Computational biochemistry ferenc Bogár György Ferency

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Two sets of points are given: A = (a₁, a₂,… a_n) and B = (b₁, b₂,… b_n) in 3D. The optimal part set of A(P) and B(Q) (absolute value) are searched. We try to find the optimal rigid body transformations (G_opt) between A(P) and B(Q) sets which gives the minimal distances (D) by the rigid body transformations..

To compare the structures there are some softwares: Dali [2], CE CALCULATOR [3], MATRAS [4], SSAP (CATH) [5], TIP-STRUCTFAST [6], SuperPose [7], VAST [8.] (see Table 7.4.)

If the sequence identity is less than 30%, our modells are unreliable, between 30-60% the modell is reliable, buti t has unreliable regions, at larger than 60% our modell is reliable. We have to be careful if homology modelling is near the binding pocket. Binding pocket is sensitive enough, we have to „positively believe” in our results and handle with critics.

Table 7.3. Some softwares to compare the protein structures

Name of the software	Input	Output
Dali [2]	pdb file/pdb code	structure fitting and alignment
Cath (SSAP) [5]	pdb file/pdb code	structure fitting and pairwise alignment
Ce calculator [3]	pdb file/pdb code	pdb file, structure alignment (Rasmol)
Matras [4]	pdb file/pdb code	structure fitting and pairwise alignment, pairwise 3D alignment
SuperPose [7]	pdb file/pdb code	sequence fitting and alignment (PDB), RMSD

The results of the homology modelling with different servers of BSA (Bovine Serum Albumine) from HSA (Human Serum Albumine) structure) are described in Figure 7.5.-Figure 7.10. As it can be seen the structures are similar after homology modelling but we can find differences int he positions of secondary structure. Table 7.5 includes the frequencies of aminoacids in BSA and HSA for modelling homology modelling. As it can be seen, the frequency of aminoacids is very similar between BSA and HSA.

Table 7.4. The frequency and the number of aminoacids in BSA and HSA

Aminosav	HSA	BSA	Aminosav	HSA	BSA
Alanin (A)	0,103	0,079	Alanin (A)	63	48
Cisztein (C)	0,057	0,058	Cisztein (C)	35	35
Aszparginsav (D)	0,069	0,066	Aszparginsav (D)	36	40
Glutaminsav (E)	0,102	0,097	Glutaminsav (E)	62	59
Fenilalanin (F)	0,057	0,049	Fenilalanin (F)	35	30
Glicin (G)	0,021	0,028	Glicin (G)	13	17
Hisztidin (H)	0,026	0,028	Hisztidin (H)	16	17
Izolucein (I)	0,015	0,025	Izolucein (I)	9	15
Lizin (K)	0,099	0,099	Lizin (K)	60	60
Leucin (L)	0,105	0,107	Leucin (L)	64	65
Metionin (M)	0,011	0,008	Metionin (M)	7	5
Aszpargin (N)	0,028	0,023	Aszpargin (N)	17	14
Prolin (P)	0,039	0,045	Prolin (P)	24	28
Glutamin (G)	0,033	0,033	Glutamin (G)	20	20
Arginin (R)	0,044	0,043	Arginin (R)	27	26
Szerin (S)	0,046	0,053	Szerin (S)	28	32
Treonin (T)	0,048	0,056	Treonin (T)	29	34
Valanin (V)	0,071	0,063	Valanin (V)	43	38
Triptofán (W)	0,003	0,005	Triptofán (W)	2	3
Tirozin (Y)	0,031	,0035	Tirozin (Y)	19	21

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