BioMed Research International

Research Article

Predicting Protein Interactions by Brownian Dynamics Simulations

Table 1

Summary of redocking results.


Complex PDB	Res (Å)	Receptorname	Ligandname	Docking results		Crystal structures
Complex PDB	Res (Å)	Receptorname	Ligandname	RMSD^a (Å)	Interaction energy (kcal mol⁻¹)	RMSD (Å)	Interaction energy (kcal mol⁻¹)	Sequence number/total number^b

Protease-inhibitor
1CA0	2.10	Chymotrypsin	APPI	1.27	−93.70	0.84	−93.22	116522/492124
1CBW	2.60	Chymotrypsin	BPTI	0.54	−83.51	0.19	−85.02	171485/456398
1ACB	2.00	Chymotrypsin	Eglin C	1.00	−103.41	0.70	−103.49	382613/513612
1CHO	1.80	Chymotrypsin	Ovonmuciod	0.30	−102.35	0.38	−102.42	302176/406978
1CGI	2.30	Chymotrypsinogen	HPTI	0.18	−147.17	0.15	−147.10	34660/494274
2KAI	2.50	Kallikrein A	BPTI	1.10	−114.68	0.21	−113.85	422991/576133
2SNI	2.10	Subtilisin BPN	CI-2	0.27	−108.81	0.28	−108.86	232574/428140
2SIC	1.80	Subtilisin BPN	SSI	0.89	−94.41	0.20	−104.20	109196/440000
1CSE	1.20	Subtilisin Carlsberg	Eglin C	1.24	−98.28	0.088	−103.19	284340/470409
2TEC	1.98	Thermitase	Eglin C	0.44	−108.55	0.68	−109.99	341844/565586
1TAW	1.80	Trypsin (bovine)	APPI	1.10	−97.13	0.86	−97.14	374416/448887
2PTC	1.90	Trypsin (bovine)	BPTI	0.98	−96.22	0.36	−96.25	269684/377757
3TGI	1.80	Trypsin (rat)	BPTI	0.39	−102.43	0.52	−102.44	232589/511269
1BRC	2.50	Trypsin (rat)	APPI	1.43	−90.55	0.55	−90.04	120053/527160

Enzyme-inhibitor
1FSS	3.00	Acetylcholinesterase	Fasciculin II	0.17	−137.88	0.20	−137.88	356416/364018
1BVN	2.50	α-Amylase	Tendamistat	0.25	−142.67	0.24	−142.51	202279/297696
1BGS	2.60	Barnase	Barstar	0.48	−112.46	0.57	−112.37	326865/408756
1AY7	1.70	Ribonuclease sa	Barstar	0.49	−77.41	0.51	−77.37	9999/356359
2B5R	1.70	TEM-1 lactamase	BLIP	0.78	−154.04	0.37	−158.39	369/464219
1UGH	1.90	UDG	UGI	0.54	−135.58	0.51	−135.43	120973/427026

Electron transport
2PCB^c	2.80	Cyt c Peroxidase	Cytochrome c	1.98	−87.18	0.22	−81.79	6060/416861
2PCF	NMR	Cytochrome f	Plastocyanin	0.28	−118.96	0.23	−119.32	83197/208700

Antibody-antigen
1MLC	2.10	Fab D44.1	Lysozyme	1.59	−93.99	0.44	−95.80	75843/344243
1VFB^d	1.80	Fv D1.3	Lysozyme	0.53	−84.78	0.43	−84.59	517225/1195007

^aRMSDs are calculated for the atoms of the ligand protein since the receptor proteins are always fixed during the simulations. ^bSequence number denotes which sequence is the predicted conformation belonging to the BD sampling. Each conformation has unique sequence number as a label. Total number denotes how many compact complexes were obtained. From this column one can see where the final predicted complex(es) come from and how many compact complexes can be obtained from one million BD runs. These data are collected to demonstrate the necessary and sufficient condition for one million BD runs. ^cThe conformation presented here is the 9th conformation by energy ranking. The top 8 conformations are regarded as one cluster RMSD around 30 Å from the crystal structure (see Section 4). ^dThree million BD runs were conducted for this complex. Usually one million is enough for most complexes; however, due to the positive electrostatics 1.61 kcal mol⁻¹ for this complex, the sampled near-native conformation appeared at around 1.4 million runs.