Metal-Containing Enzymes (eBook)

Front Cover 1
Metal-Containing Enzymes 4
Copyright 5
Contents 6
Contributors 8
Preface 10
Chapter 1: Type-3 Copper Proteins: Recent Advances on Polyphenol Oxidases 12
1. Introduction 13
2. Primary Structure and Molecular Weights of PPOs 18
2.1. General sequence structure 18
2.2. Core domain, C-terminal domain, and its proteolytic cleavage site 18
2.3. Conserved amino acid motifs in the core domain 19
2.4. Conserved amino acid motifs in the C-terminal domain 20
2.5. Transit peptide and location of PPOs 20
2.6. Sequence homologies within PPOs 22
2.7. In vitro activation of PPOs 27
2.8. In vivo activation of PPOs 27
2.9. Mutants of PPOs 27
2.9.1. Mutants of plant PPOs 27
2.9.2. Mutants of fungal PPOs 27
2.9.3. Mutants of bacterial PPOs 28
3. Oxo Complex 28
3.1. Oxo complex investigated by UV/vis absorption spectroscopy 29
3.2. Oxo complex investigated by CD spectroscopy 29
3.3. Oxo complex investigated by resonance Raman spectroscopy 29
3.4. Oxo complex of catechol oxidase 30
3.5. Oxo complex of tyrosinase 30
3.6. Oxo complex of aureusidin synthase 33
3.7. Oxo complex of hemocyanin 33
4. X-ray Crystallographic Structural Data of PPOs and Hemocyanins 33
4.1. Published structures in the protein data bank 33
4.1.1. Published structures in the PDB of hemocyanins 33
4.1.2. Published structures in the PDB of catechol oxidases 33
4.1.3. Published structures in the PDB of tyrosinases 38
4.2. Structural differences of tyrosinases and catechol oxidases 40
5. Conclusions and Outlook 41
Acknowledgments 41
References 41
Chapter 2: Biophysical Studies of Matrix Metalloproteinase/Triple-Helix Complexes 48
1. MMPs and Collagen Hydrolysis 48
2. Structures of Full-Length, Collagenolytic MMPs in Solution and in the Solid State 49
3. Structural Evaluation of MMP Interactions with Collagen 52
4. Mechanism of Collagenolysis 54
5. Heterogeneity in MMP Structures 57
Acknowledgment 58
References 58
Chapter 3: Catalytic Mechanisms of Metallohydrolases Containing Two Metal Ions 60
1. Introduction 61
2. Metallo-ß-Lactamases, Major Culprits in the Emergence of Antibiotic Resistance 61
3. Methionine Aminopeptidase, a Target for Novel Anticancer Drugs 68
4. Glycerophosphodiesterase, a Very Promiscuous Potential Bioremediator 71
5. PAP, an Alternative Target to Treat Osteoporosis 76
6. Conclusions and Outlook: Agmatinase, an Emerging Target for Biotechnological Applications 80
Acknowledgments 82
References 83
Chapter 4: Applications of Quantum Mechanical/Molecular Mechanical Methods to the Chemical Insertion Step of DNA and RNA ... 94
1. Introduction 96
2. Methods for Describing Reactive Pathways 96
3. DNA Polymerase ß 98
3.1. Abashkin, Erickson, and Burt (2001): A cluster QM calculation at steps along a proposed reaction path 98
3.2. Rittenhouse, Apostoluk, Miller, and Straatsma (2003): A cluster QM calculation on the prechemistry complex of Pol ß 100
3.3. Sawaya et al., 1997) 100
3.4. Batra et al., 2006) 101
3.5. Batra et al., 2008) 105
3.6. Batra et al. (2013): A QM/MM study based on the X-ray crystal structure of the Pol ß variant D256E 106
3.7. The broader picture: Pol ß 108
4. Application of QM/MM to Systems Similar to Pol ß 109
4.1. Pol . insertion 109
4.2. Dpo4 insertion 111
4.3. Pol . insertion 112
5. RNA Polymerase 114
6. Thoughts for Future QM/MM Simulations on Ternary Substrate Complexes of Nucleic Acid Polymerases 117
7. Conclusions 120
Acknowledgments 120
References 120
Chapter 5: Monitoring the Biomolecular Interactions and the Activity of Zn-Containing Enzymes Involved in Conformational ... 126
1. Zn-Metalloproteases and Conformational Diseases 127
2. Analytical Techniques Used to Study ZnMPs-Substrate/Inhibitors Interactions 131
2.1. Studying ZnMPs at atomic level 132
2.1.1. Nuclear magnetic resonance 132
2.1.2. X-ray crystallography 134
2.2. Analytical techniques able to provide information on binding affinities, activities, and substrate-induced conformat... 136
2.2.1. Surface plasmon resonance 136
2.2.2. Other optical methods 138
2.3. Mass spectrometry and ZnMPs 142
3. Conclusions and Future Perspectives 146
References 146
Author Index 154
Subject Index 170