A method for partitioning the information contained in a protein sequence between its structure and function

被引：5
|
作者：
Possenti, Andrea [1 ,2 ,3 ,4 ]
Vendruscolo, Michele [4 ]
Camilloni, Carlo [5 ]
Tiana, Guido [1 ,2 ,3 ]
机构：
[1] Univ Milan, Ctr Complex & Biosyst, Via Celoria 16, I-20133 Milan, Italy
[2] Univ Milan, Dept Phys, Via Celoria 16, I-20133 Milan, Italy
[3] INFN, Via Celoria 16, I-20133 Milan, Italy
[4] Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England
[5] Univ Milan, Dipartimento Biosci, Via Celoria 26, I-20133 Milan, Italy
来源：
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2018年 / 86卷 / 09期
关键词：
designed proteins; information content; intrinsically disordered proteins; protein folding/function; structure prediction; TRANSITION-STATE; PREDICTION; RESIDUES; ENTROPY; AGGREGATION; FRUSTRATION; PRINCIPLES; STABILITY; MECHANISM; DATABASE;
D O I：
10.1002/prot.25527
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance between the amount of information supplied by the sequence and that left after that the protein has folded into its structure. We study the amount of information necessary to specify the protein structure, providing an estimate that keeps into account the thermodynamic properties of protein folding. We thus show that the information remaining in the protein sequence after encoding for its structure (the information gap') is very close to what needed to encode for its function and interactions. Then, by predicting the information gap directly from the protein sequence, we show that it may be possible to use these insights from information theory to discriminate between ordered and disordered proteins, to identify unknown functions, and to optimize artificially-designed protein sequences.
引用
收藏
页码：956 / 964
页数：9
相关论文
共 50 条
  • [21] PROTEIN FUNCTION PREDICTION FROM STRUCTURE IN STRUCTURAL GENOMICS AND ITS CONTRIBUTION TO THE STUDY OF HEALTH AND DISEASE
    Watson, James D.
    Thornton, Janet M.
    FROM MOLECULES TO MEDICINES: STRUCTURE OF BIOLOGICAL MACROMOLECULES AND ITS RELEVANCE IN COMBATING NEW DISEASES AND BIOTERRORISM, 2009, : 201 - 215
  • [22] ProFPred: a two-step protein function prediction model based on sequence and evolutionary information
    Ge, Ruiquan
    feng, Guanwen
    Wang, Pu
    Miao, Qiguang
    2020 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, 2020, : 1372 - 1376
  • [23] Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function
    Hensen, Ulf
    Meyer, Tim
    Haas, Juergen
    Rex, Rene
    Vriend, Gert
    Grubmueller, Helmut
    PLOS ONE, 2012, 7 (05):
  • [24] Improving protein structure similarity searches using domain boundaries based on conserved sequence information
    Thompson, Kenneth Evan
    Wang, Yanli
    Madej, Tom
    Bryant, Stephen H.
    BMC STRUCTURAL BIOLOGY, 2009, 9
  • [25] PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms
    Sengupta, Kaustav
    Saha, Sovan
    Halder, Anup Kumar
    Chatterjee, Piyali
    Nasipuri, Mita
    Basu, Subhadip
    Plewczynski, Dariusz
    FRONTIERS IN GENETICS, 2022, 13
  • [26] Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra?
    Spencer, Simon E. F.
    Rodger, Alison
    ANALYTICAL METHODS, 2021, 13 (03) : 359 - 368
  • [27] SARS-CoV-2 Spike Protein Post Translational Modification Landscape and Its Impact on Protein Structure and Function via Computational Prediction
    Liang, Buwen
    Shi, Wenhao
    Ni, Can
    Tan, Bowen
    Zhu, Yiying
    Tang, Shaojun
    RESEARCH, 2023, 2023
  • [28] Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure
    Gupta, Munishwar Nath
    Uversky, Vladimir N.
    PROTEIN SCIENCE, 2024, 33 (04)
  • [29] Correlation between sequence, structure and function for trisporoid processing proteins in the model zygomycete Mucor mucedo
    Ellenberger, Sabrina
    Schuster, Stefan
    Woestemeyer, Johannes
    JOURNAL OF THEORETICAL BIOLOGY, 2013, 320 : 66 - 75
  • [30] Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function
    Villegas-Morcillo, Amelia
    Makrodimitris, Stavros
    van Ham, Roeland C. H. J.
    Gomez, Angel M.
    Sanchez, Victoria
    Reinders, Marcel J. T.
    BIOINFORMATICS, 2021, 37 (02) : 162 - 170
12345