Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding
Kinetic partitioning between competing routes is present in many biological processes. Here, we propose a methodology to characterize kinetic partitioning through site-directed mutagenesis and apply it to parallel routes for unfolding of the TI I27 protein and for recognition of its target DNA by th...
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2011
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17410126_v24_n1-2_p179_Sanchez http://hdl.handle.net/20.500.12110/paper_17410126_v24_n1-2_p179_Sanchez |
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paper:paper_17410126_v24_n1-2_p179_Sanchez2023-06-08T16:26:58Z Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding kinetic partitioning point mutation protein design protein folding protein-DNA binding Biological process Human papillomavirus Mutational analysis Mutational effects New parameters Parallel route Point mutations protein design protein-DNA binding Rational design Reaction routes Site directed mutagenesis Wild types Design Protein folding DNA article chemical reaction gene targeting kinetics molecular recognition mutational analysis nonhuman point mutation priority journal protein DNA binding protein folding quantitative analysis site directed mutagenesis wild type DNA DNA-Binding Proteins Humans Models, Molecular Muscle Proteins Mutagenesis, Site-Directed Oncogene Proteins, Viral Papillomaviridae Point Mutation Protein Binding Protein Denaturation Protein Folding Protein Kinases Thermodynamics Human papillomavirus Kinetic partitioning between competing routes is present in many biological processes. Here, we propose a methodology to characterize kinetic partitioning through site-directed mutagenesis and apply it to parallel routes for unfolding of the TI I27 protein and for recognition of its target DNA by the human papillomavirus E2 protein. The balance between the two competing reaction routes can be quantified by the partitioning constant Kp. Kp is easily modulated by point mutations, opening the way for the rational design of kinetic partitioning. Conserved wild-type residues strongly favor one of the two competing reactions, suggesting that in these systems there is an evolutionary pressure to shift partitioning towards a certain route. The mutations with the largest effects on partitioning cluster together in space, defining the protein regions most relevant for the modulation of partitioning. Such regions are neither fully coincident with nor strictly segregated from the regions that are important from each competing reaction. We dissected the mutational effects on partitioning into the contributions from each competing route using a new parameter called pi-value. The results suggest how the design of kinetic partitioning may be approached in each case. © The Author 2010. Published by Oxford University Press. All rights reserved. 2011 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17410126_v24_n1-2_p179_Sanchez http://hdl.handle.net/20.500.12110/paper_17410126_v24_n1-2_p179_Sanchez |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
kinetic partitioning point mutation protein design protein folding protein-DNA binding Biological process Human papillomavirus Mutational analysis Mutational effects New parameters Parallel route Point mutations protein design protein-DNA binding Rational design Reaction routes Site directed mutagenesis Wild types Design Protein folding DNA article chemical reaction gene targeting kinetics molecular recognition mutational analysis nonhuman point mutation priority journal protein DNA binding protein folding quantitative analysis site directed mutagenesis wild type DNA DNA-Binding Proteins Humans Models, Molecular Muscle Proteins Mutagenesis, Site-Directed Oncogene Proteins, Viral Papillomaviridae Point Mutation Protein Binding Protein Denaturation Protein Folding Protein Kinases Thermodynamics Human papillomavirus |
| spellingShingle |
kinetic partitioning point mutation protein design protein folding protein-DNA binding Biological process Human papillomavirus Mutational analysis Mutational effects New parameters Parallel route Point mutations protein design protein-DNA binding Rational design Reaction routes Site directed mutagenesis Wild types Design Protein folding DNA article chemical reaction gene targeting kinetics molecular recognition mutational analysis nonhuman point mutation priority journal protein DNA binding protein folding quantitative analysis site directed mutagenesis wild type DNA DNA-Binding Proteins Humans Models, Molecular Muscle Proteins Mutagenesis, Site-Directed Oncogene Proteins, Viral Papillomaviridae Point Mutation Protein Binding Protein Denaturation Protein Folding Protein Kinases Thermodynamics Human papillomavirus Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding |
| topic_facet |
kinetic partitioning point mutation protein design protein folding protein-DNA binding Biological process Human papillomavirus Mutational analysis Mutational effects New parameters Parallel route Point mutations protein design protein-DNA binding Rational design Reaction routes Site directed mutagenesis Wild types Design Protein folding DNA article chemical reaction gene targeting kinetics molecular recognition mutational analysis nonhuman point mutation priority journal protein DNA binding protein folding quantitative analysis site directed mutagenesis wild type DNA DNA-Binding Proteins Humans Models, Molecular Muscle Proteins Mutagenesis, Site-Directed Oncogene Proteins, Viral Papillomaviridae Point Mutation Protein Binding Protein Denaturation Protein Folding Protein Kinases Thermodynamics Human papillomavirus |
| description |
Kinetic partitioning between competing routes is present in many biological processes. Here, we propose a methodology to characterize kinetic partitioning through site-directed mutagenesis and apply it to parallel routes for unfolding of the TI I27 protein and for recognition of its target DNA by the human papillomavirus E2 protein. The balance between the two competing reaction routes can be quantified by the partitioning constant Kp. Kp is easily modulated by point mutations, opening the way for the rational design of kinetic partitioning. Conserved wild-type residues strongly favor one of the two competing reactions, suggesting that in these systems there is an evolutionary pressure to shift partitioning towards a certain route. The mutations with the largest effects on partitioning cluster together in space, defining the protein regions most relevant for the modulation of partitioning. Such regions are neither fully coincident with nor strictly segregated from the regions that are important from each competing reaction. We dissected the mutational effects on partitioning into the contributions from each competing route using a new parameter called pi-value. The results suggest how the design of kinetic partitioning may be approached in each case. © The Author 2010. Published by Oxford University Press. All rights reserved. |
| title |
Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding |
| title_short |
Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding |
| title_full |
Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding |
| title_fullStr |
Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding |
| title_full_unstemmed |
Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding |
| title_sort |
mutational analysis of kinetic partitioning in protein folding and protein-dna binding |
| publishDate |
2011 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17410126_v24_n1-2_p179_Sanchez http://hdl.handle.net/20.500.12110/paper_17410126_v24_n1-2_p179_Sanchez |
| _version_ |
1768541675007770624 |