Professor in Theoretical Chemistry
Vacant Ph.D. positionA vacant Ph.D. position is available in our group.
Apply before June 25, 2015.
See https://lu.mynetworkglobal.com/se/what:job/jobID:67449/ for further information. You must apply from that web page.
Research interestsBiochemical 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
- 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.
Projectswith references to my list of publications
- Ligand-binding affinity
- Chlorophyll 
- Hydrogenase 
- Development of accurate force fields (NEMO) 
- Superoxide dismuatases [83,84]
- Multi-copper oxidases 
- QM/MM free energies (QTCP) [75,78,82]
- The binding of O2 to haem proteins [65,70]
- Cytochrome P450 
- Metallo beta-lactamase [54,69]
- Porphyrin metallation and ferrochelatase [53,56,66,72,80]
- Cyclams 
- Quantum refinement and combinations of QM/MM methods with NMR and EXAFS
- Coenzyme B12 proteins [46,55,59,61,76]
- Electron-transfer proteins (iron-sulphur, cytochromes, and CuA) [42-44]
- Carboxylate shifts in zinc proteins 
- Discrimination between O2 and CO by myoglobin [31,48]
- Methods to determine atomic charges for simulations [25,45]
- QM/MM methods [20,40,51,60]
- Porphyrin proteins [43,55,57,64,71,79]
- Blue copper proteins [21,22,26-30,32,34,35,38-41,43,44,49,63]
- Simulations of protein mutants 
- Calicheamicin 
- Interpretation of PAC experiments [18,24,33]
- Alcohol dehydrogenase [15-17,19,20,24,67]
- Oscillations in biochemical systems [7,11-14]
- The Calvin cycle [1-6,8-10]
- 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
- 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
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
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
- SH2, SH-, MeSH, MeS-, EtSH, EtS-
- Samuel Genheden (PhD student 2008-2012)
- Paulius Mikulskis (PhD student 2011-2015)
- Marie-Céline van Severen (Postdoc 2009-2011)
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)
- Music (I play the piano, church organ, and sing in choirs)
- Botany (plants, especially blackberries, and fungi)
- How to use our programs
- List of my publications
- Advices for supervisors
- Krypbjörnbär i Sverige (Rubus Corylifolii in Sweden)