- Open Access
Stabilization of zwitterionic versus canonical proline by water molecules
© Yang et al. 2016
- Received: 2 November 2015
- Accepted: 28 December 2015
- Published: 6 January 2016
At physiological conditions, a majority of biomolecules (e.g., amino acids, peptides and proteins) exist predominantly in the zwitterionic form that usually decides the biological functions. However, zwitterionic amino acids are not geometrically stable in gas phase and this seriously hampers the understanding of their structures, properties and biological functions. To this end, one of the recent research focuses is to demonstrate the stabilization effects of zwitterionic amino acids. Relative stabilities of canonical conformers are dependent on water contents, while zwitterionic stability improves monotonously and pronouncedly with increase of water contents. We find that one water molecule can render zwitterionic proline geometrically stable, and stabilities of different zwitterionic amino acids increase as glycine <proline <arginine. In addition, we have determined the numbers of water molecules required for zwitterionic proline to be energetically preferential and conformationally predominant, respectively as four and five. Five water molecules are enough to fill up the first shell of proline functional sites (carboxylic and amido), which is in line with the results of glycine. At any water content, zwitterionic formation will not be hindered kinetically because of rather low activation barriers, and the distribution of zwitterionic amino acids will be largely dependent on their thermodynamic stabilities.
In aqueous solutions, a wide range of biomolecules (e.g., amino acids, peptides and proteins) exist predominantly in the zwitterionic form, and water molecules are essential to maintain their native conformations and physiological functions (Timasheff 1970; Rand 2004). Interaction of biomolecules and water has attracted general interest (Teeter 1991; Levy and Onuchic 2004; Corradini et al. 2013), and amino acids, the structural unit of proteins, are generally the protypes for ab initio and density functional investigation of peptides and proteins (Császár 1992; Hu et al. 1995; Yu et al. 1995; Zhang and Chung-Phillips 1998; Remko and Rode 2001; Hoyau and Ohanessian 1998; Ai et al. 2003; Constantino et al. 2005; Remko and Rode 2006).
On the other hand, amino acids in gas phase consist entirely of canonical conformers (Császár 1992; Hu et al. 1995; Yu et al. 1995), which is totally different from the condition in aqueous solutions. This is obviously an obstacle for us to comprehend the electronic properties and biological functions of zwitterionic structures. Zwitterions can generate strong electric fields around that usually decide the biological functions of biomolecules. Owing to the particular importance, one of the recent research focuses is to demonstrate the stabilization effects of zwitterionic amino acids (Yu et al. 1995; Zhang and Chung-Phillips 1998; Remko and Rode 2001; Hoyau and Ohanessian 1998; Ai et al. 2003; Constantino et al. 2005; Remko and Rode 2006; Corral et al. 2006; Yang et al. 2009; Jensen and Gordon 1995; Snoek et al. 2002; Yamabe et al. 2003; Balta and Aviyente 2004; Im et al. 2008; Gutowski et al. 2000; Rimola et al. 2008; Wu and McMahon 2007; Rimola et al. 2013; Kass 2005; Yang et al. 2008; Tian et al. 2009; Hwang et al. 2011; Li et al. 2011; Kim et al. 2014; Yang and Zhou 2014), and a variety of attempts have been made in this aspect, such as protonation and deprotonation (Yu et al. 1995; Zhang and Chung-Phillips 1998), metalation (Hoyau and Ohanessian 1998; Ai et al. 2003; Constantino et al. 2005; Remko and Rode 2006; Corral et al. 2006; Yang et al. 2009), hydration (Jensen and Gordon 1995; Snoek et al. 2002; Yamabe et al. 2003; Balta and Aviyente 2004; Im et al. 2008; Hwang et al. 2011; Li et al. 2011; Kim et al. 2014) and anion attachment (Kass 2005; Yang et al. 2008; Tian et al. 2009). A minimum of two water molecules is required to stabilize glycine in the zwitterionic form (Jensen and Gordon 1995), while one is enough to cause zwitterionic arginine as the lowest-energy conformer (Im et al. 2008). Interaction of proline and water has been investigated by different groups (Li et al. 2011; Kim et al. 2014), and two water molecules were considered necessary for rendering zwitterionic proline to be geometrically stable.
In this work, density functional calculations were employed to comprehend the gas-phase interaction of different proline conformers and water with a wide range of contents (n = 0–5). Five water molecules were found enough to fill up the first shell of proline functional sites (carboxylic and amido), as in the case of glycine (Kokpol et al. 1988). We determined that one water molecule can stabilize proline in zwitterionic form; meanwhile, stabilities of zwitterionic glycine, proline and arginine were compared with each other. Then, the numbers of water molecules necessary to render zwitterionic proline energetically preferential and conformationally predominant were respectively determined, and the relationship of zwitterionic stability vs. water content was demonstrated. Finally, transition states for the transformation from canonical to zwitterionic proline at all water contents were located, testifying that zwitterionic formation in gas phase is impeded mainly by the thermodynamic rather than kinetic stability.
B3LYP density functional, in combination with 6-31+G (d,p) basis set, was used for structural optimizations and frequency calculations (Frisch et al. 2013). Energy minima were confirmed to have all positive frequencies while transition states displayed a single imaginary frequency corresponding to the eigenvector along the reaction path, and the assignment of each transition sate was verified by perturbing the structure along both directions of products and reactants with subsequent structural optimizations. Single-point energy calculations at the B3LYP/6-311++G (2df, 2pd) and MP2/6-311++G (2df, 2pd) levels of theory were then carried out on these optimized structures. Afterwards, the 6-31+G(d,p) and 6-311++G (2df, 2pd) basis sets were respectively designated as bs1 and bs2, and unless otherwise noted, all energies were reported at the B3LYP/bs2//B3LYP/bs1 level, which has been sufficiently validated before (Li et al. 2011; Kim et al. 2014; Yang et al. 2009; Rankin et al. 2002; Yang et al. 2010; Ajitha and Suresh 2011) and in this work.
Results and discussion
Relative stabilities for interacted structures of different proline conformers (E RS) and water with a wide range of contents (n = 0–5)
n = 0a
n = 1
n = 2
n = 3
n = 4
n = 5
P A nW I
P C nW I
For each proline confirmer, interactions with water can result in the various structures that are discerned by suffixing nW N , wherein n (n = 1, 2, …) represents the number of water molecules and N (=I, II, …) ranks the stability of different structures. For instance, P A 2W III /P C 5W I stands for the third/first stable conformer for P A /P C interactions with two/five water molecules.
Necessary for zwitterionic stabilization
It is interesting to find that one water molecule can stabilize proline in the zwitterionic form. In P C 1W I , two H-bonds are constructed for water with the carboxylic and amido sites of proline (NH2•••O3 and O3H3•••O1) that resemble the condition in P B 1W III ; however, both H-bonds have been significantly reinforced, with the distances being optimized respectively at 2.255 and 1.925 Å vs. 2.470 and 2.322 Å in P B 1W III . Despite that, P C 1W I still has a much higher energy than P B 1W I (8.7 kcal/mol, see Table 1 and Additional file 1: Table S2). For glycine, arginine and proline, relative stabilities of their zwitterionic conformers should differ from each other. Both zwitterionic proline and arigine require one water molecule in order to remain geometrically stable, while zwitterionic glycine necessitates two water molecules (Jensen and Gordon 1995; Im et al. 2008). In addition, one water molecule is already sufficient to cause zwitterionic arginine as the global energy minimum (Im et al. 2008). Accordingly, relative stabilities of these zwitterionic conformers should increase in the order as glycine <proline <arginine.
Introduction of more water molecules
In P B 2W I and P B 2W II , one water molecule forms H-bond with the carboxylic-O site of proline while the other forms H-bond with the amido site, and two water molecules are connected with each other by one strong H-bond. In P C 2W I , the intermolecular H-bonding interactions between proline and water resemble those in P B 2W II and also in P C 1W I while are greatly consolidated as compared to P C 1W I , and the zwitterionic stability improves accordingly (Table 1). Unlike the case of one water, zwitterions (P C 2W IV and P C 2W VII ) that have H-bonds only at the carboxylic site of proline remain geometrically stable, as a result of enhanced intermolecular interactions.
Transformation to zwitterionic proline
Activation barriers (E A) and reaction heats (E R) for transformation from canonical (P B ) to zwitterionic (P C ) proline with presence of water molecules
One water molecule
P B 1W III → [TS1W III–I ]≠ → P C 1W I
Two water molecules
P B 2W II → [TS2W II–I ]≠ → P C 2W I
P B 2W I → [TS2W I–II ]≠ → P C 2W II
P B 2W VI → [TS2W VI–III ]≠ → P C 2W III
P B 2W III → [TS2W III–IV ]≠ → P C 2W IV
P B 2W VII → [TS2W VII–V ]≠ → P C 2W V
P B 2W V → [TS2W V–VI ] → P C 2W VI
P B 2W IV → [TS2W IV–VII ]≠ → P C 2W VII
Three water molecules
P B 3W II → [TS3W II–I ]≠ → P C 3W I
P B 3W I → [TS3W I–II ] ≠ → P C 3W II
P B 3W III → [TS3W III–III ] ≠ → P C 3W III
P B 3W III → [TS3W III–IV ] ≠ → P C 3W IV
P B 3W IV → [TS3W IV–V ] ≠ → P C 3W V
Four water molecules
P B 4W I → [TS4W I–I ] ≠ → P C 4W I
P B 4W II → [TS4W II–I ] ≠ → P C 4W I
P B 4W II → [TS4W II–III ] ≠ → P C 4W III
P B 4W III → [TS4W III–IV ] ≠ → P C 4W IV
Five water molecules
P B 5W I → [TS5W I–I ] ≠ → P C 5W I
P B 5W II → [TS5W II–II ] ≠ → P C 5W II
Conformational analyses are performed for interacted structures of proline conformers (P A , P B and P C ) and water with a wide range of contents (n = 1–5). Five water molecules are enough to fill up the first shell of proline functional sites (carboxylic and amido). The conformational preferences of proline are altered by gradual increase of water contents, and intermolecular H-bonds play a crucial role in deciding their relative stabilities.
It is interesting to find that one water molecule has already rendered zwitterionic proline to be geometrically stable with formation of two strong intermolecular H-bonds. Unlike the canonical conformers, the relative stabilities of zwitterionic proline improve monotonously and pronouncedly with gradual increase of water contents. Zwitterionic proline is energetically preferential over canonical structures at n = 4 and conformationally predominant at n = 5; in these cases, rather complex H-bonding networks are constructed between water and proline. Zwitterionic stabilities of different amino acids differ substantially and increase in the order of glycine <proline <arginine.
At a given water content, the activation barriers for transformation from canonical to zwitterionic conformers are significantly dependent on reaction paths; nonetheless, the activation barriers are rather low for all water contents. It is thus demonstrated that the zwitterionic distribution, at any water content (n ≥ 0), will be determined mainly by the thermodynamic rather than kinetic factor.
GY performed the experiments, analyzed the data and drafted the manuscript. LJZ and YC helped analyze the data and contributed in writing the manuscript. All authors read and approved the final manuscript.
This work was sponsored by the National Natural Science Foundation of China (21473137) and Fourth Excellent Talents Program of Higher Education in Chongqing (2014-03) and Fundamental Research Funds for the Central Colleges (SWU113049 and XDJK2014C106).
The authors declare that they have no competing interests.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
- Ai HQ, Bu YX, Han KL (2003) Glycine-Zn+/Zn2+ and their hydrates: on the number of water molecules necessary to stabilize the switterionic glycine-Zn+/Zn2+ over the nonzwitterionic ones. J Chem Phys 118:10973–10985View ArticleGoogle Scholar
- Ajitha MJ, Suresh CH (2011) A higher energy conformer of (S)-proline is the active catalyst in intermolecular aldol reaction: evidence from DFT calculations. J Mol Catal A: Chem 345:37–43View ArticleGoogle Scholar
- Alln WD, Czinki E, Csásázr AG (2004) Molecular structure of proline. Chem Eur J 10:4512–4517View ArticleGoogle Scholar
- Balta B, Aviyente V (2004) Solvent Effects on Glycine II. Water-assisted Tautomerization. J Comput Chem 15:690–703View ArticleGoogle Scholar
- Constantino E, Rodriguez-Santiago L, Sodupe M, Tortajada J (2005) Interaction of Co+ and Co2+ with Glycine. A Theoretical Study. J Phys Chem A 109:224–230View ArticleGoogle Scholar
- Corradini D, Strekalova EG, Stanley HE, Gallo P (2013) Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose. Sci Rep 3:1218View ArticleGoogle Scholar
- Corral L, Mό O, Yáňez M, Moran D, Radom L, Salpin JY, Tortajada J (2006) An experimental and theoretical investigation of gas-phase reactions of Ca2+ with glycine. Chem Eur J 12:6787–6796View ArticleGoogle Scholar
- Császár AG (1992) Conformers of gaseous glycine. J Am Chem Soc 114:9568–9575View ArticleGoogle Scholar
- Eszter C, Czinki E, Csásázr AG (2003) Conformers of gaseous proline. Chem Eur J 9:1008–1019View ArticleGoogle Scholar
- Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Cheeseman MAJR, Scalmani G, Barone V, Mennucci B, Petersson GA et al (2013) Gaussian 09, Revision A.9. Gaussian, Inc., WallingfordGoogle Scholar
- Gutowski M, Skurski P, Simons J (2000) Dipole-bound anions of glycine based on the zwitterion and neutral structures. J Am Chem Soc 122:10159–10162View ArticleGoogle Scholar
- Hoyau S, Ohanessian G (1998) Interaction of alkali metal cations (Li+-Cs+) with glycine in the gas phase: a theoretical study. Chem Eur J 4:1561–1569View ArticleGoogle Scholar
- Hu CH, Shen M, Schaefer HF III (1995) Glycine conformational analysis. J Am Chem Soc 115:2923–2929View ArticleGoogle Scholar
- Hwang TK, Eom GY, Choi MS, Jang SW, Kim JY, Lee S (2011) Microsolvation of lysine by water: computational study of stabilized zwitterion. J Phys Chem B 115:10147–10153View ArticleGoogle Scholar
- Im S, Jang SW, Lee S, Lee Y, Kim B (2008) Arginine zwitterion is more stable than the canonical form when solvated by a water molecule. J Phys Chem A 112:9767–9770View ArticleGoogle Scholar
- Jensen JH, Gordon MS (1995) On the number of water molecules necessary to stabilize the glycine zwitterion. J Am Chem Soc 117:8159–8170View ArticleGoogle Scholar
- Kapitán J, Baumruk V, Kopecký V Jr, Pohl R, Bouř P (2006) Proline zwitterion dynamics in solution, glass and crystalline state. J Am Chem Soc 128:13451–13462View ArticleGoogle Scholar
- Kass SR (2005) Zwitterion-dianion complexes and anion-anion clusters with negative dissociation energies. J Am Chem Soc 127:13098–13099View ArticleGoogle Scholar
- Kim JY, Lee Y, Lee S (2014) Effects of microsolvation on the relative stability of zwitterionic vs canonical proline. Chem Phys Lett 608:177–185View ArticleGoogle Scholar
- Kokpol SU, Doungdee PB, Hannongbua SV, Rode BM, Imtrakul LJP (1988) Ab initio study of the hydration of the glycine zwitterion. J Chem Soc Faraday Trans 2(84):1789–1792View ArticleGoogle Scholar
- Levy Y, Onuchic JN (2004) Water and proteins: a love-hate relationship. Proc Natl Acad Sci USA 101:3325–3326View ArticleGoogle Scholar
- Li XJ, Zhong ZJ, Wu HZ (2011) DFT and MP2 investigations of l-proline and its hydrated complexes. J Mol Model 17:2623–2630View ArticleGoogle Scholar
- Rand RP (2004) Probing the role of water in protein conformation and function. Philos Trans R Soc Lond B Biol Sci 359:1277–1284View ArticleGoogle Scholar
- Rankin KN, Gauld JW, Boyd RJ (2002) Density functional study of the proline-catalyzed direct aldol reaction. J Phys Chem A 106:5155–5159View ArticleGoogle Scholar
- Remko M, Rode BM (2001) Catalyzed peptide bond formation in the gas phase. Phys Chem Chem Phys 3:4667–4673View ArticleGoogle Scholar
- Remko M, Rode BM (2006) Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure of glycine and zwitterionic glycine. J Phys Chem A 110:1960–1967View ArticleGoogle Scholar
- Rimola A, Corno M, Zicovich-Wilson CM, Ugliengo P (2008) Ab initio modeling of protein/biomaterial interactions: glycine adsorption at hydroxyapatite surfaces. J Am Chem Soc 130:16181–16183View ArticleGoogle Scholar
- Rimola A, Costa D, Sodupe M, Lambert JF, Ugliengo P (2013) Silica surface features and their role in the adsorption of biomolecules: computational modeling and experiments. Chem Rev 113:42160–44313View ArticleGoogle Scholar
- Snoek LC, Kroemery RT, Simons JPA (2002) Spectroscopic and computational exploration of tryptophan-water cluster structures in the gas phase. Phys Chem Chem Phys 4:2130–2139View ArticleGoogle Scholar
- Teeter MM (1991) Water-protein interactions: theory and experiment. Annu Rev Biophys Biophys Chem 20:577–600View ArticleGoogle Scholar
- Tian SX, Li HB, Yang JL (2009) Monoanion BH4 − can stabilize zwitterionic glycine with dihydrogen bonds. Chemphyschem 10:1435–1437View ArticleGoogle Scholar
- Timasheff SN (1970) Protein-solvent interactions and protein conformation. Acc Chem Res 3:62–68View ArticleGoogle Scholar
- Wu RH, McMahon TB (2007) Stabilization of the zwitterionic structure of proline by an alkylammonium ion in the gas phase. Angew Chem Int Ed Engl 46:3668–3671View ArticleGoogle Scholar
- Yamabe S, Ono N, Tsuchida N (2003) Molecular interactions between glycine and h2o affording the zwitterion. J Phys Chem A 107:7915–7922View ArticleGoogle Scholar
- Yang G, Zhou LJ (2014) Zwitterionic versus canonical amino acids over the various defects in zeolites: a two-layer ONIOM calculation. Sci Rep 4:6594View ArticleGoogle Scholar
- Yang G, Zu YG, Liu CB, Fu YJ, Zhou LJ (2008) Stabilization of amino acid zwitterions with varieties of anionic species: the intrinsic mechanism. J Phys Chem B 112:7104–7110View ArticleGoogle Scholar
- Yang G, Zu YG, Fu YJ, Zhou LJ, Zhu RX, Liu CB (2009a) Assembly and stabilization of multi-amino acid zwitterions by the zn(ii) ion: a computational exploration. J Phys Chem B 113:4899–4906View ArticleGoogle Scholar
- Yang ZW, Wu XM, Zhou LJ, Yang G (2009b) A Proline-based neuraminidase inhibitor: DFT studies on the zwitterion conformation, stability and formation. Int J Mol Sci 10:3918–3930View ArticleGoogle Scholar
- Yang G, Yang ZW, Zhou LJ, Zhu RX, Liu CB (2010) A revisit to proline-catalyzed aldol reaction: interactions with acetone and catalytic mechanisms. J Mol Catal A: Chem 316:112–117View ArticleGoogle Scholar
- Yang G, Zhu C, Zhou LJ (2015) Stabilization of zwitterionic proline by DMSO. Int J Quantum Chem 115:1746–1752View ArticleGoogle Scholar
- Yu D, Rauk A, Armstrong DA (1995) Radicals and ions of glycine: an ab initio study of the structures and gas-phase thermochemistry. J Am Chem Soc 117:1789–1996View ArticleGoogle Scholar
- Zhang K, Chung-Phillips A (1998) Conformers of gaseous protonated glycine. J Comput Chem 19:1862–1876View ArticleGoogle Scholar