Quantitative In silico analysis of mammalian serine racemase activity

Serine racemase (SR) is a pyridoxal 5’phosphate (PLP)-dependent enzyme catalyzing the racemization of S-serine to R-serine, and also oxidizes Rserine to pyruvate; however, the enzymatic racemization reaction is not fully understood. Therefore, quantitative in silico analysis of mammalian SR was performed followed byD-amino acid oxidase (DAO) analysis.The downloaded stereo structures of Rattus norvegicus (PBD ID: 3hmk) and mammalian (PDB ID: 3l6r and 3l6b) SR were optimized using molecular mechanic (MM2) calculation. Furthermore, the stereo structure of mammalian SR was constructed using 3hmk and the amino acid sequence data. The atomic partial charge (apc) of the target atoms was calculated using MOPAC-PM5. The atomic distances, bond angles, and apc of the mutants were used to study the enzyme reaction mechanism.The serine carboxyl group contacted lysine-56, where its amino group contacted the oxygen molecules of PLP aldehyde. The apc of C indicated that S-serine was selectively oxidized. Manganese located at another side of PLP is directly involved in the serine racemization by forming bonding with the hydroxyl group of serine. The enzyme racemization activity was quantitatively related to the bond angle of the substituted serine rather than to that of alanine. However, 316r and 316b lack several amino acid residues; therefore, the selective oxidation of S84 mutants was not clearly demonstrated. Keywords— Mammalian serine racemase, Quantitative analysis, Enzyme activity, in silico.


INTRODUCTION
Substantial levels of R-serine in the mammalian brain were discovered in 1992 [1].Mammalian SR (hSR) was first purified fro m rat brain and functionally characterized in 1999 [2].The serine racemase synthesizes R-serine fro m S-serine,and controls the R-serine level by oxidation ofR-serine to pyruvate.R-Serine is the main endogenous coagonist of the N-methyl-D-aspartate (NMDA)-type glutamate receptor (NMDA R) involved in important functions such as synaptic plasticity, learn ing, memory, and excitotoxicity.The x-ray crystal structure of mammalian and rat serine racemase were determined to provide a mo lecular basis for rat ional drug design.The residues 69-73 of hRS were found to be disordered; therefore, these residues were not included in the final model.The associated reaction mechanisms have been reported and the structure described in detail.The domains of SR were connected by a flexib le linker and could adopt different orientations with respect to each other.The crystal structures corresponded to biophysical data and confirmed the dimeric state of the en zy me.The racemizat ion reaction was critically dependent on the proximity of the catalytic S82 to the substrate as shown by the closed ligand-bound structures.[3].SR was most active as a noncovalent dimer containing one or mo re free sulfhydryls in the enzyme's active center or a modulatory site.The reco mbinant hSR was sensitive to o xidative stress in vivo, perhaps consistent with a scenario in which such modification plays a role in feedback or other forms of regulation [4].A decrease in R-serine concentration was reported in psychiatric d iseases such as schizophrenia and bipolar disorder: association studies had linked DAO and the primate-specific gene 72 (p LG72) with schizophrenia susceptibility.The opportunity to regu late DAO act ivity opened the way to R-serine level in vivo and thus to act on different pathological states involving the alteration in the NM DAR function.R-serine levels were decreased in cells over expression hDAO, wh ile cotransfection with pLG restored R-serine levels and decreases the hDAO activity.The results highlight the cellu lar function of hDAO in R-serine catabolis m and confirm the role of pLG72 as a negative effector of the flavorenzy me.The interaction of p LG72 to hDAO on the cytosolic side of the outer mitochondrial memb rane induced enzyme inactivation and speeded up its degradation.In this way cytosolic R-serine was preserved and cells were p rotected fro m o xidative stress by hydrogen peroxide generated by the flavoprotein in cytosol.pLG72 inhib ited hDAO and highlighted the specificity of class C compounds as they did not inhibit glucose oxidase or D-aspartate oxidase [5].The potential involvement of R-serine in neurodegenerative diseases pertains to the impaired act ivity of DAO, which has potential fo r develop ment as a therapeutic agent in Amyotrophic lateral Sclerosis.An up-regulation of Rserine caused either by impaired metabolis m of R-serine by DAO or increased biosynthesis by SR [6].Serine racemase was a PLP-dependent enzyme cataly zing the racemizat ion of S-serine to R-serine; however, the enzy matic racemization reaction was not fully understood [7].Therefore, the bi-functional reaction mechanisms of mammalian SR were quantitatively analyzed in silico as was the case for R-amino acid o xidase [8][9][10] and alan ine racemase [11].
II. EXPERIMENTAL The stereo structure of hSR was constructed by homology modeling using Rattus norvegicus (PBD ID: 3h mk).The homology model of hSR and R-and S-amino acid complexes were optimized using MM2 force-field parameters of version 6.1 CA Che MM 2 (Fu jitsu, Japan).The a mino acid residues present within 3Å of a substituted amino acid group were ext racted with the coenzy me PLP, then locked the molecules, prio r to being optimized using the M OPAC PM5 program.The differences in the apc values of key atoms and their relationships with en zy me activit ies were analyzed.Calculations were performed using a DCPIx86-based PC with an Intel Core™i7-2600 3.40 GHz CPU.The minimum energy level was 10 -7 kcal mol -1 .

III. RESULTS AND DISCUSSION
The downloaded stereo structure of hSR (PDB, ID: 3l6r) [12] lacks seven residue amino acids P69-K75.Furthermore, so me methionines were not identified.V68 was d irectly connected to P76.Therefore, the lack of these residues shortens the distance of these two loops, a long right-handed alpha and a short -parallel loop.This results in R135 and PLP getting closer to each other.Another hSR (PDB ID: 3l6b) [12] lacks five amino acid residues (P69 -E73); in addition, C6 appeared as D6.The location of R135 is similar to that of 3l6r.The conformat ion of PLP lacks the carbonyl group, and the substrate is malonate.Therefore, the stereo structure of hSR was reconstructed using that of Rattus norvegicus SR (PDB, ID: 3h mk) [12].The homology model of hSR was defined as h3hmk.The conformation of the key mo lecules is shown in Figure 1, and that of 3l6b in Figure 2.
However, Rattus norvegicus SR lacks a substrate; therefore, malonate was inserted at the same location as the malonate (inhib itor) being held in h SR, and the complex was optimized using MM2 calcu lations prior to being replacedby serine.Alanine was used as a blank amino acid.The o xidation reaction of SR was first analyzed as with the case of DAO, where FAD is the coenzy me and the carbonyl group of the flavin ring is the electron-transferfor the deamination of R-amino acids  Arginine R275 is the key amino acid residue holdingthe R-amino acid carbo xyl group in the DA O reaction chamber [8][9][10].However, there is no arginine close to the PLP site of 3h mk and h3h mk.R135 is far fro m PLP in 3hmk and h3hmk (see Figure 1).The atomic distance between the oxygen of PLP aldehyde and the center carbon of the R135 guanidyl group is 15.1 Å; corresponding distance in 3l6b and 3l6r were 7.76 and 6.72 Å (see Figure 2), respectively.In addition, the atomic distance between the aldehyde oxygen and C of S84 were 10.1, 7.78, and 7.14 Å for h3hmk, 3l6b, and 3l6r, respectively.Indeed, the conformat ion of h3hmk is very different fro m the stereo structure of the down loaded hSR 316b and 3l6r.In the case of the latter, R135 is located close to PLP; this should facilitate the trapping of substrate serine carbo xyl groups.The atomic distances between PLP phosphine andthe R135 guanidyl group center carbon were 18.8 Å 10.5, and 9.85 Å fo r h3h mk, 3l6b, and 3l6r, respectively.The carbo xyl group of the serine substitute superimposed on the carboxy l group of the orig inal substrate malonate; then, the complex structure was optimized to analyse the oxidation activity.The carbo xyl group of the serine substrate was located near the amino group of K56.
The apc values of amino acids were calculated using these downloaded structures containing the fragmental lib rary of the CA Che program.The downloaded structures were locked prior to the MOPA C calculation.The R-form amino acids were converted fro m the orig inal S-form amino acids.The apc values of S-and R-alanines were the same, but those of R-serine were a little d ifferent.The apc value of S-serine C was 0.20 au, while those of R-serine, S-and R-alan ines were 0.20, 0.17, and 0.18 au, respectively.However, the amino group of S-alanine contacted with G239, and that of R-alanine did not face to the oxygen of PLP aldehyde.When the original apc value (-0.384 au) of S-serine were used, the apc of R-serine was smaller (0.19 au) than that of S-serine.The result supported the fact that SR relatively o xid ized S-serine at the location.Normally hSR favors S-serine elimination activity over SR activity [13].
The oxidation activity was further studied using hSR mutants, S84A, S84D, S84N, and S84T [13].The Kcat/Km values of WT and S84N were about five t imes higher than those of S84A, S84D, and S84T.However, such reaction selectivity was not obtained from the apcs of the Cs of R-and S-serines.apc was key to exp laining the selective oxidation of R-amino acids in DAO [10].However, such a change was observed while the apc was calcu lated using the 3l6r model.The d ifference should be the ato mic distance between the C of S84 and the aldehyde oxygen of PLP.The d istances in h3hkm, 3l6b, and 3l6r were 10.1, 7.78 and 7.14 Å, respectively.S84 is located near PLP in 3l6b and 3l6r and may contribute to the selective reaction of mutants, but it is far fro m the reaction center of the aldehyde oxygen in h3hkm as shown in Figure 3.The apc values of C are similar for R-and S-serines, about 0.2 au, and did not indicate the selectivity of these mutants.The reason is R135 and S84 are located far fro m the PLP in the h 3h mk structure.This conformation d iffers fro m those of 3l6r and 3l6b.In 3l6b, the apcs of the Cs of R-and S-serines in S84N, S84A, S84D, and S84T were 0.20, 0.20, 0.18, 0.16, and 0.18, respectively.Sserine amino group did not face the aldehyde o xygen.Similar results were obtained for 3l6r.In addition, S83 and S84 are connected to the G82 of -parallel and G85 right-handed alpha helix, respectively; therefore, S84 should cause a conformation change in the mutants.R135 is a part of the right-handed alpha loop; therefore this residue has no flexib ility of movement on its own.Consequently, the flexibility of these serine residues is limited.One of the reasons why no clear selectivity among the mutants was observed is that the K56 amino group contacts with both the serine amino group and PLP aldehyde in these conformat ions.This structure differs fro m that observed in DA O, where the key amino acid residue guanidyl group was far fro m the flavin carbonyl group.Here, the flexible conformation of PLP did not clearly demonstrate the localizat ion of electron.Unfortunately, the amino acid sequence data of these mutants were not presented to justify this speculation.
Deprotonation of the C and the format ion of imine are the basic mechanisms underlying alan ine racemase reactivity.The atomic distance between H and C, and the apc of H changed little in the conformation of the mo lecular forms o f PLP.The apc of the alan ine C was well correlated with the reactivity, and the value was high for R-alanine.The alanine carbo xyl and amino groups contact the oppositely charged residue's cation and anion for the electron transfer.The bond angles of the substitute alanine were well correlated with mutant reactivity.The bond angle, therefore, can be used for quantitative analysis of the reactivity [11].The observation was applied to analy ze the racemization mechanis m o f serine racemaze.
Metals often function as efficient and select ive promoters of catalysis.Why does this enzyme require manganese as an essential element?Does it functions to maintain a suitable stereo structure or is directly involved in the reaction?Another side of PLP is the oxidation reaction center with the K56 amino group.Manganese forms a complex using the hydroxy l group as a ligand [14].The possible conformat ion indicates that the hydroxyl group of serine may indeed contribute as a ligand.Serine was non-enzy matically o xidized to pyruvate at the sites where metal ions exist.Ho wever, the metal ion is located near the PLPcarbonyl group according to the schematic exp lanation.Manganese is located at the site opposite to the oxidation reaction center in the en zy matic react ion.Fu rthermore, the catalytic activity of manganese is weak co mpared to alu minu m, copper, and iron, where the metals are involved in the deamination of serine, but not racemizat ion [15].Manganese forms mu lti-ligands with water mo lecule [16][17][18].Therefore, the manganese site may not be the oxidation reaction center in the enzymatic reaction; the stereo structure was then optimized using the MM calculations.The structure change in serine was measured as with the case of alanine in an alanine racemase [11].Alanine was used as a blank substrate.
Therefore, serine and alanine were located between manganese and PLP phosphate in h3hmk to study the contribution of manganese.The ato mic d istance between manganese and phosphine was 9.1Å for both 3h mk and h3h mk.The atomic distance was a little longer for the mutants, 9.4 Å for S84D and 9.7 Å for S84A, S84N, and S84T.The hydroxyl group of serine may conjugate with manganese as a ligand, but such a phenomenon should not be expected in the case of alanine.The amino group of serine and alanine should face the PLP phosphate; then, the complexes were optimized.After optimization S-serine became flat, and the total angle increased fro m 328.3 to 341.87° at site B. However, the angle was changed a little for S-alanine.The conformat ion is such that the amino acid amino group is held by the PLP phosphate, and the carboxyl group of alanine faced manganese, while the hydroxy l group of serine faced the metal.When the carbo xyl group of serine faced the phosphate, and the amino group is faced the metal, the change in angle was only 1.9°.The angle change in the case of S-alanine was -0.1°.The changes in angle for R-serine and R-alanine were 11.9 and 9.5°.Since serine became flat at site A. However, the o xidation changes serine to pyruvate at site A. If serine racemase handles both reactions simultaneously, racemization may occur at site B where the flatness of serine is high compared to that of alanine.

IV.
CONCLUSION Deprotonation of the C and the formation of imine are the basic mechanis ms underlying racemase reactivity.The serine carboxyl and amino groups contact the oppositely charged cation and anion of the residue for electrontransfer.The bond angles of the serine substitute indicated the location of o xidation and racemization.The bond angle, therefore, can be used for the quantitative analysis of racemization.The substrate serine formed a complexwith PLP.Calcu lations were performed without considering the solvent (water).The results may notdirectly compare with those in vivo.The Lewis acidbase interaction is the strongest; however, because water mo lecules cannot interrupt this interaction, they may function as a bridge to fill the gap.Here, we performed aquantitative analysis of the selective reactivity o f serine racemase.The S-form of serine was more stable in complexes containing this enzyme due to the favorability of the enzyme structure.The probability depends on the reality of the stereo structure.The apc values among the mutants were small, and the downloaded stereo structures lacked several amino acid residues; therefore, the selectivity could not be justified without their amino acid sequence data.

Fig. 1 .
Fig. 1.Conformation of selected molecules in mammalian serine racemase h3hmk.Black color balls: oxygen or phosphine, gray color balls: nitrogen, white color large and small balls: carbon and hydrogen.Indicated atomic distance: Å.

Fig. 2 .
Fig. 2. A and B are conformation of selected molecules in mammalian serine racemase 3l6b and 3l6r.Symbols: see Figure 1.

Table . 1
: Observed and change of dihedral angle (DA/ DA) and atomic partial charge (apc) oxidation reaction site; site B: manganese-phosphate site.Site B # : Serine carboxyl and ammonium groups contacted with manganese and phosphate, respectively.