1 2.0 0.2

79.1 16.3 4.5 0.1

is given in Tables S1 and S2. In general, the fluctuations are slightly larger for the ψ torsions than for the ϕ torsions and the largest fluctuations are observed in region C for the anti-ψ states; the latter is contrasted by the fluctuations in anti-ϕ state D for which the torsional flexibility of ψ < ϕ. At this point, we compare MD simulations with the experimentally derived distance H1[5],H4[6], which is 2.2 ± 0.1 Å,21 consistent with high population of conformational states A and B, being 2.28 and 2.19 Å, respectively (Table 2). How well does the conformational distribution of states from MD simulation (Table 1) agree with that obtained from experimental SAXS data? The small-angle scattering profiles were theoretically calculated for each frame of the MD simulation, together with the radius of gyration (Rg) of the decasaccharide structures. From MD simulation, conformational states A−D at each of the nine glycosidic linkages between sugar residues were monitored, binned, and ranked according to population (Table S3, covering >95%). The highest-populated state was “all-A” present to 9.3%. A range of states containing a mixture of A and B in the interval 3.6−1.2% was then presented before a conformational state having an anti-ψ torsion was observed, viz., “AAAAAAACAA” to 1.1%. Analyzing the goodness of fit, χ2, versus radius of gyration, Rg, for conformations of the decasaccharide from the MD simulation shows Rg ≈ 13 Å for populations (P) having χ2 < 0.007 (Figure 4). Notably, at this level of fit, essentially all conformations have at least one of their glycosidic linkages in an anti-ψ state and the C state is increased compared to that from the MD simulation per se (Table 1). The top five conformations of the decasaccharide from the MD simulation having a C state as part of the sequence and P (χ2 < 0.007) are shown in Figure 5 (cf. also Table S3). Thus, employing SAXS data in the analysis of oligosaccharide conformation shows that anti-ψ conformational states are present and as such the flexibility aspects should be considered when addressing the three-dimensional structure of carbohydrates. Mixed-linkage (1→3),(1→4)-β- D -glucans (MLG) are present as cell wall polysaccharides in cereals,49 grasses,50 ferns,51 and lichens (mosses),52 where the ratio of (1→4)/(1→ 3)-linked residues is >1, typically on the order of 2−4 but in some cases significantly higher. The polysaccharide structure is

Figure 4. Goodness of fit, χ2, vs radius of gyration, Rg, (Å) for conformations of 1 from MD simulation where the blue color indicates high probability and the white color corresponds to low probability.

consequently a mixture of cellulose and curdlan with shared physical and physiological properties.53 Interestingly, bacterium Sinorhizobium meliloti produces under regulation of the secondary messenger cyclic diguanolate an MLG that markedly enhances the attachment to the host plant root as well as formation of dense biofilms on the surface of roots.54 The MLG produced consists of a disaccharide repeating unit with alternating linkages, viz., →4)-β-D-Glcp-(1→3)-β-D-Glcp-(1→, i.e., the same repeat as in the decasaccharide studied herein. The conformational preferences deduced for decasaccharide 1 thus have implications on polysaccharide structures from the plant kingdom and when they are produced by bacteria.

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CONCLUSIONS The conformational analysis of oligosaccharides in solution to a large extent relies on acquiring experimental NMR data that subsequently may be interpreted using molecular modeling techniques. The information that can be gained across the glycosidic linkage to assess the conformational aspects is in many cases short-ranged, which leads to difficulties when addressing larger oligosaccharides; the use of NMR residual dipolar couplings is an exception. MD simulations are powerful in obtaining models in which dynamics is also considered in the analysis, yielding information on the presence of anticonformational states. 55 It is encouraging that the CHARMM36 force field for carbohydrates utilized herein describes results from 1H, 1H NOE data very well and that the populations of the structures sampled in the MD simulation per se are close to those obtained when SAXS data was used in obtaining information on the overall structure of the

Table 2. Conformational-State-Dependent Glycosidic Torsion Angles (deg) and Effective Interproton Distance (Å) of Decasaccharide 1a β-(1→4) ϕ

state A B C D a

50.6 32.1 56.4 167.8

(10.4) (12.2) (14.5) (11.5)

β-(1→3) ψ −2.2 −34.6 −163.5 2.8

ϕ (11.6) (13.1) (16.8) (7.9)

51.6 32.4 48.4 169.4

(12.2) (12.8) (15.7) (13.7)

reff ψ 9.8 −27.8 −178.4 9.6

H1[5],H4[6] (14.2) (14.5) (19.8) (11.4)

2.280 2.193 3.583 3.575

(0.003) (0.006) (0.005) (0.017)

The standard deviation in each state is given in parentheses. 1172


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Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC0206CH11357.

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(1) Chen, H. Chemical Composition and Structure of Natural Lignocellulose. In Biotechnology of Lignocellulose: Theory and Practice; Springer Science+Business Media: Dordrecht, 2014; pp 25−71. (2) Berglund, J.; Angles d’Ortoli, T.; Vilaplana, F.; Widmalm, G.; Bergenstråhle-Wohlert, M.; Lawoko, M.; Henriksson, G.; Lindström, M.; Wohlert, J. A Molecular Dynamics Study of the Effect of Glycosidic Linkage Type in the Hemicellulose Backbone on the Molecular Chain Flexibility. Plant J. 2016, 88, 56−70. (3) Adibekian, A.; Stallforth, P.; Hecht, M.-L.; Werz, D. B.; Gagneux, P.; Seeberger, P. H. Comparative Bioinformatics Analysis of the Mammalian and Bacterial Glycomes. Chem. Sci. 2011, 2, 337−344. (4) NMR in Glycoscience and Glycotechnology; Kato, K., Peters, T., Eds.; Royal Society of Chemistry: Cambridge, 2017. (5) Dalheim, M.; Arnfinnsdottir, N. B.; Widmalm, G.; Christensen, B. E. The Size and Shape of Three Water-Soluble, Non-Ionic Polysaccharides Produced by Lactic Acid Bacteria: A Comparative Study. Carbohydr. Polym. 2016, 142, 91−97. (6) Andersson, M.; Kenne, L.; Stenutz, R.; Widmalm, G. Synthesis Of, and NMR and CD Studies On, Methyl 4-O-[(R)- and (S)-1Carboxyethyl]-α-L-Rhamnopyranoside and Methyl 6-O-[(R)- and (S)-1-Carboxyethyl]-α-D-Galactopyranoside. Carbohydr. Res. 1994, 254, 35−41. (7) Wiercigroch, E.; Szafraniec, E.; Czamara, K.; Pacia, M. Z.; Majzner, K.; Kochan, K.; Kaczor, A.; Baranska, M.; Malek, K. Raman and Infrared Spectroscopy of Carbohydrates: A Review. Spectrochim. Acta, Part A 2017, 185, 317−335. (8) Trewhella, J. Small-Angle Scattering and 3D Structure Interpretation. Curr. Opin. Struct. Biol. 2016, 40, 1−7. (9) Perkins, S. J.; Nan, R.; Li, K.; Khan, S.; Abe, Y. Analytical Ultracentrifugation Combined with X-Ray and Neutron Scattering: Experiment and Modelling. Methods 2011, 54, 181−199. (10) Clifton, L. A.; Sanders, M. R.; Castelletto, V.; Rogers, S. E.; Heenan, R. K.; Neylon, C.; Frazier, R. A.; Green, R. J. Puroindoline-A, a Lipid Binding Protein from Common Wheat, Spontaneously Forms Prolate Protein Micelles in Solution. Phys. Chem. Chem. Phys. 2011, 13, 8881−8888. (11) Guttman, M.; Weinkam, P.; Sali, A.; Lee, K. K. All-Atom Ensemble Modeling to Analyze Small-Angle X-Ray Scattering of Glycosylated Proteins. Structure 2013, 21, 321−331. (12) Widmalm, G. A Perspective on the Primary and ThreeDimensional Structures of Carbohydrates. Carbohydr. Res. 2013, 378, 123−132. (13) Yongye, A. B.; Gonzalez-Outeiriño, J.; Glushka, J.; Schultheis, V.; Woods, R. J. The Conformational Properties of Methyl α-(2,8)-Di/ trisialosides and Their N-Acyl Analogues: Implications for AntiNeisseria meningitidis B Vaccine Design. Biochemistry 2008, 47, 12493− 12514. (14) Ochsenbein, P.; Bonin, M.; Schenk-Joß, K.; El-Hajji, M. The 2SO Skew-Boat Conformation in L-Iduronic Acid. Angew. Chem., Int. Ed. 2011, 50, 11637−11639. (15) Thorsheim, K.; Siegbahn, A.; Johnsson, R. E.; Stålbrand, H.; Manner, S.; Widmalm, G.; Ellervik, U. Chemistry of Xylopyranosides. Carbohydr. Res. 2015, 418, 65−88. (16) Soltesova, M.; Kowalewski, J.; Widmalm, G. Dynamics of Exocyclic Groups in the Escherichia coli O91 O-Antigen Polysaccharide in Solution Studied by Carbon-13 NMR Relaxation. J. Biomol. NMR 2013, 57, 37−45. (17) Dabrowski, J.; Grosskurth, H.; Kožaŕ , T.; Nifant’ev, N. E. Conformational Mobility of Oligosaccharides: Experimental Evidence for the Existence of an “Anti” Conformer of the Galβl-3Glcβ1-OMe Disaccharide. J. Am. Chem. Soc. 1995, 117, 5534−5539. (18) Landersjö, C.; Stenutz, R.; Widmalm, G. Conformational Flexibility of Carbohydrates: A Folded Conformer at the φ Dihedral

Figure 5. Five molecular models of decasaccharide 1 consistent with χ2 < 0.007 for which R g is spanning 13.0−13.1 Å, namely, “AAAAAACAA”, “AAAACAAAA”, “AABAAACAA”, “AAAAAAAAC”, and “AAAACABAA”, from top to bottom.

decasaccharide. Most importantly, to account for the SAXS data well, the presence of anti-ψ conformational states is essential, confirming by an “orthogonal” biophysical technique to what has been used previously the importance of these states and that oligosaccharides, as well as polysaccharides,56,57 should be described as dynamic molecules with inherent high flexibility.

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ASSOCIATED CONTENT

* Supporting Information S

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcb.7b11085. Tables of glycosidic torsion angles’ averages and of populated states (PDF)

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REFERENCES

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. ORCID

Göran Widmalm: 0000-0001-8303-4481 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work was supported by grants from the Swedish Research Council 2013-4859 (G.W.), NSF DBI-1707207, XSEDE MCB070009 (W.I.) and used resources of the Argonne 1173


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The Journal of Physical Chemistry B Angle of a Glycosidic Linkage. J. Am. Chem. Soc. 1997, 119, 8695− 8698. (19) Larsson, E. A.; Staaf, M.; Soderman, P.; Höög, C.; Widmalm, G. Determination of the Conformational Flexibility of Methyl αCellobioside in Solution by NMR Spectroscopy and Molecular Simulations. J. Phys. Chem. A 2004, 108, 3932−3937. (20) Martín-Pastor, M.; Canales, A.; Corzana, F.; Asensio, J. L.; Jiménez-Barbero, J. Limited Flexibility of Lactose Detected from Residual Dipolar Couplings Using Molecular Dynamics Simulations and Steric Alignment Methods. J. Am. Chem. Soc. 2005, 127, 3589− 3595. (21) Lycknert, K.; Maliniak, A.; Widmalm, G. Analysis of Oligosaccharide Conformation by NMR Spectroscopy Utilizing 1H,1H and 1H,13C Residual Dipolar Couplings in a Dilute Liquid Crystalline Phase. J. Phys. Chem. A 2001, 105, 5119−5122. (22) Hällgren, C.; Widmalm, G. Synthesis of a Site-Specific Deuterium Substituted Methyl β-D-Glucan Decasaccharide. J. Carbohydr. Chem. 1993, 12, 309−333. (23) Inoue, K.; Doutch, J.; Terrill, N. The Current Status of SmallAngle X-Ray Scattering Beamline at Diamond Light Source. Bunseki Kagaku 2013, 62, 565−570. (24) Hamley, I. W.; Dehsorkhi, A.; Castelletto, V.; Walter, M. N. M.; Connon, C. J.; Reza, M.; Ruokolainen, J. Self-Assembly and CollagenStimulating Activity of a Peptide Amphiphile Incorporating a Peptide Sequence from Lumican. Langmuir 2015, 31, 4490−4495. (25) Sharma, U.; Carrique, L.; Vadon-Le Goff, S.; Mariano, N.; Georges, R. N.; Delolme, F.; Koivunen, P.; Myllyharju, J.; Moali, C.; Aghajari, N.; et al. Structural Basis of Homo- and Heterotrimerization of Collagen I. Nat. Commun. 2017, 8, No. 14671. (26) Konarev, P. V.; Volkov, V. V.; Sokolova, A. V.; Koch, M. H. J.; Svergun, D. I. PRIMUS: A Windows PC-Based System for SmallAngle Scattering Data Analysis. J. Appl. Crystallogr. 2003, 36, 1277− 1282. (27) Jo, S.; Im, W. Glycan Fragment Database: A Database of PDBBased Glycan 3D Structures. Nucleic Acids Res. 2013, 41, D470−D474. (28) Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; et al. CHARMM. J. Comput. Chem. 2009, 30, 1545−1614. (29) Jo, S.; Song, K. C.; Desaire, H.; MacKerell, A. D., Jr.; Im, W. Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins. J. Comput. Chem. 2011, 32, 3135−3141. (30) Jo, S.; Kim, T.; Iyer, V. G.; Im, W. CHARMM-GUI: A WebBased Graphical User Interface for CHARMM. J. Comput. Chem. 2008, 29, 1859−1865. (31) Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD. J. Comput. Chem. 2005, 26, 1781− 1802. (32) Lee, J.; Cheng, X.; Swails, J. M.; Yeom, M. S.; Eastman, P. K.; Lemkul, J. A.; Wei, S.; Buckner, J.; Jeong, J. C.; Qi, Y.; et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J. Chem. Theory Comput. 2016, 12, 405−413. (33) Guvench, O.; Hatcher, E. R.; Venable, R. M.; Pastor, R. W.; Mackerell, A. D., Jr. CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J. Chem. Theory Comput. 2009, 5, 2353−2370. (34) Patel, D. S.; Pendrill, R.; Mallajosyula, S. S.; Widmalm, G.; Mackerell, A. D., Jr. Conformational Properties of α- or β-(1→6)Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments. J. Phys. Chem. B 2014, 118, 2851−2871. (35) Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926−935.

(36) Steinbach, P. J.; Brooks, B. R. New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation. J. Comput. Chem. 1994, 15, 667−683. (37) Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089−10092. (38) Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23, 327−341. (39) Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method. J. Chem. Phys. 1995, 103, 4613−4621. (40) Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms. J. Chem. Phys. 1994, 101, 4177− 4189. (41) Huang, X.; Hagen, M.; Kim, B.; Friesner, R. A.; Zhou, R.; Berne, B. J. Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems. J. Phys. Chem. B 2007, 111, 5405−5410. (42) Wang, L.; Friesner, R. A.; Berne, B. J. Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2). J. Phys. Chem. B 2011, 115, 9431−9438. (43) Jo, S.; Jiang, W. A Generic Implementation of Replica Exchange with Solute Tempering (REST2) Algorithm in NAMD for Complex Biophysical Simulations. Comput. Phys. Commun. 2015, 197, 304−311. (44) Jo, S.; Qi, Y.; Im, W. Preferred Conformations of N-Glycan Core Pentasaccharide in Solution and in Glycoproteins. Glycobiology 2016, 26, 19−29. (45) Svergun, D.; Barberato, C.; Koch, M. H. CRYSOL - A Program to Evaluate X-Ray Solution Scattering of Biological Macromolecules from Atomic Coordinates. J. Appl. Crystallogr. 1995, 28, 768−773. (46) Yang, M.; Angles d’Ortoli, T.; Säwén, E.; Jana, M.; Widmalm, G.; MacKerell, A. D., Jr. Delineating the Conformational Flexibility of Trisaccharides from NMR Spectroscopy Experiments and Computer Simulations. Phys. Chem. Chem. Phys. 2016, 18, 18776−18794. (47) Shimada, J.; Kaneko, H.; Takada, T.; Kitamura, S.; Kajiwara, K. Conformation of Amylose in Aqueous Solution: Small-Angle X-Ray Scattering Measurements and Simulations. J. Phys. Chem. B 2000, 104, 2136−2147. (48) Khan, S.; Gor, J.; Mulloy, B.; Perkins, S. J. Semi-Rigid Solution Structures of Heparin by Constrained X-Ray Scattering Modelling: New Insight into Heparin-Protein Complexes. J. Mol. Biol. 2010, 395, 504−521. (49) Carpita, N. C. Structure and Biogenesis of the Cell Walls of Grasses. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1996, 47, 445−476. (50) Vogel, J. Unique Aspects of the Grass Cell Wall. Curr. Opin. Plant Biol. 2008, 11, 301−307. (51) Xue, X.; Fry, S. C. Evolution of Mixed-Linkage (1→3, 1→4)-βD-Glucan (MLG) and Xyloglucan in Equisetum (Horsetails) and Other Monilophytes. Ann. Bot. 2012, 109, 873−886. (52) Simmons, T. J.; Uhrín, D.; Gregson, T.; Murray, L.; Sadler, I. H.; Fry, S. C. An Unexpectedly Lichenase-Stable Hexasaccharide from Cereal, Horsetail and Lichen Mixed-Linkage β-Glucans (MLGs): Implications for MLG Subunit Distribution. Phytochemistry 2013, 95, 322−332. (53) Lazaridou, A.; Biliaderis, C. G.; Micha-Screttas, M.; Steele, B. R. A Comparative Study on Structure-Function Relations of MixedLinkage (1→3), (1→4) Linear β-D-Glucans. Food Hydrocolloids 2004, 18, 837−855. (54) Pérez-Mendoza, D.; Á ngel Rodríguez-Carvajal, M.; RomeroJiménez, L.; de Araujo Farias, G.; Lloret, J.; Trinidad Gallegos, M.; Sanjuán, J. Novel Mixed-Linkage β-Glucan Activated by c-Di-GMP in Sinorhizobium meliloti. Proc. Natl. Acad. Sci. U.S.A. 2015, 112, E757− E765. (55) Höög, C.; Landersjö, C.; Widmalm, G. Oligosaccharides Display Both Rigidity and High Flexibility in Water as Determined by 13C NMR Relaxation and 1H,1H NOE Spectroscopy: Evidence of Anti-φ and Anti-ψ Torsions in the Same Glycosidic Linkage. Chem. − Eur. J. 2001, 7, 3069−3077. 1174


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