A salt-bridge structure in solution revealed by 2D-IR spectroscopy

Huerta-Viga, Adriana; Domingos, Sérgio R.; Amirjalayer, Saeed; Woutersen, Sander

doi:10.1039/c4cp00233d

Cited by 15 publications

(23 citation statements)

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“…The salt-bridge structure is also investigated in this spectroscopic region. 37 To our best knowledge, the 2000-2800 frequency region has not been systematically used for identification of salt bridges and ionic interactions in peptides and proteins, e.g., see Refs. 103 and 104.…”

Section: Discussionmentioning

confidence: 99%

“…According to a systematic geometric analysis of the Brookhaven Protein Data Bank, the stereochemistry of the side-chain H-bonds of proteins was pointed out to be characterized by at least three factors: (a) the electronic configuration of the H-bond acceptor atoms, (b) the steric accessibility of the H-bond donor atoms, and (c) the conformation of amino acid side-chains. 27 There have also been a number of theoretical studies aimed at quantifying the strength of interaction of small ions, 9,15,26,[28][29][30][31][32][33][34][35][36][37] mimicking the salt bridges between the CO − 2 side group of glutamate or asparate and the guanidinium side group of the arginine. In particular, the interaction energy in the Arg-Glu salt bridge varies from 35 [45][46][47][48][49] The IR spectrum was evaluated in some papers; 45,49 however, the 2000-2800 frequency region was not considered.…”

Section: Introductionmentioning

confidence: 99%

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The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Vener

Odinokov

Wehmeyer

et al. 2015

The Journal of Chemical Physics

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Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short (+)N-H⋯O(-) bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm(-1). It is caused by the asymmetric stretching vibrations of the (+)N-H⋯O(-) fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Vener

Odinokov

Wehmeyer

et al. 2015

The Journal of Chemical Physics

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“…2D IR spectroscopy has been similarly applied to characterize the ligand exchange and solvation dynamics of a wide variety of ion pairs. 28, 39, 40 …”

Section: Applications Of 2d Ir Spectroscopymentioning

confidence: 99%

Applications of two-dimensional infrared spectroscopy

Sueur

Horness

Thielges

2015

Analyst

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“…30 We found that two degenerate CN 3 D In the calculated spectra, the splitting between the MeGdm + and Ac − bands is larger for the side-on geometry, which indicates that the coupling strength is larger in this configuration than in the end-on geometry. For both geometries, a value for the coupling between the vibrational modes of MeGdm + and Ac − is difficult to estimate directly from the changes in the IR frequencies upon salt-bridge formation.…”

Section: A Isolated Salt Bridgementioning

confidence: 86%

“…30 In the ab initio calculation, the monodentate geometry of Figure 1(c) was not a global energy minimum (∆E > 9 kcal/mol), and therefore it is probably not significantly populated. However, it is worth noting that in this geometry, the high-frequency MeGdm Table S1 in the supplementary material 33 for the atom participation in the normal modes for all geometries).…”

Section: A Isolated Salt Bridgementioning

confidence: 99%

The structure of salt bridges between Arg+ and Glu− in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries

Huerta-Viga

Amirjalayer

Domingos

et al. 2015

The Journal of Chemical Physics

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The structure of salt bridges between Arg+ and Glu-in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries Huerta Viga, A.; Amirjalayer, S.; Rosa Domingos, S.M.; Meuzelaar, H.; Rupenyan, A.B.; Woutersen, S. Published in:Journal of Chemical Physics DOI:10.1063/1.4921064 Link to publication Citation for published version (APA):Huerta-Viga, A., Amirjalayer, S., Domingos, S. R., Meuzelaar, H., Rupenyan, A., & Woutersen, S. (2015). The structure of salt bridges between Arg+ and Glu-in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries. Journal of Chemical Physics, 142(21). DOI: 10.1063/1.4921064 General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Download date: 12 May 2018THE JOURNAL OF CHEMICAL PHYSICS 142, 212444 (2015) The structure of salt bridges between Arg Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu − ) and arginine (Arg + ) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu − and Arg + , which provide a sensitive structural probe of Glu − · · · Arg + salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra-and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License. [http://dx

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A salt-bridge structure in solution revealed by 2D-IR spectroscopy

Abstract: We determine the spatial structure of a guanidinium:acetate salt bridge in solution from cross peaks in its 2D-IR spectrum.

Cited by 15 publications

References 16 publications

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Applications of two-dimensional infrared spectroscopy

The structure of salt bridges between Arg+ and Glu− in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries

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