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SUMMARY:Quantum refinement used for time-resolved crystallography
DTSTART;VALUE=DATE-TIME:20250923T094500Z
DTEND;VALUE=DATE-TIME:20250923T100000Z
DTSTAMP;VALUE=DATE-TIME:20260526T135934Z
UID:indico-contribution-1850@lindico453.srv.lu.se
DESCRIPTION:Speakers: Gayathri Yuvaraj (Lund University)\nIn standard crys
 tallographic refinement of proteins\, the experimental data are normally n
 ot enough to unambiguously decide the positions of all atoms. Therefore\, 
 the crystallographic data are supplemented by a set of empirical restraint
 s that ensure that bond lengths and angles make chemical sense. To obtain 
 more accurate results\, we have suggested that this potential can be repla
 ced by more accurate quantum-mechanical (QM) calculations for a small\, bu
 t interesting part of the protein\, giving the method of quantum refinemen
 t.1 Our group has shown that quantum refinement can locally improve crysta
 l structures\,2 decide protonation state of metal-bound ligands\,3–6 oxi
 dation state of metal sites\,7\,8 detect photoreduction of metal ions7\,9 
 and solve scientific problems regarding what is really is seen in crystal 
 structures.9–11 Several other groups have implemented this and similar a
 pproaches.12 We investigate how quantum refinement can be used for time-re
 solved crystallography. In time-resolved crystallography\, the obtained el
 ectron-density maps will typically involve a mixture of several states (un
 reacted state\, intermediates and products). Therefore\, the structures wi
 ll heavily depend on the empirical potential and the expectations of the c
 rystallographer. The QM calculations will give more accurate results\, esp
 ecially if there are intermediates with unusual (e.g. twisted) structures 
 or if metal sites are involved (which are hard to describe with general re
 straints). Moreover\, we will couple the structural interpretations with e
 xpectations from kinetic models of the studied reaction. I will present so
 me preliminary applications on cytochrome c oxidase\, xylose isomerase and
  bacteriorhodopsin.\n\nReferences\n1. U. Ryde\, L. Olsen\, K. Nilsson\, 20
 02\, J. Comput. Chem. 23\, 1058.\n2. U. Ryde\, K. Nilsson J. Am. Chem. Soc
 . 2003\, 125\, 14232.\n3. K. Nilsson\, U. Ryde\, J. Inorg. Biochem.\, 2004
 \, 98\, 1539\n4. L. Cao\, O. Caldararu\, U. Ryde\, J. Phys. Chem B\, 2017\
 , 121\, 8242.\n5. L. Cao\, O. Caldararu\, U. Ryde\, J. Chem. Theory Comput
 .\, 2018\, 14\, 6653.\n6. O. Caldararu\, M. Feldt\, D. Cioloboc\, M.-C.van
  Severen\, K. Starke\, E. Nordlander\, et al. Sci. Rep. 2018\, 8\, 4684\n7
 . L. Rulíšek\, U. Ryde\, J. Phys. Chem. B\, 2006\, 110\, 11511\n8. L. Ca
 o\, Börner\, M. C.\, Bergmann\, J.\, Caldararu\, O. & U. Ryde\, Inorg. Ch
 em. 2019\, 58\, 9672.\n9. P. Söderhjelm\, U. Ryde\, J. Mol. Struct. Theoc
 hem\, 2006\, 770\, 199\n10. L. Cao\, O. Caldararu\, A. C. Rosenzweig\, U. 
 Ryde\, 2018\, Angew. Chem. Int. Ed.\, 57\,162.\n11. J. Bergmann\, E. Oksan
 en & U. Ryde\, J. Biol. Inorg. Chem. 2021\, 26\, 341.\n12. J. Bergmann\, E
 . Oksanen\, U. Ryde\, Curr. Opin. Struct. Biol. 2022\, 72\, 18.\n\n\nAutho
 rs:\nGayathri Yuvaraj\, Ulf Ryde\nCo-authors:\nKristoffer Lundgren\, Esko 
 Oksanen\n\nhttps://lindico453.srv.lu.se/event/583/contributions/1850/
LOCATION:LINXS at The Loop
URL:https://lindico453.srv.lu.se/event/583/contributions/1850/
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