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Ulf Ryde

Professor in Theoretical Chemistry



Research interests

Biochemical molecules studied by theoretical methods
  • Enzyme mechanisms
  • The influence of the protein on bound metals, ligands and chromophores
  • The relation between structure and function of proteins
  • Ligand-binding affinities
  • Nature's design of proteins (Why was that metal or amino acid selected?)
  • QM/MM methods
  • Combination of QM methods and experimental methods: e.g. crystallographic refinement, NMR, and EXAFS

Selected publications

  • U. Ryde, M. H. M. Olsson, K. Pierloot & B. O. Roos (1996) "The cupric geometry of blue copper proteins is not strained". J. Mol. Biol. 261, 586-596. DOI: 10.1006/jmbi.1996.0484
  • U. Ryde, L. Olsen & K. Nilsson (2002) "Quantum chemical geometry optimisations in proteins using crystallographic raw data", J. Comp. Chem., 23, 1058-1070. DOI 10.1002/jcc.10093 .
  • T. H. Rod & U. Ryde (2005) "Free energy barriers at the density functional theory level: methyl transfer catalyzed by catechol O-methyltransferase", J. Chem. Theory Comput., 1, 1240-1251; DOI:10.1021/ct0501102.
  • P. Söderhjelm, U. Ryde (2009) "How accurate can a force field become? - A polarizable multipole model combined with fragment-wise quantum-mechanical calculations" J. Phys. Chem. A, 113, 617-627; DOI: 10.1021/jp8073514.

Projects

with references to my list of  publications

Proteins

  • blue copper proteins, e.g. plastocyanin, nitrite reducates, and azurin
  • porphyrin proteins, e.g. myoglobin, Fe/Mg-chelatase, cytochrome P450, cytochromes, peroxidases, catalases, vitamin B12 and coenzyme F430 enzymes
  • catechol O-methyl transferase
  • iron-sulphur clusters
  • superoxide dismuatases (Cu/Zn, Fe, Mn, or Ni)
  • Ni-Fe and iron-only hydrogenases
  • multi-copper oxidases
  • zinc enzymes, e.g. alcohol dehydrogenase, metallo-beta-lactamase, carbanhydrase, thermolysin, and carboxypeptidase

Methods

  • ab initio quantum chemistry (HF to CASPT2)
  • density functional theory, preferably B3LYP and BP86/RI
  • molecular dynamics
  • molecular mechanics
  • free energy perturbation
  • combined quantum chemical and classical methods (QM/MM)
  • combined quantum chemical and crystallographic refinement methods (Quantum refinement)
  • QM/MM combined with NMR refinement 
  • QM and QM/MM combined with EXAFS refinement
  • QM/MM free energy methods (QTCP)
  • Accurate force fields

Method developments

We develop methods to be used in simulations of proteins. Here are some of them.

  • ComQum, a combined quantum chemical and molecular mechanical (QM/MM) geometry optimisation program.
  • ComQum-X , a combined quantum chemical and crystallographic refinement program
  • ComQum-N, a combined quantum chemical and NMR program
  • ComQum-EXAFS, a combined quantum chemical and EXAFS program
  • Chargefit, a program to fit atomic charges to electrostatic moments or potential, e.g. the methods CHELMO and CHELP-BOW.
  • QTCP, a method for high-level QM/MM free energies
More about software.

Parameterisations

We also have done some parameterisation of protein ligands. These are most of them. Please, contact me if you are interested in the parameters.

  • A four- or five-coordinate zinc ion with His, Cys, water, and hydroxide ligands. (to be used for alcohol dehydrogenase)
  • Cu(II) ions with His, Cys, Met, and water ligands; (to be used for blue copper sites, the type 2 copper site in nitrite reductase, and Cu-substituted alcohol dehydrogenase)
  • Negatively charged Cys
  • NADH, NAD+, NADPH, and NADP+
  • Neutral Arg and Lys
  • DMSO
  • SH2, SH-, MeSH, MeS-, EtSH, EtS-
  • Xylose


Group members

Former group members

  • LiHong Hu (postdoc 2010-2011).
  • Dr. Jimmy Heimdal (PhD student 2006-2010), currently in Copenhagen
  • Dr. Maryam Farrokhnia (Postdoc 2009)
  • Dr. Pär Söderhjelm (PhD student 2003-2008), currently PostDoc in Parrinello's group in Lugano.
  • Dr. Jacob Kongsted (Postdoc 2007-2008), currently in Odense.
  • Dr. Patrik Rydberg (PhD student 2002-2007), currently in Copenhagen
  • Dr. Marcus Kaukonen (Postdoc 2006-2008), Currently in Helsinki.
  • Kambiz Katebzadeh (Project worker 2005-2006)
  • Aaron Weis (Diploma worker 2005)
  • Dr. Thomas H. Rod (Postdoc 2003-2005).
  • Dr. Ya-Wen Hsiao (Postdoc 2003-2005), Currently at AstraZeneca, Södertälje.
  • Dr. Yong Shen (Postdoc 2003-2004)
  • Dr. Kasper Planeta Jensen (PhD student 2001-2004), Postdoc Yale university (Jorgensen group). Currently at DTU.
  • Dr. Lubomir Rulisek  (Postdoc 2002-2004), Currently at UOCHB AV CR in Prague, Czech Republic
  • Dr. Kristina Nilsson (PhD student 1998-2003), "Quantum chemical interpretations of protein crystal structures", Lund, December 12, 2003; Currently at AstraZeneca, Mölndal.
  • Dr. Torben Rasmussen  (Postdoc 2002-2003), Currently at Linköping supercomputer centre.
  • Dr. Emma Sigfridsson  (PhD student 1997-2001),  now Emma Evertsson, "Theoretical studies of porphyrin proteins", Lund, September 21, 2001. Currently at AstraZeneca, Mölndal.
  • Dr. Mats Olsson  (PhD student 1995-2000) "Theoretical studies of blue copper proteins", Lund, March 3, 2000. Post doc in A. Warshel's group, University of South California. Postdoc in Jan Jensen's group in Copenhagen.
  • Jan O. A. De Kerpel (PhD student in Leuven 1995-1999), "Molecular and electronic modeling of blue copper proteins", Leuven Jan 1999. Currently at Devgen, Belgium.
  • Dr. Conrad Newton (postdoc 1998-1999)
  • Dr. Antonio Carlos Borin (postdoc 1996-1997), currently in Sao Paolo, Brazil
  • Dr. Lars Hemmingsen (postdoc 1996), currently at DTU, Lyngby, Denmark

Degrees & Titles

  • Master of Scence in Chemistry (Dec. 12, 1986)
  • Doctor of Philosophy in Biochemistry (Oct. 9, 1991)
  • Docent in Theoretical Chemistry (Mar. 20, 1996)
  • Assistant Professor (July 1, 1992; Forskarassistent)
  • Associate Professor (Feb. 1, 2000; Lektor)
  • Advisor for PhD students at the Chemical Section in Lund university (May 1, 2000- Dec. 12 2001; studierektor)
  • Senior research position in bioinorganic chemistry, Lund university (July 1, 2001-2007; Särskild forskare)
  • Professor in Theoretical Chemistry (Mar. 1, 2004)


Hobbies

  • Music (I play the piano, church organ, and sing in choirs)
  • Botany (plants, especially blackberries, and fungi)

Links


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