Inferring repeat-protein energetics from evolutionary information
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that...
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| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_1553734X_v13_n6_p_Espada |
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todo:paper_1553734X_v13_n6_p_Espada2023-10-03T16:25:28Z Inferring repeat-protein energetics from evolutionary information Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U. ankyrin leucine rich repeat protein polypeptide protein repeat protein tetratricopeptide repeat protein unclassified drug protein amino acid sequence Article energy transfer evolution Monte Carlo method point mutation protein folding protein stability sequence alignment statistical model amino acid repeat astronomy chemical model chemistry energy transfer genetics molecular model procedures protein conformation sequence analysis structure activity relation ultrastructure Energy Transfer Evolution, Chemical Models, Chemical Models, Molecular Point Mutation Protein Conformation Protein Folding Proteins Repetitive Sequences, Amino Acid Sequence Analysis, Protein Structure-Activity Relationship Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that fold into the same structural topology show different stabilization energies, and these are often related to their physiological behavior. We propose a description for the energetic variation given by sequence modifications in repeat proteins, systems for which the overall problem is simplified by their inherent symmetry. We explicitly account for single amino acid and pair-wise interactions and treat higher order correlations with a single term. We show that the resulting evolutionary field can be interpreted with structural detail. We trace the variations in the energetic scores of natural proteins and relate them to their experimental characterization. The resulting energetic evolutionary field allows the prediction of the folding free energy change for several mutants, and can be used to generate synthetic sequences that are statistically indistinguishable from the natural counterparts. © 2017 Espada et al. Fil:Ferreiro, D.U. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_1553734X_v13_n6_p_Espada |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
ankyrin leucine rich repeat protein polypeptide protein repeat protein tetratricopeptide repeat protein unclassified drug protein amino acid sequence Article energy transfer evolution Monte Carlo method point mutation protein folding protein stability sequence alignment statistical model amino acid repeat astronomy chemical model chemistry energy transfer genetics molecular model procedures protein conformation sequence analysis structure activity relation ultrastructure Energy Transfer Evolution, Chemical Models, Chemical Models, Molecular Point Mutation Protein Conformation Protein Folding Proteins Repetitive Sequences, Amino Acid Sequence Analysis, Protein Structure-Activity Relationship |
| spellingShingle |
ankyrin leucine rich repeat protein polypeptide protein repeat protein tetratricopeptide repeat protein unclassified drug protein amino acid sequence Article energy transfer evolution Monte Carlo method point mutation protein folding protein stability sequence alignment statistical model amino acid repeat astronomy chemical model chemistry energy transfer genetics molecular model procedures protein conformation sequence analysis structure activity relation ultrastructure Energy Transfer Evolution, Chemical Models, Chemical Models, Molecular Point Mutation Protein Conformation Protein Folding Proteins Repetitive Sequences, Amino Acid Sequence Analysis, Protein Structure-Activity Relationship Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U. Inferring repeat-protein energetics from evolutionary information |
| topic_facet |
ankyrin leucine rich repeat protein polypeptide protein repeat protein tetratricopeptide repeat protein unclassified drug protein amino acid sequence Article energy transfer evolution Monte Carlo method point mutation protein folding protein stability sequence alignment statistical model amino acid repeat astronomy chemical model chemistry energy transfer genetics molecular model procedures protein conformation sequence analysis structure activity relation ultrastructure Energy Transfer Evolution, Chemical Models, Chemical Models, Molecular Point Mutation Protein Conformation Protein Folding Proteins Repetitive Sequences, Amino Acid Sequence Analysis, Protein Structure-Activity Relationship |
| description |
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that fold into the same structural topology show different stabilization energies, and these are often related to their physiological behavior. We propose a description for the energetic variation given by sequence modifications in repeat proteins, systems for which the overall problem is simplified by their inherent symmetry. We explicitly account for single amino acid and pair-wise interactions and treat higher order correlations with a single term. We show that the resulting evolutionary field can be interpreted with structural detail. We trace the variations in the energetic scores of natural proteins and relate them to their experimental characterization. The resulting energetic evolutionary field allows the prediction of the folding free energy change for several mutants, and can be used to generate synthetic sequences that are statistically indistinguishable from the natural counterparts. © 2017 Espada et al. |
| format |
JOUR |
| author |
Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U. |
| author_facet |
Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U. |
| author_sort |
Espada, R. |
| title |
Inferring repeat-protein energetics from evolutionary information |
| title_short |
Inferring repeat-protein energetics from evolutionary information |
| title_full |
Inferring repeat-protein energetics from evolutionary information |
| title_fullStr |
Inferring repeat-protein energetics from evolutionary information |
| title_full_unstemmed |
Inferring repeat-protein energetics from evolutionary information |
| title_sort |
inferring repeat-protein energetics from evolutionary information |
| url |
http://hdl.handle.net/20.500.12110/paper_1553734X_v13_n6_p_Espada |
| work_keys_str_mv |
AT espadar inferringrepeatproteinenergeticsfromevolutionaryinformation AT parrarg inferringrepeatproteinenergeticsfromevolutionaryinformation AT morat inferringrepeatproteinenergeticsfromevolutionaryinformation AT walczakam inferringrepeatproteinenergeticsfromevolutionaryinformation AT ferreirodu inferringrepeatproteinenergeticsfromevolutionaryinformation |
| _version_ |
1807316936402403328 |