UGT 2B7 enzyme-cofactor complex UGT2B7 vs. SULT1A1 substrate classification

2C1X (template) - UDPProfile alignment (FORTE) Model buildingModeller Inserting cofactor & Protein minimization (near cofactor) Why? Protein 의 rotatable side chain 이 cofactor 자리를 침범, 기타 … his 회전, hydrogen bond… Validation 1.Superimpose with 2C1X (template) 1.Checking gaps 2.Whole structure (RMSD) 3.PDF score peak 2.RMSD to 2O6L (Crystal Structure of the UDP-Glucuronic Acid Binding Domain of UDP-Glucuronosyltransferase 2B7) – partial structure Validation 1.Cofactor docking (rigid protein, rigid cofactor condition to consider the pocket availability only) 2.Comparison to initial position 3.Retains same position & structure in the result

Cofactor minimization in the protein with or without constraints on glucuronic acid group Validation 1.PROCHECK (Ramachandran plot) 2.Profile-3D score graph 3.(ProStat?) 4.Manual inspection with 2C1Z (almost similar to template) - UDP-2FGlc plus kaempferol 5.& other homologue UDP-glucuronic acid or UDP-glucose binding PDB structures (2ACW, 2VCE, 2PQ6, 1IIR, 2IYF, 2IYA, 2P6P, (2JJM?)) Validation again (if needed) 1.PROCHECK (Ramachandran plot) 2.Profile-3D score graph 3.(ProStat?) UGT + Cofactor Minimization Reliable UGT structure model with cofactor MD with explicit solvent model 1.Time(ps) to RMDS graph -> checking structure stabilization 2.Table of the total energy, van-der-Waals energy and electrostatic energy between cofactor and individual residues Substrate Docking Autodock and/or DS OR

KISTI supercomputer 슈퍼컴퓨터 사용 약정서 연구계획서 ( 상세하게 ) 학생증복사본 ( 양면 ) 사용금액 입금 –SRU(System Resource Unit) 도수요금제 – 학생회원 1 구좌 : 100 SRU time(10 만원 )

벡터컴퓨터 NEC MPP 컴퓨터 IBM p690 MPP 컴퓨터 IBM p595 Hamel (Cluster)

Gaussian(03) NAMD(V2.5) GROMAX(V3.1.4) AMBER(V7.0) SuperCHARMM(c32b1) InsightII(2000L)

나철희, 김고은 – 김두남 선배의 supercomputer account 사용 –Professor Akiyama’s supercomputer 김두남 – 슈퍼컴 유료 사용 – 병렬 컴퓨터 “ 무료 ” 사용 5 년 전 이상주 박사님 소개 KISTI 슈퍼컴퓨팅센터 기반기술개발실 이상주 슈퍼컴퓨팅 기반 가상세포 응용시스템 개발 김두남 : “ 이젠 센터장정도 되는 분인데 대학 원생이 요청하긴 좀 곤란하지 않겠는가 ?"

CHRAMm Molecular Dynamics Trials of computing hours Standard dynamics cascade –~39h, Halted to upgrade hard disk storage –100ps + α –Heating, Equilibration, Production Stopped here

Time estimation ~ 1ns production –370~390 h

Running MD Heating –2fs time step –300K –100ps –Save result each 1ps

Equilibration –2fs time step –40ps –300K –Save result each 1ps –Constant pressure condition

Production –2fs time step –1ns –300K –Save result each 1ps –NVT: Constant temperature dynamics using Berendsen weak coupling method –Nonbond List Radius 14A –Particle Mesh Ewald (PME) –Leapfrog Verlet Integrator (LEAP): the atom velocities and positions are calculated at time points that differ by a half time step. –SHAKE constraint