Prediction of tRNA secondary structure

"einverted"

with defaults didn't show any inverted patterns, so it was decided to run a program with gap penalty [4] and Minimum score threshold [10]. That run showed one inverted pattern, presented below.

SEQUENCE: Score 21: 7/7 (100%) matches, 0 gaps
       1 cggggag 7       
         |||||||
      73 gcccctc 67 
     

Zuker algorithm

Predicted structure

Stem	find_pair results	einverted results	RNAfold results
Acceptor stem	5'-4-7-3' 5'-66-69-3' 4 pairs	5'-1-7-3' 5'-66-72-3' 7 pairs	5'-1-7-3' 5'-66-72-3' 7 pairs
T-stem	5'-49-53-3' 5'-61-65-3' 5 pairs	-	5'-49-53-3' 5'-61-65-3' 4 pairs
Anticodon stem	5'-26-32-3' 5'-38-44-3' 7 pairs	-	5'-27-33-3' 5'-37-43-3' 7 pairs
D-stem	5'-10-13-3' 5'-23-26-3' 4 pairs	-	5'-10-13-3' 5'-23-26-3' 4 pairs
Amount of Watson-Crick base pairs	19	7 pairs	22 pairs

Here we can see that real secondary structure is quite similar to the RNAfold result.

DNA-protein contacts

Jmol commands for definition atom groups are presented below.
define set1 (:D.O4' or :D.O3' or :D.O5' or :C.O4' or :C.O3' or :C.O5')
define set2 (:C.OP2, :C.OP1, :D.OP2, :D.OP1)
define set3 nitrogen and dna

script1

script2

Different types of contacts in 1mhd.pdb complex

Contacts with:	Polar	Nonpolar	Total
2'-deoxyribose residues	1 contacts	9 contacts	10 contacts
phosphoric acid residues	9 contacts	2 contacts	11 contacts
nitrogenous bases residues (major groove)	8 contacts	6 contacts	14 contacts
nitrogenous bases residues (minor groove)	0 contacts	0 contacts	0 contacts

Here we can see that the highest number of contacts is shown for contacts with nitrogenous bases residues in the major groove. It must be caused by the large size of nitrogenous bases and it's big potential to form contacts due to their electrochemical structure.

nucplot

nucplot output

The output shows that the residues with the highest number of contacts(3) are Lys81A and Lys81B. So those residues must be the most important for identification. (If point mutation will suddenly happens, the conformation change will be more critical)

Aminoacid residues Lys81A and Lys81B and their iteractions with DNA

Aminoacid residues Lys81A and Lys81B and their iteractions with DNA

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© Gumerov Ruslan, 2017