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Article

Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study

Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan
*
Author to whom correspondence should be addressed.
Catalysts 2017, 7(12), 363; https://doi.org/10.3390/catal7120363
Submission received: 26 October 2017 / Revised: 16 November 2017 / Accepted: 22 November 2017 / Published: 27 November 2017

Abstract

:
Spontaneous, nonenzymatic reactions in proteins are known to have relevance to aging and age-related diseases, such as cataract and Alzheimer’s disease. Among such reactions is the racemization of Ser residues, but its mechanism in vivo remains to be clarified. The most likely intermediate is an enol. Although being nonenzymatic, the enolization would need to be catalyzed to occur at a biologically relevant rate. In the present study, we computationally found plausible reaction pathways for the enolization of a Ser residue where a dihydrogen phosphate ion, H2PO4, acts as a catalyst. The H2PO4 ion mediates the proton transfer required for the enolization by acting simultaneously as both a general base and a general acid. Using the B3LYP density functional theory method, reaction pathways were located in the gas phase and hydration effects were evaluated by single-point calculations using the SM8 continuum model. The activation barriers calculated for the reaction pathways found were around 100 kJ mol−1, which is consistent with spontaneous reactions occurring at physiological temperature. Our results are also consistent with experimental observations that Ser residue racemization occurs more readily in flexible regions in proteins.

1. Introduction

All common amino acids, except for glycine (Gly), have an asymmetric α-carbon atom, resulting in the occurrence of l- and d-forms. However, only l-amino acids are used in protein biosynthesis. Once biosynthesized, proteins, especially long-lived ones, can undergo various spontaneous reactions which are nonenzymatic and have relevance to aging and age-related diseases such as cataract and Alzheimer’s disease [1,2,3,4,5,6]. Among such reactions, racemization (or epimerization if viewed from the entire protein molecule) of amino acid residues, by which d-amino acid residues gradually accumulate, has recently attracted increasing attention [7,8,9,10,11].
Aspartic acid (Asp) residues are the most racemization-prone amino acid residues. This is due to the well-known succinimide-mediated mechanism [12,13,14,15]. In this mechanism, the actual species undergoing racemization is a succinimide intermediate which is formed from an l-Asp residue by an intramolecular cyclization with the loss of a water molecule. As a result of this mechanism, Asp racemization is coupled to the isomerization to the β-form, so that l-β-Asp, d-Asp, and d-β-Asp residues can be formed from the original l-Asp residue. These unusual amino acid residues can also be formed from asparagine (Asn) residues, since a succinimide intermediate can also be formed from them with the loss of an ammonia molecule.
Serine (Ser) residues are the second most racemization-prone amino acid residues in an overall sense. Shapira and co-workers showed that human brain myelin basic protein (MBP), a long-lived protein, undergoes racemization at Asp and Ser residues [16,17]. High levels of racemization at Asp and Ser residues were also found for amyloid β from Alzheimer’s disease brains [17,18]. Amyloid β contains two Ser residues, Ser8 and Ser26, and both residues are probably equally racemized [19]. Kaneko and co-workers proposed possible roles of racemization of Ser26 in the pathogenesis (neurodegeneration) of Alzheimer’s disease [20,21,22,23,24].
Age-dependent, progressive racemization of Ser residues was also found for lifelong proteins (crystallins) of normal human lenses by Hooi and Truscott [25]; by age 70, 4.5% of all Ser residues were shown to have converted to the d-form. In addition, the extent of racemization was significantly higher in cataract lenses than in age-matched normal lenses. Later, Ser59 and Ser62 residues in human αA-crystallin, the most abundant structural protein in the human lens, were demonstrated to be sites of racemization by Hooi and co-workers [26]; these two Ser residues reside in an unstructured region of the protein, and, in total, about 35% of both Ser residues were converted to the d-form in normal lenses by age 75. Once again, the extent of racemization was significantly higher in cataract lenses. Thus, racemization of Ser residues (and other spontaneous modifications) in crystallin proteins could be associated with the development of cataracts.
Racemization of Ser residues has also been observed for crystallin proteins from sheep, pig, and cow eye lenses, especially in structurally disordered N-terminal and C-terminal regions [27,28]. An age-dependent increase in d-Ser residues was also demonstrated for proteins in articular cartilage and tooth dentin [29,30].
Compared to Asp residue racemization, little is known about the mechanism of Ser residue racemization, although recent experimental studies using peptides suggest that a direct abstraction of the α-proton is involved in the mechanism [31,32]. A simple abstraction of the α-proton results in an enolate intermediate having a negative charge. However, at a physiological pH of 7.4, an enol species is a more likely intermediate [33,34,35,36]. The formation of the enol intermediate requires that the carbonyl oxygen of the Ser main chain be protonated (Scheme 1). Although being nonenzymatic, the enolization of a Ser residue would have to be catalyzed in order to occur at a biologically significant rate. Even two water molecules in a dimeric form may catalyze the enolization of succinimide and Ser residues [31,33,34,35].
Recently, we have computationally shown that the racemization of the succinimide residue can be efficiently catalyzed by a dihydrogen phosphate ion, H2PO4 [36]. In our proposed mechanism, this ion mediates the proton transfer required for the enolization of the Hα–Cα–C=O moiety by acting simultaneously as both a general base and a general acid. In other words, a proton relay involving the H2PO4 ion occurs, as schematically shown in Scheme 2. Our finding was consistent with the experimental observation by Tomizawa and co-workers [37] that d-Asp formation from l-Asp/l-Asn in hen egg white lysozyme was accelerated in a phosphate buffer of pH 6 (where H2PO4 is the main phosphate species). The H2PO4 ion also exists in a significant amount at a physiological pH of 7.4, and Ser residue racemization in vivo may also be catalyzed by this ion. Computational studies also suggest that the H2PO4 ion may also have catalyzed prebiotic reactions by simultaneously acting as both a general base and a general acid [38,39]. Moreover, keto–enol tautomerism of simple aldehydes (propanal, 2-methylpropanal, and butanal) has been shown to be catalyzed by a phosphate buffer of pH 7.4 [40]. Nitro–aci-nitro tautomerism is also catalyzed by phosphate buffer [41].
Miyamoto et al. [42] have recently reported the in vitro racemization of Ser residues in albumin from chicken egg white. They showed that racemization at pH 9.5 was about 4.6 times faster than at pH 7.4. This difference cannot be explained only by a specific base (OH) catalyzed mechanism. Since phosphate buffer was used for the experiment at pH 7.4, it is likely that a phosphate species acts as a catalyst for Ser residue racemization.
The purpose of the present study was to computationally find reasonable reaction pathways for Ser residue enolization catalyzed by an H2PO4 ion. By “reasonable”, we mean that the corresponding activation barrier is around 100 kJ mol−1 or less, considering activation energies for typical nonenzymatic reactions of amino acid residues [12,36,43,44,45,46]. We used the model compound shown in Figure 1, where a Ser residue is capped with acetyl (Ace) and methylamino (Nme) groups on the N- and C-termini, respectively (Ace–Ser–Nme), and the B3LYP density functional theory (DFT) method. While geometry optimizations were performed in the gas phase, the effect of hydration was evaluated by single-point calculations using the SM8 (solvation model 8) continuum model [47,48], which is one of the most accurate continuum solvation models [49] and is implemented in the Spartan ’14 [50] used in the present study (see Section 3 for details). We find three energetically close enolization pathways, which are consistent with in vivo racemization of Ser residues.

2. Results and Discussion

By preliminary conformational analyses for the model compound itself, we found the conformer shown in Figure 2 (φ = 91°, ψ = −124°, χ1 = 80°, χ2 = −63°) as one which can interact with an H2PO4 ion effectively for Ser residue enolization (see Figure 1 for definition of the main-chain dihedral angles φ and ψ, and the side-chain dihedral angles χ1 and χ2). After the zero-point energy (ZPE), thermodynamic, and hydration Gibbs energy corrections, this conformer was the fifteenth lowest among 23 conformers found, lying 10.0 kJ mol−1 above the lowest one (φ = −158°, ψ = −175°, χ1 = −167°, χ2 = 83°). This conformer can interact with an H2PO4 ion at the three points, shown by orange circles in Figure 2, and, hence, is reactive for Ser residue enolization. It should be noted that this conformer has two intramolecular hydrogen bonds involving the Ser side chain (1.763 and 1.951 Å) and is unique to Ser. Indeed, we did not find a corresponding stable conformation for the main chain of the analogous alanine (Ala)-containing compound (Ace–Ala–Nme); instead, a conformer with φ = 73° and ψ = −56° was located because of the formation of an intramolecular hydrogen bond between the oxygen of Ace and the hydrogen of Nme (1.932 Å). It has been experimentally observed that Ser residue racemization occurs mainly in flexible regions of proteins [26,27,28]. Therefore, the existence of the above reactive conformer unique to Ser may be one of the reasons why Ser residues are prone to racemization. Here, it should be noted that Ser racemization reactions in lifelong proteins are very slow; their half-lives should be longer than our life spans. Therefore, these reactions need not occur in very stable Ser conformations.
We identified three reaction pathways with low activation barriers, which we denote as pathway 1, pathway 2, and pathway 3. The energy profiles for these pathways are shown in Figure 3. In this figure, RC, TS, and PC stand for reactant complex, transition state, and product complex, respectively, and relative energies including the ZPE, thermodynamic, and hydration Gibbs energy corrections are shown in kJ mol−1, with respect to RC1 (reactant complex of pathway 1). The optimized geometries in pathway 1, pathway 2, and pathway 3 are shown in Figure 4, Figure 5 and Figure 6, respectively, and the dihedral angles defined in Figure 1 are reported in Table 1. Intrinsic reaction coordinate (IRC) calculations (followed by full geometry optimizations) were performed in order to confirm the connection of each transition state to the respective reactant and product complexes. The total energies, ZPEs, SM8 hydration Gibbs energies, and Cartesian coordinates of the optimized geometries are provided in Supplementary Materials.
The geometries of RC1, TS1 (transition state of pathway 1), and PC1 (product complex of pathway 1) are shown in Figure 4. In RC1, the model compound and the H2PO4 ion form a complex by two hydrogen bonds and a CH–O interaction. The CH–O interaction (2.003 Å) involves the Ser Cα–Hα bond and one of the deprotonated oxygens in H2PO4. The H2PO4 ion also forms a hydrogen bond (1.960 Å) to the Ser carbonyl oxygen. The additional hydrogen bond (1.873 Å) involving the Ser NH group may also contribute to stabilizing RC1. It should be noted that the H2PO4 ion in RC1 is in a pseudo-C2 symmetry, corresponding to the global minimum geometry of an isolated H2PO4 ion of C2 symmetry [51,52,53,54].
RC1 is converted to PC1 via TS1. The corresponding activation barrier was calculated to be 104.8 kJ mol−1 after the ZPE, thermodynamic, and hydration Gibbs energy corrections. This value is reasonable for a nonenzymatic reaction which occurs at physiological temperature. In TS1, abstraction of the Ser α-proton by the phosphate oxygen is almost completed, as may be seen from the relevant interatomic distances shown in Figure 4. On the other hand, the proton transfer from H2PO4 to the carbonyl oxygen is in its early stage. Therefore, the double proton transfer mediated by the H2PO4 ion is concerted but asynchronous. In TS1, the phosphate moiety has a form like an H3PO4 molecule. It should be noted that in TS1, the Ser Cα–Cβ bond is shorter and the Cβ–O bond is longer than in RC1, indicating that the Cβ–O bond may stabilize the negative charge developing at Cα by hyperconjugation. PC1 is a complex between the enol product and an H2PO4 ion formed again by a three-point interaction. In particular, the hydrogen bond between the enol hydrogen and H2PO4 is very short (1.464 Å). The ψ dihedral angle changes by more than 30° by going from RC1 to PC1 (Table 1), because the Cα atom is converted to sp2-hybridized from sp3-hybridized. The relative energy of PC1 with respect to RC1 is 97.5 kJ mol−1.
Figure 5 shows the geometries of RC2 (reactant complex of pathway 2), TS2 (transition state of pathway 2), and PC2 (product complex of pathway 2). In RC2, the H2PO4 ion is again in a pseudo-C2 symmetry, but the model compound interacts with the H2PO4 ion in a different way from RC1 at the three points shown in Figure 2. RC2 is higher in energy than RC1 by 11.2 kJ mol−1. However, the local activation barrier for pathway 2 is 98.9 kJ mol−1, which is lower than for pathway 1 by 5.9 kJ mol−1. Compared to TS1, the energy of TS2 is 5.3 kJ mol−1 higher. PC2 is only slightly more stable than PC1 by 2.1 kJ mol−1. The double proton transfer mediated by the H2PO4 ion is again concerted but asynchronous, as may be seen from the relevant interatomic distances shown in Figure 5. The side-chain Cβ–O bond again seems to stabilize the transition state hyperconjugatively. In pathway 2, a larger change in the main-chain conformation was observed compared to pathway 1; the φ and ψ dihedral angles change by 36° and 42°, respectively, when going from RC2 to PC2. In PC2, the interaction between Cα and the abstracted α-proton is weak (3.051 Å).
Figure 6 shows the geometries of RC3 (reactant complex of pathway 3), TS3 (transition state of pathway 3), and PC3 (product complex of pathway 3). RC3 and RC2 can be related to each other by a proton transfer in the phosphate moiety. RC3 is higher in energy than RC2 by 3.4 kJ mol−1. However, the local activation barrier of pathway 3 is 96.6 kJ mol−1, which is the lowest among the three pathways. Compared to TS1 and TS2, the energy of TS3 is higher by 6.4 and 1.1 kJ mol−1, respectively. PC3 is the lowest in energy among the three product complexes. In RC3, the H2PO4 ion is not in a pseudo-C2 symmetry, but in a pseudo-Cs symmetry. This is thought to be the main reason for the energy difference between RC2 and RC3 [52,53,54]. Interestingly, the H2PO4 ion is in a pseudo-C2 symmetry in PC3, consistent with its stability mentioned above. Since the three transition states (TS1, TS2, and TS3) have similar energies, all the three pathways may plausibly mimic the in vivo enolization of Ser residues. The changes in dihedral angles in pathway 3 are very similar to those in pathway 2. The hyperconjugation of the side-chain Cβ–O bond seems to be also operative in pathway 3. Compared to TS1 and TS2, TS3 has a shorter distance of the cleaving Cα–Hα bond (1.680 Å) and a longer distance of the forming enol O–H bond (1.480 Å).

3. Computational Details

Figure 1 shows the model compound used in the present study (Ace–Ser–Nme), in which a Ser residue is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Searches for the reaction pathways of Ser residue enolization were performed for complexes between the model compound and an H2PO4 ion. All calculations were carried out by DFT with the B3LYP functional using Spartan ’14 [50]. Geometry optimizations and vibrational frequency calculations were performed using the 6-31+G(d,p) basis set in the gas phase. Moreover, hydration Gibbs energies were evaluated at the gas-phase optimized geometries using the SM8 continuum model [47,48], as implemented in Spartan ’14; the 6-31G(d) basis set was employed for these calculations because it gives stable atomic charges and is recommended by the developers of the model [55]. All the optimized geometries were confirmed to be an energy minimum (with no imaginary frequency) or a transition state (with a single imaginary frequency) by the vibrational frequency calculations. The relative energies reported in this paper include the ZPE and thermodymamic corrections to give the Gibbs energy at 298.15 K and 1 atm, and the SM8 hydration Gibbs energy correction. IRC calculations (followed by full geometry optimizations) were performed from all the transition states to confirm the energy minima connected by each transition state.

4. Conclusions

We have computationally found plausible reaction pathways for Ser residue enolization where an H2PO4 ion acts as a catalyst. As in the previous study for the racemization of a succinimide residue [36], the H2PO4 ion acts both as a general base and a general acid in a single step. More specifically, it abstracts the α-proton from the Ser residue, and donates a proton of its own to the Ser carbonyl oxygen. It seems that an H2PO4 ion has an effective proton relay ability. It has recently been elucidated that the majority of Ser (and Asp) residues that are susceptible to racemization reside in flexible regions of proteins [26,27,28]. If a Ser residue can adopt such a conformation as shown in Figure 2 and then its α-proton and carbonyl oxygen are exposed to solvent water, it is likely to undergo enolization (and hence racemization) by the mechanism revealed in the present study. At physiological pH, there exist more HPO42− ions than H2PO4. It would be interesting to know which ion catalyzes the enolization of Ser (and other residues) more effectively, especially in the context of aging and pathologies. In order to elucidate the relative catalytic abilities of H2PO4 and HPO42−, calculations including at least several explicit water molecules will be needed. We are now planning such calculations.

Supplementary Materials

The following are available online at www.mdpi.com/2073-4344/7/12/363/s1, Table S1: Total energies (au), zero-point energies (kJ mol−1), and SM8 hydration Gibbs energies (kJ mol−1) of the B3LYP/6-31+G(d,p) optimized geometries, Table S2: Cartesian coordinates (Å) of RC1, Table S3: Cartesian coordinates (Å) of TS1, Table S4: Cartesian coordinates (Å) of PC1, Table S5: Cartesian coordinates (Å) of RC2, Table S6: Cartesian coordinates (Å) of TS2, Table S7: Cartesian coordinates (Å) of PC2, Table S8: Cartesian coordinates (Å) of RC3, Table S9: Cartesian coordinates (Å) of TS3, Table S10: Cartesian coordinates (Å) of PC3.

Acknowledgments

The authors would like to acknowledge Tohoku Medical and Pharmaceutical University for financial support.

Author Contributions

O.T. conceived and designed the calculations; O.T., R.K., and N.M. performed the calculations; O.T. wrote the paper.

Conflicts of Interest

The authors declare no conflict of interest.

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Scheme 1. Enolization of the main chain of a Ser residue. The enol form, in which the asymmetry of the α-carbon has vanished, is postulated to be the intermediate of Ser residue racemization in vivo. The asterisk indicates the asymmetric α-carbon of Ser.
Scheme 1. Enolization of the main chain of a Ser residue. The enol form, in which the asymmetry of the α-carbon has vanished, is postulated to be the intermediate of Ser residue racemization in vivo. The asterisk indicates the asymmetric α-carbon of Ser.
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Scheme 2. Enolization of the main chain of an amino acid residue catalyzed by a species which can act simultaneously as both a general base and a general acid (such as an H2PO4 ion). The asterisk indicates the asymmetric α-carbon.
Scheme 2. Enolization of the main chain of an amino acid residue catalyzed by a species which can act simultaneously as both a general base and a general acid (such as an H2PO4 ion). The asterisk indicates the asymmetric α-carbon.
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Figure 1. The model compound used in the present study (Ace–Ser–Nme, where Ace = acetyl, Ser = serine, Nme = methylamino). The φ (C–N–Cα–C) and ψ (N–Cα–C–N) dihedral angles which characterize the main-chain conformation, and the χ1 (N–Cα–Cβ–O) and χ2 (Cα–Cβ–O–H) dihedral angles which characterize the side-chain conformation are indicated. The Ser residue is in the l-configuration.
Figure 1. The model compound used in the present study (Ace–Ser–Nme, where Ace = acetyl, Ser = serine, Nme = methylamino). The φ (C–N–Cα–C) and ψ (N–Cα–C–N) dihedral angles which characterize the main-chain conformation, and the χ1 (N–Cα–Cβ–O) and χ2 (Cα–Cβ–O–H) dihedral angles which characterize the side-chain conformation are indicated. The Ser residue is in the l-configuration.
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Figure 2. A conformer of the model compound shown in Figure 1 optimized by the B3LYP/6-31+G(d,p) method (φ = 91°, ψ = −124°, χ1 = 80°, χ2 = −63°). Selected interatomic distances are shown in Å. This conformer can interact with an H2PO4 ion at the three points indicated by orange circles and is reactive for the H2PO4-catalyzed enolization. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen.
Figure 2. A conformer of the model compound shown in Figure 1 optimized by the B3LYP/6-31+G(d,p) method (φ = 91°, ψ = −124°, χ1 = 80°, χ2 = −63°). Selected interatomic distances are shown in Å. This conformer can interact with an H2PO4 ion at the three points indicated by orange circles and is reactive for the H2PO4-catalyzed enolization. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen.
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Figure 3. Energy diagrams of the three enolization pathways (pathway 1, pathway 2, and pathway 3) for the model compound. RC: reactant complex; TS: transition state; PC: product complex. The relative energies including the zero-point energy, thermodynamic, and hydration Gibbs energy corrections are shown in kJ mol−1 with respect to RC1 (reactant complex of pathway 1). The imaginary frequencies of TS1, TS2, and TS3 are 230i, 151i, and 138i cm−1, respectively.
Figure 3. Energy diagrams of the three enolization pathways (pathway 1, pathway 2, and pathway 3) for the model compound. RC: reactant complex; TS: transition state; PC: product complex. The relative energies including the zero-point energy, thermodynamic, and hydration Gibbs energy corrections are shown in kJ mol−1 with respect to RC1 (reactant complex of pathway 1). The imaginary frequencies of TS1, TS2, and TS3 are 230i, 151i, and 138i cm−1, respectively.
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Figure 4. The geometries of RC1 (reactant complex of pathway 1), TS1 (transition state of pathway 1), and PC1 (product complex of pathway 1). Selected interatomic distances are shown in Å. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen; orange: phosphorus.
Figure 4. The geometries of RC1 (reactant complex of pathway 1), TS1 (transition state of pathway 1), and PC1 (product complex of pathway 1). Selected interatomic distances are shown in Å. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen; orange: phosphorus.
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Figure 5. The geometries of RC2 (reactant complex of pathway 2), TS2 (transition state of pathway 2), and PC2 (product complex of pathway 2). Selected interatomic distances are shown in Å. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen; orange: phosphorus.
Figure 5. The geometries of RC2 (reactant complex of pathway 2), TS2 (transition state of pathway 2), and PC2 (product complex of pathway 2). Selected interatomic distances are shown in Å. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen; orange: phosphorus.
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Figure 6. The geometries of RC3 (reactant complex of pathway 3), TS3 (transition state of pathway 3), and PC3 (product complex of pathway 3). Selected interatomic distances are shown in Å. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen; orange: phosphorus.
Figure 6. The geometries of RC3 (reactant complex of pathway 3), TS3 (transition state of pathway 3), and PC3 (product complex of pathway 3). Selected interatomic distances are shown in Å. Grey: carbon; white: hydrogen; blue: nitrogen; red: oxygen; orange: phosphorus.
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Table 1. The main-chain dihedral angles φ and ψ, and the side-chain dihedral angles χ1 and χ2 (in degrees) of the optimized geometries 1.
Table 1. The main-chain dihedral angles φ and ψ, and the side-chain dihedral angles χ1 and χ2 (in degrees) of the optimized geometries 1.
PathwayGeometryφψχ1χ2
1RC180−12579−51
TS190−15189−47
PC1101−15794−50
2RC286−12679−55
TS298−15289−52
PC2122−16894−55
3RC385−12779−55
TS392−14886−51
PC3121−16794−56
1 See Figure 1 for definition of φ, ψ, χ1, and χ2.

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Takahashi, O.; Kirikoshi, R.; Manabe, N. Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study. Catalysts 2017, 7, 363. https://doi.org/10.3390/catal7120363

AMA Style

Takahashi O, Kirikoshi R, Manabe N. Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study. Catalysts. 2017; 7(12):363. https://doi.org/10.3390/catal7120363

Chicago/Turabian Style

Takahashi, Ohgi, Ryota Kirikoshi, and Noriyoshi Manabe. 2017. "Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study" Catalysts 7, no. 12: 363. https://doi.org/10.3390/catal7120363

APA Style

Takahashi, O., Kirikoshi, R., & Manabe, N. (2017). Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study. Catalysts, 7(12), 363. https://doi.org/10.3390/catal7120363

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