Lac repressor morph methods: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) →Linear Interpolation: polishing |
Eric Martz (talk | contribs) →Hydrogen Bonds: polishing |
||
| Line 20: | Line 20: | ||
===Hydrogen Bonds=== | ===Hydrogen Bonds=== | ||
There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be engaged in hydrogen bonding by inspection | There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be engaged in hydrogen bonding by inspection. | ||
===Salt Bridges=== | |||
In the nonspecific interaction, Kalodimos et al. report salt bridges to the DNA backbone phosphates involving Arg22, Arg35, Lys33, Lys37, and His29. In model 9 of 1OSL, the only two of these I could see were Arg22B.NH1 3.0 Å from A3D.O2P, and His29B.ND1 2.8 Å from G2D.O2P. Therefore I did not make an animation showing the nonspecific salt bridges. Presumably the salt bridges are more prominent in NMR models other than 9, but I did not explore this. | In the nonspecific interaction, Kalodimos et al. report salt bridges to the DNA backbone phosphates involving Arg22, Arg35, Lys33, Lys37, and His29. In model 9 of 1OSL, the only two of these I could see were Arg22B.NH1 3.0 Å from A3D.O2P, and His29B.ND1 2.8 Å from G2D.O2P. Therefore I did not make an animation showing the nonspecific salt bridges. Presumably the salt bridges are more prominent in NMR models other than 9, but I did not explore this. | ||
