Unraveling the degradation of artificial amide bonds in Nylon oligomer hydrolase: From induced-fit to acylation processes

Transcription

1 Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2015 Supporting Information for Unraveling the degradation of artificial amide bonds in Nylon oligomer hydrolase: From induced-fit to acylation processes Takeshi Baba a, b, Mauro Boero c, Katsumasa Kamiya d, Hiroyuki Ando a, Seiji Negoro e, Masayoshi Nakano a, Yasuteru Shigeta f, g a Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka , Japan. b Japan Society for the Promotion of Science (JSPS) Research Fellow. c Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, Strasbourg 23 rue du Loess, Strasbourg, France. d Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology, 1030 Shimo-Ogino, Atsugi, Kanagawa , Japan. e Department of Material Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo , Japan. f Department of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki , Japan. g JST, CREST, Honcho, Kawaguchi, Saitama , Japan.

2 SI-1 details of the QM region Details concerning the QM region of the enzyme and its boundaries are reported in Table S1. A total number of 17 monovalent hydrogen-like link atoms were used to compensate the dangling bonds at the frontier between the QM and the MM subsystems. These boundaries, cutting across chemical bond, are listed in Table S1. C and N are in all cases carbonyl carbon atoms and amide nitrogen atoms, respectively. The QM region of Ald contains atoms within two carbon and hydrogen pairs from carbonyl carbon or nitrogen atom of the amide bond. Table S1 details of the QM region Amino acid residue True bond Atom1(QM)-Atom2(MM) QM/MM border Atom1-H(cap)-Atom2 MET111 H N H N SER112 C H C LYS115 H GLU168 H TYR170 H TYR215 H SER217 N C H N H C GLN266 N H N H GLY267 C H C GLY344 N H N ILE345 C H H C

3 SI-2 Details about the parameters used in QM/MM metadynamics simulations In the practical use the extended Lagrangean for our specific simulations, (2) the single collective variable (CV) s ( = 1) evolves according to a fictitious dynamics in which the mass M and spring constant k are set to 20 a.u. and 0.24 a.u., respectively. These parameters to ensure a good control of the conserved quantities along at least for the simulation times investigated in the present work 1,2. The history dependent potential V t, s was constructed by accumulation of small Gaussian with a height of 0.5 kcal/mol and a width of 0.3 au and a new Gaussian function was added every 140 steps (13.44 fs). After the reaction occurred, and to speed up the simulations, after 226 meta-steps, we increased the height W i 1.0 kcal/mol. This does not penalize too much our simulations since, in any case, our accuracy is bound by the typical DFT error 3 bar which is at very best of the order of this order of magnitude. These simulations lasted in any case long enough to reproduce the cleavage of the amide bond.

4 SI-3 Results for the WT system Evolution of the reaction coordinate adopted for the metadynamics and the more relevant distances in case of the WT; r 1 = N3(Ald393)-C1(Ald393) in red, r 2 = OG(Ser112)-C1(Ald393) in green, r 3 = HH(Tyr215)- N3(Ald393) in blue, and r 4 = HG(Ser112)-NZ(Lys115) in magenta. Panel (i) refers to the whole simulation, panel (ii) to the specific region encircled in (i), and (iii) shows the reaction mechanism of WT going from (a) to (f). (iv) is described Free-energy surface as a function of the Ser112-O Ald-C and the Ald-N Ald-C distances based on Ref 4. The free energy value of γ between (a) and (c), between (b) and (c) are ~35 kcal/mol and ~21 kcal/mol, respectively. (i) (ii) (iii) (a) Tyr170 Tyr215 (b) Tyr170 Tyr215 O H R ' H N O H R C Lys115 :N H 2 H O O H H N R ' O H R C Lys115 :NH 2 H O Ile345 NH O NH Ser112 Ile345 NH O NH Ser112 (c) Tyr170 Tyr215 (d) Tyr170 Tyr215 Ile345 O H H N R ' NH O H R C O Lys115 :NH 2 H + O Ser112 NH Ile345 R ' O H H NH : N O H C R O - O H NH Lys115 N + H 2 Ser112 (e) Tyr170 Tyr215 (f) Tyr170 Tyr215 Ile345 O H H N R ' NH H C R O - O O H NH Lys115 N + H 2 Ser112 Ile345 O H H N R ' NH H C O R O O NH H Lys115 N + H 2 Ser112

5 (iv)

6 SI-4 Free energy profile based on QM/MM CPMD complemented with metadynamics In the present study, free energy differences have to be intended as approximate estimates based on the comparison of the maxima for the acylation of the two systems WT and Y170F. As explained in the main text, we followed the simulation until the first reaction occurs. Because of the specific choice of collective variable, the system is unable to realize the reverse reaction thus our estimations are more to be intended as an upper bound reflecting the behavior of WT and Y170F, which in any case are clearly different. SI-5 Metastable state from Open form to Close form of Y170F Monitored distances and related free energy differences for the four minima of the free energy surface of Y170F reported and discussed in the main text. Table S2. Information of meta-stable states State d a 1 d a 2 Difference of Free energy b A B C D a in Å. b in kcal/mol.

7 SI-6 IFIE DATA IFIE values between all the amino acid residues and the substrate WT ALD(1) a ALD(2) a ALD(3) a MET ASN ALA ARG SER THR GLY GLN HIS PRO ALA ARG TYR PRO GLY ALA ALA ALA GLY GLU PRO THR LEU ASP SER TRP GLN GLU PRO PRO

8 HIS ASN ARG TRP ALA PHE ALA HIS LEU GLY GLU MET VAL PRO SER ALA ALA VAL SER ARG ARG PRO VAL ASN ALA PRO GLY HIS ALA LEU ALA ARG LEU GLY ALA

9 ILE ALA ALA GLN LEU PRO ASP LEU GLU GLN ARG LEU GLU GLN THR TYR THR ASP ALA PHE LEU VAL LEU ARG GLY THR GLU VAL VAL ALA GLU TYR TYR ARG ALA

10 GLY PHE ALA PRO ASP ASP ARG HIS LEU LEU MET SER VAL SER LYN SER LEU CYS GLY THR VAL VAL GLY ALA LEU VAL ASP GLU GLY ARG ILE ASP PRO ALA GLN

11 PRO VAL THR GLU TYR VAL PRO GLU LEU ALA GLY SER VAL TYR ASP GLY PRO SER VAL LEU GLN VAL LEU ASP MET GLN ILE SER ILE ASP TYR ASN GLU ASP TYR

12 VAL ASP PRO ALA SER GLU VAL GLN THR HIS ASP ARG SER ALA GLY TRP ARG THR ARG ARG HIS GLY ASP PRO ALA ASP THR TYR GLU PHE LEU THR THR LEU ARG

13 GLY ASP GLY SER THR GLY GLU PHE GLN TYR CYS SER ALA ASN THR ASP VAL LEU ALA TRP ILE VAL GLU ARG VAL THR GLY LEU ARG TYR VAL GLU ALA LEU SER

14 THR TYR LEU TRP ALA LYS LEU ASP ALA ASP ARG ASP ALA THR ILE THR VAL ASP THR THR GLY PHE GLY PHE ALA ASN GLY GLY VAL SER CYS THR ALA ARG ASP

15 LEU ALA ARG VAL GLY ARG MET MET LEU ASP GLY GLY VAL ALA PRO GLY GLY ARG VAL VAL SER GLU ASP TRP VAL ARG ARG VAL LEU ALA GLY GLY SER HIS GLU

16 ALA MET THR ASP LYS GLY PHE THR ASN THR PHE PRO ASP GLY SER TYR THR ARG GLN TRP TRP CYS THR GLY ASN GLU ARG GLY ASN VAL SER GLY ILE GLY ILE

17 HIS GLY GLN ASN LEU TRP LEU ASP PRO LEU THR ASP SER VAL ILE VAL LYS LEU SER SER TRP PRO ASP PRO TYR THR GLU HIS TRP HIS ARG LEU GLN ASN GLY

18 ILE LEU LEU ASP VAL SER ARG ALA LEU ASP ALA VAL a unit of kcal / mol Y170F ALD(1) a ALD(2) a ALD(3) a MET ASN ALA ARG SER THR GLY GLN HIS PRO ALA ARG TYR PRO GLY ALA ALA ALA GLY

19 GLU PRO THR LEU ASP SER TRP GLN GLU PRO PRO HIS ASN ARG TRP ALA PHE ALA HIS LEU GLY GLU MET VAL PRO SER ALA ALA VAL SER ARG ARG PRO VAL ASN

20 ALA PRO GLY HIS ALA LEU ALA ARG LEU GLY ALA ILE ALA ALA GLN LEU PRO ASP LEU GLU GLN ARG LEU GLU GLN THR TYR THR ASP ALA PHE LEU VAL LEU ARG

21 GLY THR GLU VAL VAL ALA GLU TYR TYR ARG ALA GLY PHE ALA PRO ASP ASP ARG HIS LEU LEU MET SER VAL SER LYN SER LEU CYS GLY THR VAL VAL GLY ALA

22 LEU VAL ASP GLU GLY ARG ILE ASP PRO ALA GLN PRO VAL THR GLU TYR VAL PRO GLU LEU ALA GLY SER VAL TYR ASP GLY PRO SER VAL LEU GLN VAL LEU ASP

23 MET GLN ILE SER ILE ASP TYR ASN GLU ASP PHE VAL ASP PRO ALA SER GLU VAL GLN THR HIS ASP ARG SER ALA GLY TRP ARG THR ARG ARG HIS GLY ASP PRO

24 ALA ASP THR TYR GLU PHE LEU THR THR LEU ARG GLY ASP GLY SER THR GLY GLU PHE GLN TYR CYS SER ALA ASN THR ASP VAL LEU ALA TRP ILE VAL GLU ARG

25 VAL THR GLY LEU ARG TYR VAL GLU ALA LEU SER THR TYR LEU TRP ALA LYS LEU ASP ALA ASP ARG ASP ALA THR ILE THR VAL ASP THR THR GLY PHE GLY PHE

26 ALA ASN GLY GLY VAL SER CYS THR ALA ARG ASP LEU ALA ARG VAL GLY ARG MET MET LEU ASP GLY GLY VAL ALA PRO GLY GLY ARG VAL VAL SER GLU ASP TRP

27 VAL ARG ARG VAL LEU ALA GLY GLY SER HIS GLU ALA MET THR ASP LYS GLY PHE THR ASN THR PHE PRO ASP GLY SER TYR THR ARG GLN TRP TRP CYS THR GLY

28 ASN GLU ARG GLY ASN VAL SER GLY ILE GLY ILE HIS GLY GLN ASN LEU TRP LEU ASP PRO LEU THR ASP SER VAL ILE VAL LYS LEU SER SER TRP PRO ASP PRO

29 TYR THR GLU HIS TRP HIS ARG LEU GLN ASN GLY ILE LEU LEU ASP VAL SER ARG ALA LEU ASP ALA VAL a unit of kcal / mol Hyb-24 ALD(1) a ALD(2) a ALD(3) a MET ASN ALA ARG SER THR GLY GLN

30 HIS PRO ALA ARG TYR PRO GLY ALA ALA ALA GLY GLU PRO THR LEU ASP SER TRP GLN GLU PRO PRO HIS ASN ARG TRP ALA PHE ALA HIS LEU GLY GLU MET VAL

31 PRO SER ALA ALA VAL SER ARG ARG PRO VAL ASN ALA PRO GLY HIS ALA LEU ALA ARG LEU GLY ALA ILE ALA ALA GLN LEU PRO ASP LEU GLU GLN ARG LEU GLU

32 GLN THR TYR THR ASP ALA PHE LEU VAL LEU ARG GLY THR GLU VAL VAL ALA GLU TYR TYR ARG ALA GLY PHE ALA PRO ASP ASP ARG HIS LEU LEU MET SER VAL

33 SER LYN SER LEU CYS GLY THR VAL VAL GLY ALA LEU VAL ASP GLU GLY ARG ILE ASP PRO ALA GLN PRO VAL THR GLU TYR VAL PRO GLU LEU ALA GLY SER VAL

34 TYR ASP GLY PRO SER VAL LEU GLN VAL LEU ASP MET GLN ILE SER ILE ASP TYR ASN GLU ASP TYR VAL ASP PRO ALA SER GLU VAL GLN THR HIS GLY ARG SER

35 ALA GLY TRP ARG THR ARG ARG HIS GLY ASP PRO ALA ASP THR TYR GLU PHE LEU THR THR LEU ARG GLY ASP GLY SER THR GLY GLU PHE GLN TYR CYS SER ALA

36 ASN THR ASP VAL LEU ALA TRP ILE VAL GLU ARG VAL THR GLY LEU ARG TYR VAL GLU ALA LEU SER THR TYR LEU TRP ALA LYS LEU ASP ALA ASP ARG ASP ALA

37 THR ILE THR VAL ASP THR THR GLY PHE GLY PHE ALA HIS GLY GLY VAL SER CYS THR ALA ARG ASP LEU ALA ARG VAL GLY ARG MET MET LEU ASP GLY GLY VAL

38 ALA PRO GLY GLY ARG VAL VAL SER GLU ASP TRP VAL ARG ARG VAL LEU ALA GLY GLY SER HIS GLU ALA MET THR ASP LYS GLY PHE THR ASN THR PHE PRO ASP

39 GLY SER TYR THR ARG GLN TRP TRP CYS THR GLY ASN GLU ARG GLY ASN VAL SER GLY ILE GLY ILE HIS GLY GLN ASN LEU TRP LEU ASP PRO LEU THR ASP SER

40 VAL ILE VAL LYS LEU SER SER TRP PRO ASP PRO ASP THR GLU HIS TRP HIS ARG LEU GLN ASN GLY ILE LEU LEU ASP VAL SER ARG ALA LEU ASP ALA VAL a units of kcal / mol

41 References: [1] A. Laio, A. Rodriguez-Fortea, F. L. Gervasio, M. Ceccarelli, and M. Parrinello, J. Phys. Chem. B 2005, 109, [2] A. Laio and F. L. Gervasio, Rep. Prog. Phys. 2008, 71, [3] B. G. Johnson, P. M. W. Gill, and J. A. Pople, J. Chem. Phys. 1993, 98, ). [4] K. Kamiya, T. Baba, M. Boero, T. Matsui, S. Negoro, and Y. Shigeta, J. Phys. Chem. Lett., 2014, 5, 1210.