| Chapter title |
Computational Analysis of Protein Tunnels and Channels
|
|---|---|
| Chapter number | 3 |
| Book title |
Protein Engineering
|
| Published in |
Methods in molecular biology, January 2018
|
| DOI | 10.1007/978-1-4939-7366-8_3 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-7364-4, 978-1-4939-7366-8
|
| Authors |
Jan Brezovsky, Barbora Kozlikova, Jiri Damborsky, Brezovsky, Jan, Kozlikova, Barbora, Damborsky, Jiri |
| Abstract |
Protein tunnels connecting the functional buried cavities with bulk solvent and protein channels, enabling the transport through biological membranes, represent the structural features that govern the exchange rates of ligands, ions, and water solvent. Tunnels and channels are present in a vast number of known proteins and provide control over their function. Modification of these structural features by protein engineering frequently provides proteins with improved properties. Here we present a detailed computational protocol employing the CAVER software that is applicable for: (1) the analysis of tunnels and channels in protein structures, and (2) the selection of hot-spot residues in tunnels or channels that can be mutagenized for improved activity, specificity, enantioselectivity, or stability. |
Mendeley readers
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|---|---|---|
| Unknown | 38 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Bachelor | 9 | 24% |
| Researcher | 9 | 24% |
| Student > Ph. D. Student | 8 | 21% |
| Student > Master | 3 | 8% |
| Lecturer | 2 | 5% |
| Other | 2 | 5% |
| Unknown | 5 | 13% |
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|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 19 | 50% |
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| Computer Science | 1 | 3% |
| Unknown | 8 | 21% |