Computer-aided protein modelling: Applications to antibody and enzyme engineering: Dissertation

Anna-Marja Hoffren

Research output: ThesisDissertation

Abstract

Knowledge-based modelling and molecular dynamics were used in designing antibodies and enzymes for which the sequences and the known closely or distantly related crystal structures were available. The hapten binding to structural models of anti-2-phenyloxazolone antibodies in a solvent environment was studied by molecular dynamics simulations. The comparison of modelled antibody-hapten complexes of the idiotype and the high-affinity variant suggested plausible explanations for the experimentally observed increase in affinity of the variant. A structural model of the lignin peroxidase LIII from Phlebia radiata based on a distantly related crystal structure of cytochrome c peroxidase was constructed by using newly developed knowledge-based methods. Comparison of the structural model with a closely related crystal structure of the lignin peroxidase from Phanerochaete chrysosporium showed that the core of the model was predicted rather accurately. However, the last 30 amino acids at the C-terminus were modelled with less certainty owing to a lack of biochemical information about disulfide bridge formation. Cellulose-binding domains of Trichoderma reesei cellulases were homology modelled in order to predict structural correlations that would effect their binding to crystalline cellulose. Comparison of their sequences with sequences of other fungal cellulases predicted an additional disulfide bridge in several cellulose-binding domains. The three-dimensional structures of other fungal cellulose-binding domains can be expected to be similar to those of Trichoderma reesei. Mutations that improved labelling of the anti-human alpha-fetoprotein antibody were predicted on the basis of a structural model of the Fab-fragment of the alpha-fetoprotein antibody. The improved labelling efficiency of the lysine enriched anti-human alpha-fetoprotein antibody Fab-fragment was found to be promising for the development of a more sensitive immunoassays.
Original languageEnglish
QualificationDoctor Degree
Awarding Institution
  • University of Eastern Finland
Award date20 Jun 1994
Place of PublicationEspoo
Publisher
Print ISBNs951-38-4623-7
Publication statusPublished - 1994
MoE publication typeG5 Doctoral dissertation (article)

Fingerprint

Cellulose
Antibodies
Enzymes
Cellulases
Immunoglobulin Fab Fragments
Proteins
Haptens
Crystal structure
Disulfides
Labeling
Molecular dynamics
Cytochrome-c Peroxidase
alpha-Fetoproteins
Lysine
Crystalline materials
Amino Acids
Computer simulation
lignin peroxidase
human AFP protein

Keywords

  • knowledge-based systems
  • molecular models
  • crystal structure
  • antibodies
  • enzymes
  • cellulase
  • proteins

Cite this

Hoffren, A-M. (1994). Computer-aided protein modelling: Applications to antibody and enzyme engineering: Dissertation. Espoo: VTT Technical Research Centre of Finland.
Hoffren, Anna-Marja. / Computer-aided protein modelling : Applications to antibody and enzyme engineering: Dissertation. Espoo : VTT Technical Research Centre of Finland, 1994. 146 p.
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publisher = "VTT Technical Research Centre of Finland",
number = "185",
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Hoffren, A-M 1994, 'Computer-aided protein modelling: Applications to antibody and enzyme engineering: Dissertation', Doctor Degree, University of Eastern Finland, Espoo.

Computer-aided protein modelling : Applications to antibody and enzyme engineering: Dissertation. / Hoffren, Anna-Marja.

Espoo : VTT Technical Research Centre of Finland, 1994. 146 p.

Research output: ThesisDissertation

TY - THES

T1 - Computer-aided protein modelling

T2 - Applications to antibody and enzyme engineering: Dissertation

AU - Hoffren, Anna-Marja

N1 - Project code: BEL4652

PY - 1994

Y1 - 1994

N2 - Knowledge-based modelling and molecular dynamics were used in designing antibodies and enzymes for which the sequences and the known closely or distantly related crystal structures were available. The hapten binding to structural models of anti-2-phenyloxazolone antibodies in a solvent environment was studied by molecular dynamics simulations. The comparison of modelled antibody-hapten complexes of the idiotype and the high-affinity variant suggested plausible explanations for the experimentally observed increase in affinity of the variant. A structural model of the lignin peroxidase LIII from Phlebia radiata based on a distantly related crystal structure of cytochrome c peroxidase was constructed by using newly developed knowledge-based methods. Comparison of the structural model with a closely related crystal structure of the lignin peroxidase from Phanerochaete chrysosporium showed that the core of the model was predicted rather accurately. However, the last 30 amino acids at the C-terminus were modelled with less certainty owing to a lack of biochemical information about disulfide bridge formation. Cellulose-binding domains of Trichoderma reesei cellulases were homology modelled in order to predict structural correlations that would effect their binding to crystalline cellulose. Comparison of their sequences with sequences of other fungal cellulases predicted an additional disulfide bridge in several cellulose-binding domains. The three-dimensional structures of other fungal cellulose-binding domains can be expected to be similar to those of Trichoderma reesei. Mutations that improved labelling of the anti-human alpha-fetoprotein antibody were predicted on the basis of a structural model of the Fab-fragment of the alpha-fetoprotein antibody. The improved labelling efficiency of the lysine enriched anti-human alpha-fetoprotein antibody Fab-fragment was found to be promising for the development of a more sensitive immunoassays.

AB - Knowledge-based modelling and molecular dynamics were used in designing antibodies and enzymes for which the sequences and the known closely or distantly related crystal structures were available. The hapten binding to structural models of anti-2-phenyloxazolone antibodies in a solvent environment was studied by molecular dynamics simulations. The comparison of modelled antibody-hapten complexes of the idiotype and the high-affinity variant suggested plausible explanations for the experimentally observed increase in affinity of the variant. A structural model of the lignin peroxidase LIII from Phlebia radiata based on a distantly related crystal structure of cytochrome c peroxidase was constructed by using newly developed knowledge-based methods. Comparison of the structural model with a closely related crystal structure of the lignin peroxidase from Phanerochaete chrysosporium showed that the core of the model was predicted rather accurately. However, the last 30 amino acids at the C-terminus were modelled with less certainty owing to a lack of biochemical information about disulfide bridge formation. Cellulose-binding domains of Trichoderma reesei cellulases were homology modelled in order to predict structural correlations that would effect their binding to crystalline cellulose. Comparison of their sequences with sequences of other fungal cellulases predicted an additional disulfide bridge in several cellulose-binding domains. The three-dimensional structures of other fungal cellulose-binding domains can be expected to be similar to those of Trichoderma reesei. Mutations that improved labelling of the anti-human alpha-fetoprotein antibody were predicted on the basis of a structural model of the Fab-fragment of the alpha-fetoprotein antibody. The improved labelling efficiency of the lysine enriched anti-human alpha-fetoprotein antibody Fab-fragment was found to be promising for the development of a more sensitive immunoassays.

KW - knowledge-based systems

KW - molecular models

KW - crystal structure

KW - antibodies

KW - enzymes

KW - cellulase

KW - proteins

M3 - Dissertation

SN - 951-38-4623-7

T3 - VTT Publications

PB - VTT Technical Research Centre of Finland

CY - Espoo

ER -

Hoffren A-M. Computer-aided protein modelling: Applications to antibody and enzyme engineering: Dissertation. Espoo: VTT Technical Research Centre of Finland, 1994. 146 p.