Theoretical Analysis of Oxygen Diffusion in the Micro-channels of Quinoline Oxygenase†

doi:10.7503/cjcu20170202

Abstract

Abstract:

Oxygen diffusion pathways of quinoline oxygenase(HOD) were investigated by bioinformatics analysis, quantum chemical optimization, CAVER and MD pocket prediction, random accelerated molecular dynamics simulations and umbrella sampling. The results show that the pre-reaction site of oxygen does locate inside the active pocket, and there exists several possible oxygen tunnels in HOD, in which the one with shortest length has the highest priority. Random accelerated molecular dynamics proved that oxygen has the highest probability to exit from this tunnel, and umbrella sampling further verified its free energy for oxygen passing by is the lowest. The tunnel ended at the binding site of oxygen located on the Re-face of the substrate, which is consistent with previous studies. These results better illuminate the kinetics and the stereo-selectivity of the catalytic reaction in HOD, and also provide theoretical guidance to further experimentally improve the efficiency of oxygen usage by enzyme.

Key words: Quinoline oxygenase, Oxygendiffusion, Random accelerated molecular dynamics, Umbrella sampling

CLC Number:

O641

TrendMD:

ZHOU Chao, SHI Ting, ZHAO Yilei, WANG Xiaolei. Theoretical Analysis of Oxygen Diffusion in the Micro-channels of Quinoline Oxygenase^†[J]. Chem. J. Chinese Universities, 2017, 38(10): 1813.

Figures/Tables 11

Scheme 1 Degradation reaction catalyzed by HOD and its analogue enzymes, QDO and QD(A) and catalytic cycle of HOD(B)

Fig.1 Location of Cl- in the crystal structure of HODCl- is buried deeper inside the active pocket, beneath the substrate QND, which is also the putative binding site of O2. Re face and Si face of QND are labelled according to the carbonyl group.

Fig.2 Sequence alignment of HOD, QDO and QD

Fig.3 Proportion of the two pre-reaction oxygen orientations(red and purple) in total 26 optimizations(A) and their 3D structure in the active site of HOD(B)

Fig.4 25 Tunnels predicted by CAVER(A) and top 5 tunnels in rank score(B)

Table 1 25 Predicted oxygen tunnels and their bottleneck radius, length, curvature and priority

ID	Bottleneck radius/nm	Length/nm	Curvature	Priority	ID	Bottleneck radius/nm	Length/nm	Curvature	Priority
1	0.095	1.674	1.38	0.42	14	0.074	3.365	1.35	0.07
2	0.070	2.213	1.52	0.30	15	0.077	4.507	3.28	0.06
3	0.079	2.624	1.34	0.18	16	0.061	3.293	2.09	0.06
4	0.070	2.419	1.36	0.14	17	0.067	3.664	1.52	0.05
5	0.064	2.705	1.56	0.14	18	0.066	3.852	2.32	0.05
6	0.062	2.054	1.70	0.13	19	0.063	3.437	2.21	0.05
7	0.077	3.221	1.42	0.13	20	0.064	3.517	2.30	0.05
8	0.074	2.875	1.41	0.12	21	0.064	4.117	1.73	0.04
9	0.077	3.380	3.34	0.12	22	0.062	3.565	2.22	0.04
10	0.064	2.353	1.31	0.12	23	0.064	3.962	1.58	0.04
11	0.064	2.712	1.38	0.11	24	0.061	4.564	2.44	0.04
12	0.064	2.524	1.55	0.09	25	0.064	4.137	1.86	0.02
13	0.066	2.970	1.73	0.09

Fig.5 4 Pockets in HOD predicted by MDpocket(A) and the positional relationship between tunnel 1 and pocket 2(B)

Fig.6 Active site in pocket 1(A), amino acid compositions of pocket 2(B), pocket 3(C) and pocket 4(D)

Table 2 Results of the RAMD simulation

Tunnel	Time step			Sum
Tunnel	10	30	50	Sum
1	9	8	11	28
2	2	1	0	3
3	1	2	0	3
4	1	1	0	2
5	1	3	0	4
8	5	4	1	10
Others	1	1	8	10
Sum	20	20	20	60

Fig.7 Sampling distribution of the three tunnels along the reaction coordinate(A) Tunnel 1; (B) tunnel 2; (C) tunnel 8.

Fig.8 Potential mean force calculated by WHAM program

References 37

[1]	Wang L., Li Y., Yang D., Process Biochem., 2010, 45(6), 919—928
[2]	Neuwoehner J., Reineke A. K., Hollender J., Eisentraeger A., Ecotoxicol. Environ. Saf., 2009, 72(3), 819—827
[3]	Sideropoulos A. S., Specht S. M., Curr. Microbiol., 1984, 11(2), 59—65
[4]	Hirao K., Shinohara Y., Tsuda H., Fukushima S., Takahashi M., Cancer Res., 1976, 36(2 Part 1), 329—335
[5]	Betz A., Facey S. J., Hauer B., Tshisuaka B., Lingens F., J. Basic Microbiol., 2000, 40(1), 7—23
[6]	Fetzner S., Tshisuaka B., Lingens F., Kappl R., Hüttermann J., Angew. Chem., Int. Ed., 1998, 37(5), 576—597
[7]	Hernandez-Ortega A., Quesne M. G., Bui S., Heuts D. P., Steiner R. A., Heyes D. J., de Visser S. P., Scrutton N. S., J. Biol. Chem., 2014, 289(12), 8620—8632
[8]	Steiner R. A., Janssen H. J., Roversi P., Oakley A. J., Fetzner S., Proc. Natl. Acad. Sci., 2010, 107(2), 657—662
[9]	Fischer F., Künne S., Fetzner S., J. Bacteriol., 1999, 181(18), 5725—5733
[10]	Baas B. J., Poddar H., Geertsema E. M., Rozeboom H. J., de Vries M. P., Permentier H. P., Thunnissen A. M., Poelarends G. J., Biochemistry,2015, 54(5), 1219—1232
[11]	Fetzner S., Steiner R. A., Appl. Microbiol. Biotechnol., 2010, 86(3), 791—804
[12]	Frerichs-Deeken U., Fetzner S., Curr. Biol., 2005, 51(5), 344—352
[13]	Calhoun D. B., Vanderkooi J. M., Englander S. W., Biochemistry,1983, 22(7), 1533—1539
[14]	Oliveira A. S. F., Damas J. M., Baptista A. M., Soares C. M., PLoS Comput. Biol., 2014, 10(12), e1004010
[15]	Shadrina M. S., English A. M., Peslherbe G. H., J. Am. Chem. Soc., 2012, 134(27), 11177—11184
[16]	Saam J., Rosini E., Molla G., Schulten K., Pollegioni L., Ghisla S., J. Biol. Chem., 2010, 285(32), 24439—24446
[17]	Baron R., Riley C., Chenprakhon P., Thotsaporn K., Winter R. T., Alfieri A., Forneris F., van Berkel W. J., Chaiyen P., Fraaije M. W., Mattevi A., McCammon J. A., Proc. Natl. Acad. Sci., 2009, 106(26), 10603—10608
[18]	Saam J., Ivanov I., Walther M., Holzhütter H. G., Kuhn H., Proc. Natl. Acad. Sci., 2007, 104(33), 13319—13324
[19]	Klinman J. P., Acc. Chem. Res., 2007, 40(5), 325—333
[20]	Cohen J., Schulten K., Biophys. J., 2007, 93(10), 3591—3600
[21]	Pesce A., Nardini M., LaBarre M., Richard C., Wittenberg J. B., Wittenberg B. A., Guertin M., Bolognesi M., BBA-Proteins and Proteomics., 2011, 1814(6), 810—816
[22]	Milani M., Pesce A., Ouellet Y., Dewilde S., Friedman J., Ascenzi P., Guertin M., Bolognesi M., J. Biol. Chem., 2004, 279(20), 21520—21525
[23]	Colloc’h N., Gabison L., Monard G., Altarsha M., Chiadmi M., Marassio G., Sopkova-de O. S. J., El H. M., Castro B., Abraini J. H., Prangé T., Biophys. J., 2008, 95(5), 2415—2422
[24]	Boechi L., Arrar M., Martí M. A., Olson J. S., Roitberg A. E., Estrin D. A., J. Biol. Chem., 2013, 288(9), 6754—6762
[25]	Vassiliev S., Zaraiskaya T., Bruce D., BBA-Bioenergetics., 2013, 1827(10), 1148—1155
[26]	Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Mennucci B., Petersson G. A., Nakatsuji H., Caricato M., Li X., Hratchian H. P., Izmaylov A. F., Bloino J., Zheng G., Sonnenberg J. L., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Montgomery J. A. Jr., Peralta J. E., Ogliaro F., Bearpark M., Heyd J. J., Brothers E., Kudin K. N., Staroverov V. N., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J. C., Iyengar S. S., Tomasi J., Cossi M., Rega N., Millam N. J., Klene M., Knox J. E., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Martin R. L., Morokuma K., Zakrzewski V. G., Voth G. A., Salvador P., Dannenberg J. J., Dapprich S., Daniels A. D., Farkas Ö., Foresman J. B., Ortiz J. V., Cioslowski J., Fox D. J., Gaussian 09, Revision A. 1, Gaussian Inc.,Wallingford CT, 2009
[27]	Chovancova E., Pavelka A., Benes P., Strnad O., Brezovsky J., Kozlikova B., Gora A., Sustr V., Klvana M., Medek P., Biedermannova L., Sochor J., Damborsky J., PLoS Comput. Biol., 2012, 8(10), e1002708
[28]	Schmidtke P., Bidon-Chanal A., Luque F. J., Barril X., Bioinformatics,2011, 27(23), 3276—3285
[29]	Durrant J. D., Votapka L., Sørensen J., Amaro R. E., J. Chem. Theory Comput., 2014, 10(11), 5047—5056
[30]	Hamelberg D., Mongan J., McCammon J. A., J. Chem. Phys., 2004, 120(24), 11919—11929
[31]	Burendahl S., Danciulescu C., Nilsson L., Proteins: Struct., Funct., Bioinf., 2009, 77(4), 842—856
[32]	Vashisth H., Abrams C. F., Biophys. J., 2008, 95(9), 4193—4204
[33]	Schleinkofer K., Sudarko Winn P. J., Lüdemann S. K., Wade R. C., EMBO Rep., 2005, 6(6), 584—589
[34]	Case D. A., Darden T. A., Cheatham III T. E., Simmerling C. L., Wang J., Duke R. E., Luo R., Walker R. C., Zhang W., Merz K. M., Roberts B., Hayik S., Roitberg A., Seabra G., Swails J., Götz A. W., Kolossváry I., Wong K. F., Paesani F., Vanicek J., Wolf R. M., Liu J., Wu X., Brozell S. R., Steinbrecher T., Gohlke H., Cai Q., Ye X., Wang J., Hsieh M. J., Cui G., Roe D. R., Mathews D. H., Seetin M. G., Salomon-Ferrer R., Sagui C., Babin V., Luchko T., Gusarov S., Kovalenko A., Kollman P. A., AMBER 12, University of California, San Francisco, 2012
[35]	Phillips J. C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kale L., Schulten K., J. Comput. Chem., 2005, 26, 1781—1802
[36]	Grossfield A., WHAM: the Weighted Histogram Analysis Method, Version 2.0.9,
[37]	Pap J. S., Matuz A., Baráth G., Kripli B., Giorgi M., Speier G., Kaizer J., J. Inorg. Biochem., 2012, 108, 15—21