Intrinsically Disordered Protein: Difference between revisions
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<StructureSection load='1jsu' size='350' side='right' scene='37/372681/Cv/2' caption='Human CDK2 ( | <StructureSection load='1jsu' size='350' side='right' scene='37/372681/Cv/2' caption='Human CDK2 (blue) complex with cyclin-A (green) and P27 (pink) [[1jsu]]: see p27kip1 below. P27 has undergone a disorder to order transition upon encountering these partners.'> | ||
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It has long been taught that proteins must be properly folded in order to perform their functions. This paradigm derives from work by Christian B. Anfinsen and coworkers. In the 1960's, they showed that RNAse, when denatured so that 99% of its enzymatic activity was lost, could regain enzymatic activity within seconds when the denaturing agent was removed under proper conditions<ref>For the sake of brevity, this description is oversimplified. RNAse needed to be reduced to break disulfide bonds, as well as using 8 M urea, for denaturation. Oxidation without the denaturant then left an inactive enzyme because the disulfide bonds formed randomly, precluding proper folding except very slowly (many hours). Only when protein disulfide isomerase was added did the re-folding occur at a physiological rate (about a minute). The fact that RNAse could thus be trapped in an inactive conformation under physiological conditions contributed to the insights developed by Anfinsen and his team. Proteins lacking disulfides renatured in seconds. For details, see [http://nobelprize.org/nobel_prizes/chemistry/laureates/1972/anfinsen-lecexture.html Anfinsen's Nobel Lecture.]</ref><ref>A similar observation was made around the same time by then graduate student Lisa Steiner in the lab of [[Richards, Frederic M.|Fred Richards]] at Yale University. Neither Richards nor advisor Joseph Fruton thought the observation interesting enough to publish. It was an answer to a question not yet asked. This story is recounted by David Eisenberg, see the next citation.</ref><ref>PMID: 29958112</ref>. They concluded that the amino acid sequence is sufficient for a protein to fold into its functional, lowest energy conformation. This work won the [[Nobel_Prizes_for_3D_Molecular_Structure|1972 Nobel Prize]], and was subsequently confirmed and extended by many researchers. | It has long been taught that proteins must be properly folded in order to perform their functions. This paradigm derives from work by Christian B. Anfinsen and coworkers. In the 1960's, they showed that RNAse, when denatured so that 99% of its enzymatic activity was lost, could regain enzymatic activity within seconds when the denaturing agent was removed under proper conditions<ref>For the sake of brevity, this description is oversimplified. RNAse needed to be reduced to break disulfide bonds, as well as using 8 M urea, for denaturation. Oxidation without the denaturant then left an inactive enzyme because the disulfide bonds formed randomly, precluding proper folding except very slowly (many hours). Only when protein disulfide isomerase was added did the re-folding occur at a physiological rate (about a minute). The fact that RNAse could thus be trapped in an inactive conformation under physiological conditions contributed to the insights developed by Anfinsen and his team. Proteins lacking disulfides renatured in seconds. For details, see [http://nobelprize.org/nobel_prizes/chemistry/laureates/1972/anfinsen-lecexture.html Anfinsen's Nobel Lecture.]</ref><ref>A similar observation was made around the same time by then graduate student Lisa Steiner in the lab of [[Richards, Frederic M.|Fred Richards]] at Yale University. Neither Richards nor advisor Joseph Fruton thought the observation interesting enough to publish. It was an answer to a question not yet asked. This story is recounted by David Eisenberg, see the next citation.</ref><ref>PMID: 29958112</ref>. They concluded that the amino acid sequence is sufficient for a protein to fold into its functional, lowest energy conformation. This work won the [[Nobel_Prizes_for_3D_Molecular_Structure|1972 Nobel Prize]], and was subsequently confirmed and extended by many researchers. | ||
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</td></tr></table> | </td></tr></table> | ||
Many [[X-ray crystallography|crystallographic]] structures have missing loops -- that is, ranges of amino acids with no [[atomic coordinate file|atomic coordinates]] in the model. These "gaps" in the model are often thought to be artifacts of inadvertant disorder in the crystal. In some cases, these gaps may be alerting us to the presence of intrinsically disordered loops in an otherwise folded protein<ref name="IDSG" />. Such gaps are the basis for the [[#Protein disorder predictors|DISOPRED2 disorder prediction server]]. [[FirstGlance in Jmol]] offers [[Temperature_value#Missing_Residues|one method for locating and | Many [[X-ray crystallography|crystallographic]] structures have missing loops -- that is, ranges of amino acids with no [[atomic coordinate file|atomic coordinates]] in the model. These "gaps" in the model are often thought to be artifacts of inadvertant disorder in the crystal. In some cases, these gaps may be alerting us to the presence of intrinsically disordered loops in an otherwise folded protein<ref name="IDSG" />. Such gaps are the basis for the [[#Protein disorder predictors|DISOPRED2 disorder prediction server]]. [[FirstGlance in Jmol]] offers [[Temperature_value#Missing_Residues|one method for locating and visualizing such gaps]]. | ||
Despite the existence of compelling evidence for IDPs and intrinsically disordered loops beginning in 1990<ref name="struhl1990" /><ref>PMID: 2236048</ref><ref>For the ''unstructured domain'' interpretation of early work by Pontius and Berg, see the 2004 review by Tompa and Csermley, PMID: 15284216</ref>, many current textbooks of biochemistry and even some monographs on protein structure fail to mention intrinsic disorder and its importance for protein function<ref>PMID: 18831774</ref><ref>Martz, E. Book review of <i>Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M.</i>. <i>Biochem. Mol. Biol. Educ.</i> 33:144-5 (2006). [http://dx.doi.org/10.1002/bmb.2005.494033022442 DOI: 10.1002/bmb.2005.494033022442]</ref>. In 2011, Chouard provided a readable and informative overview of IDPs and how some of them function<ref>PMID: 21390105</ref>. | Despite the existence of compelling evidence for IDPs and intrinsically disordered loops beginning in 1990<ref name="struhl1990" /><ref>PMID: 2236048</ref><ref>For the ''unstructured domain'' interpretation of early work by Pontius and Berg, see the 2004 review by Tompa and Csermley, PMID: 15284216</ref>, many current textbooks of biochemistry and even some monographs on protein structure fail to mention intrinsic disorder and its importance for protein function<ref>PMID: 18831774</ref><ref>Martz, E. Book review of <i>Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M.</i>. <i>Biochem. Mol. Biol. Educ.</i> 33:144-5 (2006). [http://dx.doi.org/10.1002/bmb.2005.494033022442 DOI: 10.1002/bmb.2005.494033022442]</ref>. In 2011, Chouard provided a readable and informative overview of IDPs and how some of them function<ref>PMID: 21390105</ref>. | ||
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==Molecular Shields== | ==Molecular Shields== | ||
It appears that hundreds of IDPs that remain soluble after boiling protect folded proteins against heat-denaturation, aggregation, and loss of activity from dessication or organic solvents<ref name="hero">PMID: 32163402</ref>. They also appear to suppress neurodegeneration and extend lifespan<ref name="hero" />. They have been termed "heat-resistant obscure" (hero) proteins<ref name="hero" />. Their isoelectric pH's (pI's) form a bimodal distribution, so that most are negatively or positively charged at neutral pH<ref name="hero" />. Examples include six human proteins that were studied in detail: [https://www.uniprot.org/uniprot/Q9BUW7 C9orf16] (length 83), [https://www.uniprot.org/uniprot/Q00994 BEX3] (length 111), [https://www.uniprot.org/uniprot/O00193 C11orf58] (length 183), [https://www.uniprot.org/uniprot/Q8NC51 SERBP1] (length 408), In several test cases, scrambling the sequences of these proteins did not diminish their protective effects<ref name="hero" />. Their protective activity appears to depend on their high charge density and length, but not on a specific sequence. | It appears that hundreds of IDPs that remain soluble after boiling protect folded proteins against heat-denaturation, aggregation, and loss of activity from dessication or organic solvents<ref name="hero">PMID: 32163402</ref>. They also appear to suppress neurodegeneration and extend lifespan<ref name="hero" />. They have been termed "heat-resistant obscure" (hero) proteins<ref name="hero" />. Their isoelectric pH's (pI's) form a bimodal distribution, so that most are negatively or positively charged at neutral pH<ref name="hero" />. Examples include six human proteins that were studied in detail: [https://www.uniprot.org/uniprot/P84101 SERF2] (length 59), [https://www.uniprot.org/uniprot/Q9BUW7 C9orf16] (length 83), [https://www.uniprot.org/uniprot/Q9UNZ5 C19ofr53] (length 99), [https://www.uniprot.org/uniprot/Q00994 BEX3] (length 111), [https://www.uniprot.org/uniprot/O00193 C11orf58] (length 183), and [https://www.uniprot.org/uniprot/Q8NC51 SERBP1] (length 408)<ref name="hero" />. Estimated isoelectric points<ref>Isoelectric points were estimated with the [http://protcalc.sourceforge.net/cgi-bin/protcalc Protein Calculator].</ref> are 10.5, 4.2, 11.6, 5.5, 4.7, and 8.6 respectively. In several test cases, scrambling the sequences of these proteins did not diminish their protective effects<ref name="hero" />. Their protective activity appears to depend on their high charge density and length, but not on a specific sequence. | ||
== Protein disorder predictors == | == Protein disorder predictors == | ||
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* [http://bioinf.cs.ucl.ac.uk/disopred/ DISOPRED2] (Jones Group, University College London, UK). "DISOPRED2 was trained on a set of around 750 non-redundant sequences with high resolution X-ray structures. Disorder was identified with those residues that appear in the sequence records but with coordinates missing from the electron density map. This is an imperfect means for identifying disordered residues as missing co-ordinates can also arise as an artifact of the crystalization process. False assignment of order can also occur as a result of stabilizing interactions by ligands or other macromolecules in the complex. However, this is the simplest means for defining disorder in the absence of further experimental investigation of the protein." (Quoted from the DISOPRED2 website.) | * [http://bioinf.cs.ucl.ac.uk/disopred/ DISOPRED2] (Jones Group, University College London, UK). "DISOPRED2 was trained on a set of around 750 non-redundant sequences with high resolution X-ray structures. Disorder was identified with those residues that appear in the sequence records but with coordinates missing from the electron density map. This is an imperfect means for identifying disordered residues as missing co-ordinates can also arise as an artifact of the crystalization process. False assignment of order can also occur as a result of stabilizing interactions by ligands or other macromolecules in the complex. However, this is the simplest means for defining disorder in the absence of further experimental investigation of the protein." (Quoted from the DISOPRED2 website.) | ||
* [http:// | * [http://biomine.cs.vcu.edu/servers/flDPnn2/ flDPnn2] (putative '''f'''unction- and '''l'''inker based '''D'''isorder '''P'''rediction using deep '''n'''eural '''n'''etwork)<ref name="fldpnn">PMID: 34290238</ref>. In 2021, flDPnn, was selected as the {{font color|#c000c0|'''best disorder predictor in the first Critical Assessment of Protein Intrinsic Disorder Prediction'''}} (CAID) <ref name="caid2021">PMID: 33875885</ref>. | ||
* [ | * [https://fold.proteopedia.org/ FoldIndex]<ref name="foldindex" /> (Sussman Group, Weizmann Institute, Rehovot, Israel). FoldIndex makes predictions based on the observation that IDPs occupy the low hydrophobicity/ high net-charge portion of charge-hydrophobicity phase space. (See Figure above.) | ||
* [https://iupred2a.elte.hu/ IUPred2a] (Dosztányi, Csizmók, Tompa and Simon: Budapest, Hungary). "IUPred recognized intrinsically unstructured regions from the amino acid sequence based on the estimated pairwise energy content. The underlying assumption is that globular proteins are composed of amino acids which have the potential to form a large number of favorable interactions, whereas intrinsically disorered proteins (IDPs) adopt no stable structure because their amino acid composition does not allow sufficient favorable interactions to form." (Quoted from the IUPred website.) | |||
* [http://www.pondr.com/ PONDR] (Dunker Group, Indiana University and Molecular Kinetics, Inc., Indianapolis IN USA; Obradovic Group, Temple Univ., Philadelphia PA USA). "PONDR® functions from primary sequence data alone. The predictors are feedforward neural networks that use sequence information from windows of generally 21 amino acids. Attributes, such as the fractional composition of particular amino acids or hydropathy, are calculated over this window, and these values are used as inputs for the predictor. The neural network, which has been trained on a specific set of ordered and disordered sequences, then outputs a value for the central amino acid in the window. The predictions are then smoothed over a sliding window of 9 amino acids. If a residue value exceeds a threshold of 0.5 (the threshold used for training) the residue is considered disordered." (Quoted from the PONDR website.) | * [http://www.pondr.com/ PONDR] (Dunker Group, Indiana University and Molecular Kinetics, Inc., Indianapolis IN USA; Obradovic Group, Temple Univ., Philadelphia PA USA). "PONDR® functions from primary sequence data alone. The predictors are feedforward neural networks that use sequence information from windows of generally 21 amino acids. Attributes, such as the fractional composition of particular amino acids or hydropathy, are calculated over this window, and these values are used as inputs for the predictor. The neural network, which has been trained on a specific set of ordered and disordered sequences, then outputs a value for the central amino acid in the window. The predictions are then smoothed over a sliding window of 9 amino acids. If a residue value exceeds a threshold of 0.5 (the threshold used for training) the residue is considered disordered." (Quoted from the PONDR website.) | ||