Abstract
Different aspects of porphyrin proteins have been studied with theoretical methods. For example, we have studied:
- The importance of hydrogen bonds for the discrimination between carbon monoxide and molecular oxygen by myoglobin, the oxygen carrier in muscles, modelling the active site both in vacuum and in the protein matrix
- The inner-sphere reorganisation energy during electron transfer for cytochromes compared to other electron-transfer proteins, such as blue copper proteins and Fe-S clusters
- The role of porphyrin distortions in the reaction mechanism of ferrochelatase, the enzyme that inserts an iron ion into protoporphyrin IX to make haem
- The interaction between different metal sites in ferrochelatase
In these studies we have used density functional theory, classical force field methods, and a combination of quantum chemistry and molecular mechanics. In particular we have developed new methods for calculating charges to be used in molecular mechanics and dynamics calculations, and compared them with existing methods.
- The importance of hydrogen bonds for the discrimination between carbon monoxide and molecular oxygen by myoglobin, the oxygen carrier in muscles, modelling the active site both in vacuum and in the protein matrix
- The inner-sphere reorganisation energy during electron transfer for cytochromes compared to other electron-transfer proteins, such as blue copper proteins and Fe-S clusters
- The role of porphyrin distortions in the reaction mechanism of ferrochelatase, the enzyme that inserts an iron ion into protoporphyrin IX to make haem
- The interaction between different metal sites in ferrochelatase
In these studies we have used density functional theory, classical force field methods, and a combination of quantum chemistry and molecular mechanics. In particular we have developed new methods for calculating charges to be used in molecular mechanics and dynamics calculations, and compared them with existing methods.
| Original language | English |
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| Qualification | Doctor |
| Awarding Institution |
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| Supervisors/Advisors |
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| Award date | 2001 Sept 21 |
| Publisher | |
| ISBN (Print) | 91-7874-145-9 |
| Publication status | Published - 2001 |
Bibliographical note
Defence detailsDate: 2001-09-21
Time: 10:15
Place: sal A, Chemical Centre
External reviewer(s)
Name: Carloni, Paolo
Title: Professor
Affiliation: Trieste, Italy
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Article: I. Emma Sigfridsson and Ulf Ryde"On the significance of hydrogen bonds for the discrimination between CO and O2 bymyoglobin"J. Biol. Inorg. Chem., 4 (1999) 99-110
Article: II. Emma Sigfridsson and Ulf Ryde"Binding of O2 and CO to myoglobin studied by theoretical methods"Manuscript
Article: III. Emma Sigfridsson, Mats H. M. Olsson, and Ulf Ryde"A comparison of the inner-sphere reorganisation energies of cytochromes, iron-sulphurclusters, and blue copper proteins"J. Phys. Chem. B, 105 (2001) 5546-5552
Article: IV. David Lecerof, Michael Fodje, Román Alvarez León, Ulf Olsson, Andreas Hansson, EmmaSigfridssona, Ulf Ryde, Salam Al-Karadaghi, and Mats Hansson"Interaction between metal binding sites in Bacillus subtilis ferrochelatase"J. Biol. Chem., submitted for publication
Article: V. Emma Sigfridsson and Ulf Ryde"The importance of porphyrin distortions for the ferrochelatase reaction"Manuscript
Article: VI. Emma Sigfridsson and Ulf Ryde"A comparison of methods for deriving atomic charges from the electrostatic potentialand moments"J. Comp. Chem. 19 (1998) 377-395.
Article: VII. Emma Sigfridsson, Ulf Ryde, and Bruce L. Bush"Restrained point-charge models for disaccharides "J. Comp. Chem., submitted for publication
The information about affiliations in this record was updated in December 2015.
The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
Subject classification (UKÄ)
- Theoretical Chemistry (including Computational Chemistry)
Free keywords
- molecular mechanics
- quantum chemical calculations
- electrostatic potential charges
- atomic charges
- ferrochelatase
- cytochrome
- myoglobin
- Porphyrin
- haem
- QM/MM
- reorganisation energy
- Theoretical chemistry
- quantum chemistry
- Teoretisk kemi
- kvantkemi