Sandbox Reserved 1101: Difference between revisions
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Different types of interactions occur between specific residues during the NTD dimerization. Asp40, Lys65, Asp39 and Glu84 residues have been identified as being particularly important. | Different types of interactions occur between specific residues during the NTD dimerization. Asp40, Lys65, Asp39 and Glu84 residues have been identified as being particularly important. | ||
In one side, <scene name='82/829354/Asp40b_glu84b/1'>Asp40 and Glu84 of subunit B</scene> engage in the '''intramolecular handshake interaction'''. The '''asymmetric nature''' and the '''difference of topology''' of the subunits allow the formation of '''salt bridges'''. <scene name='82/829354/Lys_65-asp39_interaction/2'>Lys65 of subunit A and Asp39 of subunit B</scene> engage in a short-range intermolecular salt bridge of 2,6 Å. In the other side, <scene name='82/829354/Lys_65b-asp40a_interaction/1'>Asp40 of subunit A and Lys65 of subunit B</scene> engage in a short-range intermolecular salt bridge of 3,1 Å. Asp39 is not involved in this part of the dimer. The structure of ''N. clavipes'' dimer interface differs from those of other species due to the asymmetric nature of the interface and the involvement of Asp39. It has been reported that '''Asp39 is essential''' for the NTD dimerization in other species of spiders and seems to be also important in ''N.clavipes''. These interactions make subunits '''alignment better'''. Acidic residues are conserved around residues Asp39 and Asp40 and this allows the '''variability in the interactions''' that take place to Lys65. This variability provides a '''mechanism for plasticity''' in the dimer interface allowing the transition from loosely to stably associated dimer <ref name="Atkison">Atkison JH, Parnham S, Marcotte WR, Jr., and Olsen SK, 2016. Crystal Structure of the Nephila clavipes Major Ampullate Spidroin 1A N-terminal Domain Reveals Plasticity at the Dimer Interface, The Journal of Biological Chemistry, vol. | In one side, <scene name='82/829354/Asp40b_glu84b/1'>Asp40 and Glu84 of subunit B</scene> engage in the '''intramolecular handshake interaction'''. The '''asymmetric nature''' and the '''difference of topology''' of the subunits allow the formation of '''salt bridges'''. <scene name='82/829354/Lys_65-asp39_interaction/2'>Lys65 of subunit A and Asp39 of subunit B</scene> engage in a short-range intermolecular salt bridge of 2,6 Å. In the other side, <scene name='82/829354/Lys_65b-asp40a_interaction/1'>Asp40 of subunit A and Lys65 of subunit B</scene> engage in a short-range intermolecular salt bridge of 3,1 Å. Asp39 is not involved in this part of the dimer. The structure of ''N. clavipes'' dimer interface differs from those of other species due to the asymmetric nature of the interface and the involvement of Asp39. It has been reported that '''Asp39 is essential''' for the NTD dimerization in other species of spiders and seems to be also important in ''N.clavipes''. These interactions make subunits '''alignment better'''. Acidic residues are conserved around residues Asp39 and Asp40 and this allows the '''variability in the interactions''' that take place to Lys65. This variability provides a '''mechanism for plasticity''' in the dimer interface allowing the transition from loosely to stably associated dimer <ref name="Atkison">Atkison JH, Parnham S, Marcotte WR, Jr., and Olsen SK, 2016. Crystal Structure of the Nephila clavipes Major Ampullate Spidroin 1A N-terminal Domain Reveals Plasticity at the Dimer Interface, The Journal of Biological Chemistry, vol.291 no.36, p.19006-19017.</ref> | ||
Another intramolecular handshake interaction occurs also between <scene name='82/829354/Asp17a-asp53a_interaction/1'>Asp17 and Asp53 in subunit A</scene>. This interaction doesn’t exist in subunit B because of the orientation of subunit A with respect to subunit B, Asp17 and Asp53 are too far away in order to engage this interaction. <ref name="Atkison"/> | Another intramolecular handshake interaction occurs also between <scene name='82/829354/Asp17a-asp53a_interaction/1'>Asp17 and Asp53 in subunit A</scene>. This interaction doesn’t exist in subunit B because of the orientation of subunit A with respect to subunit B, Asp17 and Asp53 are too far away in order to engage this interaction. <ref name="Atkison"/> | ||
