51
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Crabtree MD, Mendonça CATF, Bubb QR, Clarke J. Folding and binding pathways of BH3-only proteins are encoded within their intrinsically disordered sequence, not templated by partner proteins. J Biol Chem 2018; 293:9718-9723. [PMID: 29716994 PMCID: PMC6016464 DOI: 10.1074/jbc.ra118.002791] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/24/2018] [Indexed: 12/03/2022] Open
Abstract
Intrinsically disordered regions are present in one-third of eukaryotic proteins and are overrepresented in cellular processes such as signaling, suggesting that intrinsically disordered proteins (IDPs) may have a functional advantage over folded proteins. Upon interacting with a partner macromolecule, a subset of IDPs can fold and bind to form a well-defined three-dimensional conformation. For example, disordered BH3-only proteins bind promiscuously to a large number of homologous BCL-2 family proteins, where they fold to a helical structure in a groove on the BCL-2–like protein surface. As two protein chains are involved in the folding reaction, and the structure is only formed in the presence of the partner macromolecule, this raises the question of where the folding information is encoded. Here, we examine these coupled folding and binding reactions to determine which component determines the folding and binding pathway. Using Φ value analysis to compare transition state interactions between the disordered BH3-only proteins PUMA and BID and the folded BCL-2–like proteins A1 and MCL-1, we found that, even though the BH3-only protein is disordered in isolation and requires a stabilizing partner to fold, its folding and binding pathway is encoded in the IDP itself; the reaction is not templated by the folded partner. We suggest that, by encoding both its transition state and level of residual structure, an IDP can evolve a specific kinetic profile, which could be a crucial functional advantage of disorder.
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Affiliation(s)
- Michael D Crabtree
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Carolina A T F Mendonça
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Quenton R Bubb
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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52
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Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners. Methods Enzymol 2018; 611:137-192. [DOI: 10.1016/bs.mie.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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53
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Salvi N, Abyzov A, Blackledge M. Atomic resolution conformational dynamics of intrinsically disordered proteins from NMR spin relaxation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:43-60. [PMID: 29157493 DOI: 10.1016/j.pnmrs.2017.06.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 05/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental approaches for investigating the conformational behaviour of intrinsically disordered proteins (IDPs). IDPs represent a significant fraction of all proteomes, and, despite their importance for understanding fundamental biological processes, the molecular basis of their activity still remains largely unknown. The functional mechanisms exploited by IDPs in their interactions with other biomolecules are defined by their intrinsic dynamic modes and associated timescales, justifying the considerable interest over recent years in the development of technologies adapted to measure and describe this behaviour. NMR spin relaxation delivers information-rich, site-specific data reporting on conformational fluctuations occurring throughout the molecule. Here we review recent progress in the use of 15N relaxation to identify local backbone dynamics and long-range chain-like motions in unfolded proteins.
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Affiliation(s)
- Nicola Salvi
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France
| | - Anton Abyzov
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France.
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54
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Saglam AS, Wang DW, Zwier MC, Chong LT. Flexibility vs Preorganization: Direct Comparison of Binding Kinetics for a Disordered Peptide and Its Exact Preorganized Analogues. J Phys Chem B 2017; 121:10046-10054. [PMID: 28992700 DOI: 10.1021/acs.jpcb.7b08486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many intrinsically disordered proteins, which are prevalent in nature, fold only upon binding their structured partner proteins. Such proteins have been hypothesized to have a kinetic advantage over their folded, preorganized analogues in binding their partner proteins. Here we determined the effects of ligand preorganization on the kon for a biomedically important system: an intrinsically disordered p53 peptide ligand and the MDM2 protein receptor. Based on direct simulations of binding pathways, computed kon values for fully disordered and preorganized p53 peptide analogues were within error of each other, indicating little if any kinetic advantage to being disordered or preorganized for binding the MDM2 protein. We also examined the effects of increasing the concentration of MDM2 on the extent to which its mechanism of binding to the p53 peptide is induced fit vs conformational selection. Results predict that the mechanism is solely induced fit if the unfolded state of the peptide is more stable than its folded state; otherwise, the mechanism shifts from being dominated by conformational selection at low MDM2 concentration to induced fit at high MDM2 concentration. Taken together, our results are relevant to any protein binding process that involves a disordered peptide of a similar length that forms a single α-helix upon binding a partner protein. Such disorder-to-helix transitions are common among protein interactions of disordered proteins and are therefore of fundamental biological interest.
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Affiliation(s)
- A S Saglam
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - D W Wang
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - M C Zwier
- Department of Chemistry, Drake University , Des Moines, Iowa 50311, United States
| | - L T Chong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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55
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Hadži S, Mernik A, Podlipnik Č, Loris R, Lah J. The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Andrej Mernik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Remy Loris
- Structural Biology Brussels; Department of Biotechnology; Vrije Universiteit Brussel and Center for Structural Biology; Vlaams Instituut voor Biotechnologie; Pleinlaan 2 1050 Brussel Belgium
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
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56
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Hadži S, Mernik A, Podlipnik Č, Loris R, Lah J. The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2017; 56:14494-14497. [DOI: 10.1002/anie.201707853] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Andrej Mernik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Remy Loris
- Structural Biology Brussels; Department of Biotechnology; Vrije Universiteit Brussel and Center for Structural Biology; Vlaams Instituut voor Biotechnologie; Pleinlaan 2 1050 Brussel Belgium
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
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57
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Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure. Proc Natl Acad Sci U S A 2017; 114:9882-9887. [PMID: 28847960 DOI: 10.1073/pnas.1705105114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of defined structure. Instead, they populate ensembles of rapidly interconverting conformations with marginal structural stabilities. Changes in solution conditions such as temperature and crowding agents consequently affect IDPs more than their folded counterparts. Here we reveal that the residual structure content of IDPs is modulated both by ionic strength and by the type of ions present in solution. We show that these ion-specific structural changes result in binding affinity shifts of up to sixfold, which happen through alteration of both association and dissociation rates. These effects follow the Hofmeister series, but unlike the well-established effects on the stability of folded proteins, they already occur at low, hypotonic concentrations of salt. We attribute this sensitivity to the marginal stability of IDPs, which could have physiological implications given the role of IDPs in signaling, the asymmetric ion profiles of different cellular compartments, and the role of ions in biology.
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58
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Lindström I, Dogan J. Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement. Biochemistry 2017; 56:4145-4153. [PMID: 28707474 DOI: 10.1021/acs.biochem.7b00428] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.
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Affiliation(s)
- Ida Lindström
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
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59
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The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease. Biochem Soc Trans 2017; 44:1185-1200. [PMID: 27911701 PMCID: PMC5095923 DOI: 10.1042/bst20160172] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/23/2022]
Abstract
In the 1960s, Christian Anfinsen postulated that the unique three-dimensional structure of a protein is determined by its amino acid sequence. This work laid the foundation for the sequence–structure–function paradigm, which states that the sequence of a protein determines its structure, and structure determines function. However, a class of polypeptide segments called intrinsically disordered regions does not conform to this postulate. In this review, I will first describe established and emerging ideas about how disordered regions contribute to protein function. I will then discuss molecular principles by which regulatory mechanisms, such as alternative splicing and asymmetric localization of transcripts that encode disordered regions, can increase the functional versatility of proteins. Finally, I will discuss how disordered regions contribute to human disease and the emergence of cellular complexity during organismal evolution.
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60
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Liu Y, Wu J, Sun N, Tu C, Shi X, Cheng H, Liu S, Li S, Wang Y, Zheng Y, Uversky VN. Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles. J Proteome Res 2017; 16:2393-2409. [PMID: 28525284 DOI: 10.1021/acs.jproteome.6b01045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100 °C for 10 min) was present in R0mm and R15mm radicles (i.e., before radicle emergence and 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%). The heat-stable proteome of soybean radicles that contain many IDPs could protect lactate dehydrogenase (LDH) during freeze-thaw cycles. Comparison of the 795 heat-stable proteins in the R0mm and R15mm soybean radicles revealed that many of these proteins changed abundance during seedling growth with 170 and 89 proteins being more abundant in R0mm and R15mm, respectively. KEGG analysis identified 18 proteins from the cysteine and methionine metabolism pathways and nine proteins from the phenylpropanoid biosynthesis pathway. As an important type of IDP related to stress, 30 late embryogenesis abundant proteins were also found. Ten selected proteins with high levels of predicted intrinsic disorder were able to efficiently protect LDH from the freeze-thaw-induced inactivation, but the protective ability was not correlated with the disorder content of these proteins. These observations suggest that protection of the enzymes and other proteins in a stressed cell can be one of the biological functions of plant IDPs.
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Affiliation(s)
- Yun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Jiahui Wu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Nan Sun
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo , 285 Kapoor Hall, Buffalo, New York14260, United States
| | - Xiaoying Shi
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Hua Cheng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Simu Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Shuiming Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Yong Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Yizhi Zheng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard MDC07, Tampa, Florida 33612, United States
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences , Institutskaya str., 7, Pushchino, Moscow region 142290, Russia
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61
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Zhang P, Tripathi S, Trinh H, Cheung MS. Opposing Intermolecular Tuning of Ca 2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides. Biophys J 2017; 112:1105-1119. [PMID: 28355539 PMCID: PMC5374985 DOI: 10.1016/j.bpj.2017.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/27/2016] [Accepted: 01/23/2017] [Indexed: 12/03/2022] Open
Abstract
We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca2+ signaling pathways in neurons. It was shown experimentally that Ca2+/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca2+-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca2+ affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng13–49), which binds to apoCaM or holoCaM with binding affinities of the same order of magnitude. Unlike the holoCaM-CaMKII peptide, whose structure can be determined by crystallography, the structural description of the apoCaM-Ng13–49 is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng13–49 structures by matching the changes in the chemical shifts of CaM upon Ng13–49 binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca2+ affinity for CaM with and without binding targets in atomistic models using Jarzynski’s equality. We discovered the molecular underpinnings of lowered affinity of Ca2+ for CaM in the presence of Ng13–49 by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+ binding loops particularly at C-domain of CaM, enabling Ca2+ release. In contrast, CaMKII peptide increases Ca2+ affinity for the C-domain of CaM by stabilizing the two Ca2+ binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng13–49 and holoCaM-CaMKII delineates the importance of CaM’s progressive mechanism of target binding on its Ca2+ binding affinities.
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Affiliation(s)
- Pengzhi Zhang
- Department of Physics, University of Houston, Houston, Texas
| | | | - Hoa Trinh
- Department of Physics, University of Houston, Houston, Texas
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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62
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Okuda M, Higo J, Komatsu T, Konuma T, Sugase K, Nishimura Y. Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH. Biophys J 2017; 111:950-62. [PMID: 27602723 DOI: 10.1016/j.bpj.2016.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 01/09/2023] Open
Abstract
General transcription factor II E (TFIIE) contains an acid-rich region (residues 378-393) in its α-subunit, comprising 13 acidic and two hydrophobic (Phe387 and Val390) residues. Upon binding to the p62 subunit of TFIIH, the acidic region adopts an extended string-like structure on the basic groove of the pleckstrin homology domain (PHD) of p62, and inserts Phe387 and Val390 into two shallow pockets in the groove. Here, we have examined the dynamics of this interaction by NMR and molecular dynamics (MD) simulations. Although alanine substitution of Phe387 and/or Val390 greatly reduced binding to PHD, the binding mode of the mutants was similar to that of the wild-type, as judged by the chemical-shift changes of the PHD. NMR relaxation dispersion profiles of the interaction exhibited large amplitudes for residues in the C-terminal half-string in the acidic region (Phe387, Glu388, Val390, Ala391, and Asp392), indicating a two-site binding mode: one corresponding to the final complex structure, and one to an off-pathway minor complex. To probe the off-pathway complex structure, an atomically detailed free-energy landscape of the binding mode was computed by all-atom multicanonical MD. The most thermodynamically stable cluster corresponded to the final complex structure. One of the next stable clusters was the off-pathway structure cluster, showing the reversed orientation of the C-terminal half-string on the PHD groove, as compared with the final structure. MD calculations elucidated that the C-terminal half-acidic-string forms encounter complexes mainly around the positive groove region with nearly two different orientations of the string, parallel and antiparallel to the final structure. Interestingly, the most encountered complexes exhibit a parallel-like orientation, suggesting that the string has a tendency to bind around the groove in the proper orientation with the aid of Phe387 and/or Val390 to proceed smoothly to the final complex structure.
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Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Tadashi Komatsu
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Tsuyoshi Konuma
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kenji Sugase
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan.
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63
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Olsen JG, Teilum K, Kragelund BB. Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness. Cell Mol Life Sci 2017; 74:3175-3183. [PMID: 28597296 PMCID: PMC5533869 DOI: 10.1007/s00018-017-2560-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not, by themselves, fold into a compact globular structure. They are extremely dynamic and flexible, and are typically involved in signalling and transduction of information through binding to other macromolecules. The reason for their existence may lie in their malleability, which enables them to bind several different partners with high specificity. In addition, their interactions with other macromolecules can be regulated by a variable amount of chemically diverse post-translational modifications. Four kinetically and energetically different types of complexes between an IDP and another macromolecule are reviewed: (1) simple two-state binding involving a single binding site, (2) avidity, (3) allovalency and (4) fuzzy binding; the last three involving more than one site. Finally, a qualitative definition of fuzzy binding is suggested, examples are provided, and its distinction to allovalency and avidity is highlighted and discussed.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
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64
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Fox SJ, Kannan S. Probing the dynamics of disorder. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:57-62. [PMID: 28554553 DOI: 10.1016/j.pbiomolbio.2017.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/25/2016] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
Intrinsically disordered proteins (IDPs) play an important role in many diseases. IDPs are a large and important class of proteins; estimated to represent a significant fraction of many genomes. In contrast to protein-protein interactions between well-folded proteins, IDPs typically bind to targets using short consecutive stretches of amino acids. Structures of IDPs complexed with a target have shown great diversity in binding modes. However, how this binding diversity is achieved at the molecular level is not well understood. Unfortunately, the prediction and detailed characterization of IDPs experimentally is still a very challenging task; however molecular mechanics based molecular dynamics simulation are well suited for studying the dynamic behavior of IDPs. We look into the current state for force fields for simulating IDPs and an example of how these methods have been applied to the p53 protein. p53 is one of the most extensively studied IDPs, with multiple intrinsically disordered regulatory domains that mediate its interactions with many other proteins engaged in multiple biological pathways. We show how molecular dynamics simulations can be used to elucidate on the mechanisms involved in selection of the different binding partners.
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Affiliation(s)
- Stephen John Fox
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.
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65
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Crabtree MD, Borcherds W, Poosapati A, Shammas SL, Daughdrill GW, Clarke J. Conserved Helix-Flanking Prolines Modulate Intrinsically Disordered Protein:Target Affinity by Altering the Lifetime of the Bound Complex. Biochemistry 2017; 56:2379-2384. [PMID: 28425697 PMCID: PMC5467178 DOI: 10.1021/acs.biochem.7b00179] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Appropriate
integration of cellular signals requires a delicate
balance of ligand–target binding affinities. Increasing the
level of residual structure in intrinsically disordered proteins (IDPs),
which are overrepresented in these cellular processes, has been shown
previously to enhance binding affinities and alter cellular function.
Conserved proline residues are commonly found flanking regions of
IDPs that become helical upon interacting with a partner protein.
Here, we mutate these helix-flanking prolines in p53 and MLL and find
opposite effects on binding affinity upon an increase in free IDP
helicity. In both cases, changes in affinity were due to alterations
in dissociation, not association, rate constants, which is inconsistent
with conformational selection mechanisms. We conclude that, contrary
to previous suggestions, helix-flanking prolines do not regulate affinity
by modulating the rate of complex formation. Instead, they influence
binding affinities by controlling the lifetime of the bound complex.
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Affiliation(s)
- Michael D Crabtree
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Wade Borcherds
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida , Tampa, Florida 33620, United States.,Florida Center for Drug Discovery and Innovation, University of South Florida , Tampa, Florida 33612, United States
| | - Anusha Poosapati
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida , Tampa, Florida 33620, United States.,Florida Center for Drug Discovery and Innovation, University of South Florida , Tampa, Florida 33612, United States
| | - Sarah L Shammas
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Gary W Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida , Tampa, Florida 33620, United States.,Florida Center for Drug Discovery and Innovation, University of South Florida , Tampa, Florida 33612, United States
| | - Jane Clarke
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
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66
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Neukirchen S, Krieger V, Roschger C, Schubert M, Elsässer B, Cabrele C. Impact of the amino acid sequence on the conformation of side chain lactam-bridged octapeptides. J Pept Sci 2017; 23:587-596. [PMID: 28370688 DOI: 10.1002/psc.2997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 01/22/2023]
Abstract
Synthetic helical peptides are valuable scaffolds for the development of modulators of protein-protein interactions involving helical motifs. Backbone-to-side chain or side chain-to-side chain constraints have been and still are intensively exploited to stabilize short α-helices. Very often, these constraints have been combined with backbone modifications induced by Cα-tetrasubstituted, β-, or γ-amino acids, which facilitate the α-peptide or α/β/γ-peptide adopting an α-helical conformation. In this work, we investigated the helical character of octapeptides that were cyclized by a Lys-Asp-(i,i + 4)-lactam bridge. We started with two sequences extracted from the helix-loop-helix region of the Id proteins, which are inhibitors of cell differentiation during development and in cancer. Nineteen analogs containing the lactam bridge at different positions and displaying different amino acid core triads (i + 1,2,3) as well as outer residues were prepared by solid-phase methodology. Their conformation in water and water/2,2,2-trifluoroethanol mixtures was investigated by circular dichroism (CD) spectroscopy. The cyclopeptides could be grouped in helix-prone and non-helix-prone structures. Both the amino acid core triad (i + 1,2,3) and the pendant residues positively or negatively affected the formation of a helical structure. Computational studies based on the NMR-derived helical structure of a cyclopeptide containing Aib at position (i + 2) of the triad were generally in agreement with the secondary structure propensity of the cyclopeptides observed by CD spectroscopy. In conclusion, the Lys-Asp-(i,i + 4)-lactam bridge may succeed or fail in the stabilization of short helices, depending on the primary structure. Moreover, computational methods may be valuable tools to discriminate helix-prone from non-helix-prone peptide-based macrolactams. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Saskia Neukirchen
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.,Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Viktoria Krieger
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.,Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Cornelia Roschger
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Mario Schubert
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Brigitta Elsässer
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Chiara Cabrele
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
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67
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Koide H, Yoshimatsu K, Hoshino Y, Lee SH, Okajima A, Ariizumi S, Narita Y, Yonamine Y, Weisman AC, Nishimura Y, Oku N, Miura Y, Shea KJ. A polymer nanoparticle with engineered affinity for a vascular endothelial growth factor (VEGF 165). Nat Chem 2017. [PMID: 28644480 DOI: 10.1038/nchem.2749] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein affinity reagents are widely used in basic research, diagnostics and separations and for clinical applications, the most common of which are antibodies. However, they often suffer from high cost, and difficulties in their development, production and storage. Here we show that a synthetic polymer nanoparticle (NP) can be engineered to have many of the functions of a protein affinity reagent. Polymer NPs with nM affinity to a key vascular endothelial growth factor (VEGF165) inhibit binding of the signalling protein to its receptor VEGFR-2, preventing receptor phosphorylation and downstream VEGF165-dependent endothelial cell migration and invasion into the extracellular matrix. In addition, the NPs inhibit VEGF-mediated new blood vessel formation in Matrigel plugs in vivo. Importantly, the non-toxic NPs were not found to exhibit off-target activity. These results support the assertion that synthetic polymers offer a new paradigm in the search for abiotic protein affinity reagents by providing many of the functions of their protein counterparts.
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Affiliation(s)
- Hiroyuki Koide
- Department of Medical Biochemistry, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8526, Japan.,Department of Chemistry, University of California Irvine, Irvine, California 92697, USA
| | - Keiichi Yoshimatsu
- Department of Chemistry, University of California Irvine, Irvine, California 92697, USA
| | - Yu Hoshino
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Shih-Hui Lee
- Department of Chemistry, University of California Irvine, Irvine, California 92697, USA
| | - Ai Okajima
- Department of Medical Biochemistry, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8526, Japan
| | - Saki Ariizumi
- Department of Medical Biochemistry, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8526, Japan
| | - Yudai Narita
- Department of Medical Biochemistry, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8526, Japan
| | - Yusuke Yonamine
- Department of Chemistry, University of California Irvine, Irvine, California 92697, USA
| | - Adam C Weisman
- Department of Chemistry, University of California Irvine, Irvine, California 92697, USA
| | - Yuri Nishimura
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Naoto Oku
- Department of Medical Biochemistry, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8526, Japan
| | - Yoshiko Miura
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Kenneth J Shea
- Department of Chemistry, University of California Irvine, Irvine, California 92697, USA
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68
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DeForte S, Uversky VN. Quarterly intrinsic disorder digest (April-May-June, 2014). INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1287505. [PMID: 28321370 DOI: 10.1080/21690707.2017.1287505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This is the 6th issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Département De Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute of Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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69
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Baliga C, Varadarajan R, Aghera N. Homodimeric Escherichia coli Toxin CcdB (Controller of Cell Division or Death B Protein) Folds via Parallel Pathways. Biochemistry 2016; 55:6019-6031. [PMID: 27696818 DOI: 10.1021/acs.biochem.6b00726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The existence of parallel pathways in the folding of proteins seems intuitive, yet remains controversial. We explore the folding kinetics of the homodimeric Escherichia coli toxin CcdB (Controller of Cell Division or Death B protein) using multiple optical probes and approaches. Kinetic studies performed as a function of protein and denaturant concentrations demonstrate that the folding of CcdB is a four-state process. The two intermediates populated during folding are present on parallel pathways. Both form by rapid association of the monomers in a diffusion limited manner and appear to be largely unstructured, as they are silent to the optical probes employed in the current study. The existence of parallel pathways is supported by the insensitivity of the amplitudes of the refolding kinetic phases to the different probes used in the study. More importantly, interrupted refolding studies and ligand binding studies clearly demonstrate that the native state forms in a biexponential manner, implying the presence of at least two pathways. Our studies indicate that the CcdA antitoxin binds only to the folded CcdB dimer and not to any earlier folding intermediates. Thus, despite being part of the same operon, the antitoxin does not appear to modulate the folding pathway of the toxin encoded by the downstream cistron. This study highlights the utility of ligand binding in distinguishing between sequential and parallel pathways in protein folding studies, while also providing insights into molecular interactions during folding in Type II toxin-antitoxin systems.
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Affiliation(s)
- Chetana Baliga
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O., Bangalore 560 004, India
| | - Nilesh Aghera
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India
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70
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Song T, Wang Z, Zhang Z. Substituted indole Mcl-1 inhibitors: a patent evaluation (WO2015148854A1). Expert Opin Ther Pat 2016; 26:1227-1238. [DOI: 10.1080/13543776.2016.1240786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ting Song
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian, China
| | - Ziqian Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian, China
| | - Zhichao Zhang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian, China
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71
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Mollica L, Bessa LM, Hanoulle X, Jensen MR, Blackledge M, Schneider R. Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment. Front Mol Biosci 2016; 3:52. [PMID: 27668217 PMCID: PMC5016563 DOI: 10.3389/fmolb.2016.00052] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022] Open
Abstract
In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context.
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Affiliation(s)
- Luca Mollica
- CompuNet, Drug Discovery and Development, Istituto Italiano di Tecnologia Genova, Italy
| | - Luiza M Bessa
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
| | - Xavier Hanoulle
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
| | | | - Martin Blackledge
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes Grenoble, France
| | - Robert Schneider
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
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72
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Harmon TS, Crabtree MD, Shammas SL, Posey AE, Clarke J, Pappu RV. GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins. Protein Eng Des Sel 2016; 29:339-46. [PMID: 27503953 DOI: 10.1093/protein/gzw034] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 06/21/2016] [Indexed: 01/15/2023] Open
Abstract
Many intrinsically disordered proteins (IDPs) participate in coupled folding and binding reactions and form alpha helical structures in their bound complexes. Alanine, glycine, or proline scanning mutagenesis approaches are often used to dissect the contributions of intrinsic helicities to coupled folding and binding. These experiments can yield confounding results because the mutagenesis strategy changes the amino acid compositions of IDPs. Therefore, an important next step in mutagenesis-based approaches to mechanistic studies of coupled folding and binding is the design of sequences that satisfy three major constraints. These are (i) achieving a target intrinsic alpha helicity profile; (ii) fixing the positions of residues corresponding to the binding interface; and (iii) maintaining the native amino acid composition. Here, we report the development of a G: enetic A: lgorithm for D: esign of I: ntrinsic secondary S: tructure (GADIS) for designing sequences that satisfy the specified constraints. We describe the algorithm and present results to demonstrate the applicability of GADIS by designing sequence variants of the intrinsically disordered PUMA system that undergoes coupled folding and binding to Mcl-1. Our sequence designs span a range of intrinsic helicity profiles. The predicted variations in sequence-encoded mean helicities are tested against experimental measurements.
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Affiliation(s)
- Tyler S Harmon
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael D Crabtree
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Ammon E Posey
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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73
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Eustache S, Leprince J, Tufféry P. Progress with peptide scanning to study structure-activity relationships: the implications for drug discovery. Expert Opin Drug Discov 2016; 11:771-84. [PMID: 27310575 DOI: 10.1080/17460441.2016.1201058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Peptides have gained renewed interest as candidate therapeutics. However, to bring them to a broader clinical use, challenges such as the rational optimization of their pharmacological properties remain. Peptide scanning techniques offer a systematic framework to gain information on the functional role of individual amino acids of a peptide. Due to progress in mastering new chemical synthesis routes targeting amino acid backbone, they are currently diversified. Structure-activity relationship (SAR) analyses such as alanine- or enantioneric- scanning can now be supplemented by N-substitution, lactam cyclisation- or aza-amino scanning procedures addressing not only SAR considerations but also the peptide pharmacological properties. AREAS COVERED This review highlights the different scanning techniques currently available and illustrates how they can impact drug discovery. EXPERT OPINION Progress in peptide scanning techniques opens new perspectives for peptide drug development. It comes with the promise of a paradigm change in peptide drug design in which peptide drugs will be closer to the parent peptides. However, scanning still remains assimilable to a trial and error strategy that could benefit from being combined with specific in silico approaches that start reaching maturity.
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Affiliation(s)
- Stéphanie Eustache
- a INSERM UMR-S 973 , University Paris-Diderot, Sorbonne Paris Cité , Paris , France
| | - Jérôme Leprince
- b INSERM U982 , Regional Platform for Cell Imaging of Normandy (PRIMACEN), University Rouen-Normandy , Mont-Saint-Aignan, France
| | - Pierre Tufféry
- a INSERM UMR-S 973 , University Paris-Diderot, Sorbonne Paris Cité , Paris , France
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74
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NMR Meets Tau: Insights into Its Function and Pathology. Biomolecules 2016; 6:biom6020028. [PMID: 27338491 PMCID: PMC4919923 DOI: 10.3390/biom6020028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/02/2016] [Accepted: 05/26/2016] [Indexed: 12/21/2022] Open
Abstract
In this review, we focus on what we have learned from Nuclear Magnetic Resonance (NMR) studies on the neuronal microtubule-associated protein Tau. We consider both the mechanistic details of Tau: the tubulin relationship and its aggregation process. Phosphorylation of Tau is intimately linked to both aspects. NMR spectroscopy has depicted accurate phosphorylation patterns by different kinases, and its non-destructive character has allowed functional assays with the same samples. Finally, we will discuss other post-translational modifications of Tau and its interaction with other cellular factors in relationship to its (dys)function.
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75
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Abyzov A, Salvi N, Schneider R, Maurin D, Ruigrok RWH, Jensen MR, Blackledge M. Identification of Dynamic Modes in an Intrinsically Disordered Protein Using Temperature-Dependent NMR Relaxation. J Am Chem Soc 2016; 138:6240-51. [PMID: 27112095 DOI: 10.1021/jacs.6b02424] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dynamic modes and time scales sampled by intrinsically disordered proteins (IDPs) define their function. Nuclear magnetic resonance (NMR) spin relaxation is probably the most powerful tool for investigating these motions delivering site-specific descriptions of conformational fluctuations from throughout the molecule. Despite the abundance of experimental measurement of relaxation in IDPs, the physical origin of the measured relaxation rates remains poorly understood. Here we measure an extensive range of auto- and cross-correlated spin relaxation rates at multiple magnetic field strengths on the C-terminal domain of the nucleoprotein of Sendai virus, over a large range of temperatures (268-298 K), and combine these data to describe the dynamic behavior of this archetypal IDP. An Arrhenius-type relationship is used to simultaneously analyze up to 61 relaxation rates per amino acid over the entire temperature range, allowing the measurement of local activation energies along the chain, and the assignment of physically distinct dynamic modes. Fast (τ ≤ 50 ps) components report on librational motions, a dominant mode occurs on time scales around 1 ns, apparently reporting on backbone sampling within Ramachandran substates, while a slower component (5-25 ns) reports on segmental dynamics dominated by the chain-like nature of the protein. Extending the study to three protein constructs of different lengths (59, 81, and 124 amino acids) substantiates the assignment of these contributions. The analysis is shown to be remarkably robust, accurately predicting a broad range of relaxation data measured at different magnetic field strengths and temperatures. The ability to delineate intrinsic modes and time scales from NMR spin relaxation will improve our understanding of the behavior and function of IDPs, adding a new and essential dimension to the description of this biologically important and ubiquitous class of proteins.
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Affiliation(s)
- Anton Abyzov
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Robert Schneider
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Damien Maurin
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Rob W H Ruigrok
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
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76
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Cuevas-Velazquez CL, Saab-Rincón G, Reyes JL, Covarrubias AA. The Unstructured N-terminal Region of Arabidopsis Group 4 Late Embryogenesis Abundant (LEA) Proteins Is Required for Folding and for Chaperone-like Activity under Water Deficit. J Biol Chem 2016; 291:10893-903. [PMID: 27006402 DOI: 10.1074/jbc.m116.720318] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Indexed: 11/06/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are a conserved group of proteins widely distributed in the plant kingdom that participate in the tolerance to water deficit of different plant species. In silico analyses indicate that most LEA proteins are structurally disordered. The structural plasticity of these proteins opens the question of whether water deficit modulates their conformation and whether these possible changes are related to their function. In this work, we characterized the secondary structure of Arabidopsis group 4 LEA proteins. We found that they are disordered in aqueous solution, with high intrinsic potential to fold into α-helix. We demonstrate that complete dehydration is not required for these proteins to sample ordered structures because milder water deficit and macromolecular crowding induce high α-helix levels in vitro, suggesting that prevalent conditions under water deficit modulate their conformation. We also show that the N-terminal region, conserved across all group 4 LEA proteins, is necessary and sufficient for conformational transitions and that their protective function is confined to this region, suggesting that folding into α-helix is required for chaperone-like activity under water limitation. We propose that these proteins can exist as different conformers, favoring functional diversity, a moonlighting property arising from their structural dynamics.
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Affiliation(s)
| | - Gloria Saab-Rincón
- Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250 Cuernavaca, México
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77
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Shimojo H, Kawaguchi A, Oda T, Hashiguchi N, Omori S, Moritsugu K, Kidera A, Hiragami-Hamada K, Nakayama JI, Sato M, Nishimura Y. Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail. Sci Rep 2016; 6:22527. [PMID: 26934956 PMCID: PMC4776139 DOI: 10.1038/srep22527] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/15/2016] [Indexed: 11/09/2022] Open
Abstract
The chromodomain of HP1α binds directly to lysine 9-methylated histone H3 (H3K9me). This interaction is enhanced by phosphorylation of serine residues in the N-terminal tail of HP1α by unknown mechanism. Here we show that phosphorylation modulates flexibility of HP1α's N-terminal tail, which strengthens the interaction with H3. NMR analysis of HP1α's chromodomain with N-terminal tail reveals that phosphorylation does not change the overall tertiary structure, but apparently reduces the tail dynamics. Small angle X-ray scattering confirms that phosphorylation contributes to extending HP1α's N-terminal tail. Systematic analysis using deletion mutants and replica exchange molecular dynamics simulations indicate that the phosphorylated serines and following acidic segment behave like an extended string and dynamically bind to H3 basic residues; without phosphorylation, the most N-terminal basic segment of HP1α inhibits interaction of the acidic segment with H3. Thus, the dynamic string-like behavior of HP1α's N-terminal tail underlies the enhancement in H3 binding due to phosphorylation.
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Affiliation(s)
- Hideaki Shimojo
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ayumi Kawaguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Nobuto Hashiguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Satoshi Omori
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akinori Kidera
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kyoko Hiragami-Hamada
- Division of Genome Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501, Japan
| | - Mamoru Sato
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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78
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Jhong SR, Li CY, Sung TC, Lan YJ, Chang KJ, Chiang YW. Evidence for an Induced-Fit Process Underlying the Activation of Apoptotic BAX by an Intrinsically Disordered BimBH3 Peptide. J Phys Chem B 2016; 120:2751-60. [PMID: 26913490 DOI: 10.1021/acs.jpcb.6b00909] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Apoptotic BAX protein functions as a critical gateway to mitochondria-mediated apoptosis. A diversity of stimuli has been implicated in initiating BAX activation, but the triggering mechanism remains elusive. Here we study the interaction of BAX with an intrinsically disordered BH3 motif of Bim protein (BimBH3) using ESR techniques. Upon incubation with BAX, BimBH3 binds to BAX at helices 1/6 trigger site to initiate conformational changes of BAX, which in turn promotes the formation of BAX oligomers. The study strategy is twofold: while BAX oligomerization was monitored through spectral changes of spin-labeled BAX, the binding kinetics was studied by observing time-dependent changes of spin-labeled BimBH3. Meanwhile, conformational transition between the unstructured and structured BimBH3 was measured. We show that helical propensity of the BimBH3 is increased upon binding to BAX but is then reduced after being released from the activated BAX; the release is due to the BimBH3-induced conformational change of BAX that is a prerequisite for the oligomer assembling. Intermediate states are identified, offering a key snapshot of the coupled folding and binding process. Our results provide a quantitative mechanistic description of the BAX activation and reveal new insights into the mechanism underlying the interactions between BAX and BH3-mimetic peptide.
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Affiliation(s)
- Siao-Ru Jhong
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Ching-Yu Li
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Tai-Ching Sung
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Kuo-Jung Chang
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan
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79
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Miles JA, Yeo DJ, Rowell P, Rodriguez-Marin S, Pask CM, Warriner SL, Edwards TA, Wilson AJ. Hydrocarbon constrained peptides - understanding preorganisation and binding affinity. Chem Sci 2016; 7:3694-3702. [PMID: 28970875 PMCID: PMC5618334 DOI: 10.1039/c5sc04048e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/15/2016] [Indexed: 12/19/2022] Open
Abstract
The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-alkenylglycine derived amino acid to synthesise hydrocarbon constrained BH3-family sequences (BIM and BID). Our biophysical and structural analyses illustrate that whilst the introduction of the constraint increases the population of the bioactive α-helical conformation of the peptide in solution, it does not enhance the inhibitory potency against pro-apoptotic Bcl-xL and Mcl-1 PPIs. SPR analyses indicate binding occurs via an induced fit mechanism whilst X-ray analyses illustrate none of the key interactions between the helix and protein are disturbed. The behaviour derives from enthalpy-entropy compensation which may be considered in terms of the ground state energies of the unbound constrained and unconstrained peptides; this has implications for the design of preorganised peptides to target protein-protein interactions.
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Affiliation(s)
- Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - David J Yeo
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Philip Rowell
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Silvia Rodriguez-Marin
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Christopher M Pask
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
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80
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Shammas SL, Crabtree MD, Dahal L, Wicky BIM, Clarke J. Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies. J Biol Chem 2016; 291:6689-95. [PMID: 26851275 PMCID: PMC4807256 DOI: 10.1074/jbc.r115.692715] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of persistent structure. Since their identification more than a decade ago, many questions regarding their functional relevance and interaction mechanisms remain unanswered. Although most experiments have taken equilibrium and structural perspectives, fewer studies have investigated the kinetics of their interactions. Here we review and highlight the type of information that can be gained from kinetic studies. In particular, we show how kinetic studies of coupled folding and binding reactions, an important class of signaling event, are needed to determine mechanisms.
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Affiliation(s)
- Sarah L Shammas
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael D Crabtree
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Liza Dahal
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Basile I M Wicky
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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81
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Gianni S, Dogan J, Jemth P. Coupled binding and folding of intrinsically disordered proteins: what can we learn from kinetics? Curr Opin Struct Biol 2016; 36:18-24. [DOI: 10.1016/j.sbi.2015.11.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/13/2015] [Accepted: 11/26/2015] [Indexed: 12/16/2022]
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82
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Kvansakul M, Hinds MG. The Bcl-2 family: structures, interactions and targets for drug discovery. Apoptosis 2015; 20:136-50. [PMID: 25398535 DOI: 10.1007/s10495-014-1051-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Two phylogenetically and structurally distinct groups of proteins regulate stress induced intrinsic apoptosis, the programmed disassembly of cells. Together they form the B cell lymphoma-2 (Bcl-2) family. Bcl-2 proteins appeared early in metazoan evolution and are identified by the presence of up to four short conserved sequence blocks known as Bcl-2 homology (BH) motifs, or domains. The simple BH3-only proteins bear only a BH3-motif and are intrinsically disordered proteins and antagonize or activate the other group, the multi-motif Bcl-2 proteins that have up to four BH motifs, BH1-BH4. Multi-motif Bcl-2 proteins are either pro-survival or pro-apoptotic in action and have remarkably similar α-helical bundle structures that provide a binding groove formed from the BH1, BH2, and BH3-motifs for their BH3-bearing antagonists. In mammals a network of interactions between Bcl-2 members regulates mitochondrial outer membrane permeability (MOMP) and efflux of cytochrome c and other death inducing factors from mitochondria to initiate the apoptotic caspase cascade, but the molecular events leading to MOMP are uncertain. Dysregulation of the Bcl-2 family occurs in many diseases and pathogenic viruses have assimilated pro-survival Bcl-2 proteins to evade immune responses. Their role in disease has made the Bcl-2 family the focus of drug design attempts and clinical trials are showing promise for 'BH3-mimics', drugs that mimic the ability of BH3-only proteins to neutralize selected pro-survival proteins to induce cell death in tumor cells. This review focuses on the structural biology of Bcl-2 family proteins, their interactions and attempts to harness them as targets for drug design.
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Affiliation(s)
- Marc Kvansakul
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, 3086, Australia,
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83
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Sherry KP, Johnson SE, Hatem CL, Majumdar A, Barrick D. Effects of Linker Length and Transient Secondary Structure Elements in the Intrinsically Disordered Notch RAM Region on Notch Signaling. J Mol Biol 2015; 427:3587-3597. [PMID: 26344835 DOI: 10.1016/j.jmb.2015.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/26/2015] [Accepted: 09/02/2015] [Indexed: 12/14/2022]
Abstract
Formation of the bivalent interaction between the Notch intracellular domain (NICD) and the transcription factor CBF-1/RBP-j, Su(H), Lag-1 (CSL) is a key event in Notch signaling because it switches Notch-responsive genes from a repressed state to an activated state. Interaction of the intrinsically disordered RBP-j-associated molecule (RAM) region of NICD with CSL is thought to both disrupt binding of corepressor proteins to CSL and anchor NICD to CSL, promoting interaction of the ankyrin domain of NICD with CSL through an effective concentration mechanism. To quantify the role of disorder in the RAM linker region on the effective concentration enhancement of Notch transcriptional activation, we measured the effects of linker length variation on activation. The resulting activation profile has general features of a worm-like chain model for effective concentration. However, deviations from the model for short sequence deletions suggest that RAM contains sequence-specific structural elements that may be important for activation. Structural characterization of the RAM linker with sedimentation velocity analytical ultracentrifugation and NMR spectroscopy reveals that the linker is compact and contains three transient helices and two extended and dynamic regions. To test if these secondary structure elements are important for activation, we made sequence substitutions to change the secondary structure propensities of these elements and measured transcriptional activation of the resulting variants. Substitutions to two of these nonrandom elements (helix 2, extended region 1) have effects on activation, but these effects do not depend on the nature of the substituting residues. Thus, the primary sequences of these elements, but not their secondary structures, are influencing signaling.
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Affiliation(s)
- Kathryn P Sherry
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Scott E Johnson
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Christine L Hatem
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Ananya Majumdar
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Doug Barrick
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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84
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Rogers JM, Suga H. Discovering functional, non-proteinogenic amino acid containing, peptides using genetic code reprogramming. Org Biomol Chem 2015; 13:9353-63. [PMID: 26280393 DOI: 10.1039/c5ob01336d] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The protein synthesis machinery of the cell, the ribosome and associated factors, is able to accurately follow the canonical genetic code, that which maps RNA sequence to protein sequence, to assemble functional proteins from the twenty or so proteinogenic amino acids. A number of innovative methods have arisen to take advantage of this accurate, and efficient, machinery to direct the assembly of non-proteinogenic amino acids. We review and compare these routes to 'reprogram the genetic code' including in vitro translation, engineered aminoacyl tRNA synthetases, and RNA 'flexizymes'. These studies show that the ribosome is highly tolerant of unnatural amino acids, with hundreds of unusual substrates of varying structure and chemistries being incorporated into protein chains. We also discuss how these methods have been coupled to selection techniques, such as phage display and mRNA display, opening up an exciting new avenue for the production of proteins and peptides with properties and functions beyond that which is possible using proteins composed entirely of the proteinogenic amino acids.
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Affiliation(s)
- J M Rogers
- Department of Chemistry, The University of Tokyo, Graduate School of Science, Tokyo, Japan.
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85
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Dogan J, Jonasson J, Andersson E, Jemth P. Binding Rate Constants Reveal Distinct Features of Disordered Protein Domains. Biochemistry 2015; 54:4741-50. [DOI: 10.1021/acs.biochem.5b00520] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jakob Dogan
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Josefin Jonasson
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Eva Andersson
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Per Jemth
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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86
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Berlow RB, Dyson HJ, Wright PE. Functional advantages of dynamic protein disorder. FEBS Lett 2015; 589:2433-40. [PMID: 26073260 DOI: 10.1016/j.febslet.2015.06.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered proteins participate in many important cellular regulatory processes. The absence of a well-defined structure in the free state of a disordered domain, and even on occasion when it is bound to physiological partners, is fundamental to its function. Disordered domains are frequently the location of multiple sites for post-translational modification, the key element of metabolic control in the cell. When a disordered domain folds upon binding to a partner, the resulting complex buries a far greater surface area than in an interaction of comparably-sized folded proteins, thus maximizing specificity at modest protein size. Disorder also maintains accessibility of sites for post-translational modification. Because of their inherent plasticity, disordered domains frequently adopt entirely different structures when bound to different partners, increasing the repertoire of available interactions without the necessity for expression of many different proteins. This feature also adds to the faithfulness of cellular regulation, as the availability of a given disordered domain depends on competition between various partners relevant to different cellular processes.
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Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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87
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Chebaro Y, Ballard AJ, Chakraborty D, Wales DJ. Intrinsically disordered energy landscapes. Sci Rep 2015; 5:10386. [PMID: 25999294 PMCID: PMC4441119 DOI: 10.1038/srep10386] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/10/2015] [Indexed: 12/19/2022] Open
Abstract
Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such 'intrinsically disordered' landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an α-helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium.
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Affiliation(s)
- Yassmine Chebaro
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
| | - Andrew J Ballard
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
| | - Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
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88
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Dogan J, Jemth P. Only kinetics can prove conformational selection. Biophys J 2015; 107:1997-1998. [PMID: 25418181 DOI: 10.1016/j.bpj.2014.08.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jakob Dogan
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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89
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Abstract
Intrinsically disordered proteins (IDPs) are important components of the cellular signalling machinery, allowing the same polypeptide to undertake different interactions with different consequences. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and providing a mechanism for tissue-specific signalling. These proteins participate in the assembly of signalling complexes and in the dynamic self-assembly of membrane-less nuclear and cytoplasmic organelles. Experimental, computational and bioinformatic analyses combine to identify and characterize disordered regions of proteins, leading to a greater appreciation of their widespread roles in biological processes.
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90
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Blair LJ, Baker JD, Sabbagh JJ, Dickey CA. The emerging role of peptidyl-prolyl isomerase chaperones in tau oligomerization, amyloid processing, and Alzheimer's disease. J Neurochem 2015; 133:1-13. [PMID: 25628064 DOI: 10.1111/jnc.13033] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/12/2014] [Accepted: 01/05/2015] [Indexed: 12/20/2022]
Abstract
Peptidyl-prolyl cis/trans isomerases (PPIases), a unique family of molecular chaperones, regulate protein folding at proline residues. These residues are abundant within intrinsically disordered proteins, like the microtubule-associated protein tau. Tau has been shown to become hyperphosphorylated and accumulate as one of the two main pathological hallmarks in Alzheimer's disease, the other being amyloid beta (Ab). PPIases, including Pin1, FK506-binding protein (FKBP) 52, FKBP51, and FKBP12, have been shown to interact with and regulate tau biology. This interaction is particularly important given the numerous proline-directed phosphorylation sites found on tau and the role phosphorylation has been found to play in pathogenesis. This regulation then affects downstream aggregation and oligomerization of tau. However, many PPIases have yet to be explored for their effects on tau biology, despite the high likelihood of interaction based on proline content. Moreover, Pin1, FKBP12, FKBP52, cyclophilin (Cyp) A, CypB, and CypD have been shown to also regulate Ab production or the toxicity associated with Ab pathology. Therefore, PPIases directly and indirectly regulate pathogenic protein multimerization in Alzheimer's disease and represent a family rich in targets for modulating the accumulation and toxicity.
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Affiliation(s)
- Laura J Blair
- Department of Molecular Medicine, Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, USA
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91
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Gibbs EB, Showalter SA. Quantitative biophysical characterization of intrinsically disordered proteins. Biochemistry 2015; 54:1314-26. [PMID: 25631161 DOI: 10.1021/bi501460a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) are broadly defined as protein regions that do not cooperatively fold into a spatially or temporally stable structure. Recent research strongly supports the hypothesis that a conserved functional role for structural disorder renders IDPs uniquely capable of functioning in biological processes such as cellular signaling and transcription. Recently, the frequency of application of rigorous mechanistic biochemistry and quantitative biophysics to disordered systems has increased dramatically. For example, the launch of the Protein Ensemble Database (pE-DB) demonstrates that the potential now exists to refine models for the native state structure of IDPs using experimental data. However, rigorous assessment of which observables place the strongest and least biased constraints on those ensembles is now needed. Most importantly, the past few years have seen strong growth in the number of biochemical and biophysical studies attempting to connect structural disorder with function. From the perspective of equilibrium thermodynamics, there is a clear need to assess the relative significance of hydrophobic versus electrostatic forces in IDP interactions, if it is possible to generalize at all. Finally, kinetic mechanisms that invoke conformational selection and/or induced fit are often used to characterize coupled IDP folding and binding, although application of these models is typically built upon thermodynamic observations. Recently, the reaction rates and kinetic mechanisms of more intrinsically disordered systems have been tested through rigorous kinetic experiments. Motivated by these exciting advances, here we provide a review and prospectus for the quantitative study of IDP structure, thermodynamics, and kinetics.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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92
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Schneider R, Maurin D, Communie G, Kragelj J, Hansen DF, Ruigrok RWH, Jensen MR, Blackledge M. Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR. J Am Chem Soc 2015; 137:1220-9. [PMID: 25551399 DOI: 10.1021/ja511066q] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite playing important roles throughout biology, molecular recognition mechanisms in intrinsically disordered proteins remain poorly understood. We present a combination of (1)H(N), (13)C', and (15)N relaxation dispersion NMR, measured at multiple titration points, to map the interaction between the disordered domain of Sendai virus nucleoprotein (NT) and the C-terminal domain of the phosphoprotein (PX). Interaction with PX funnels the free-state equilibrium of NT by stabilizing one of the previously identified helical substates present in the prerecognition ensemble in a nonspecific and dynamic encounter complex on the surface of PX. This helix then locates into the binding site at a rate coincident with intrinsic breathing motions of the helical groove on the surface of PX. The binding kinetics of complex formation are thus regulated by the intrinsic free-state conformational dynamics of both proteins. This approach, providing high-resolution structural and kinetic information about a complex folding and binding interaction trajectory, can be applied to a number of experimental systems to provide a general framework for understanding conformational disorder in biomolecular function.
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93
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Chen T, Song J, Chan HS. Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding. Curr Opin Struct Biol 2014; 30:32-42. [PMID: 25544254 DOI: 10.1016/j.sbi.2014.12.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 11/29/2022]
Abstract
The diverse biological functions of intrinsically disordered proteins (IDPs) have markedly raised our appreciation of protein conformational versatility, whereas the existence of energetically favorable yet functional detrimental nonnative interactions underscores the physical limitations of evolutionary optimization. Here we survey recent advances in using biophysical modeling to gain insight into experimentally observed nonnative behaviors and IDP properties. Simulations of IDP interactions to date focus mostly on coupled folding-binding, which follows essentially the same organizing principle as the local-nonlocal coupling mechanism in cooperative folding of monomeric globular proteins. By contrast, more innovative theories of electrostatic and aromatic interactions are needed for the conceptually novel but less-explored 'fuzzy' complexes in which the functionally bound IDPs remain largely disordered.
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Affiliation(s)
- Tao Chen
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Jianhui Song
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada.
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94
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Affiliation(s)
- Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; and
| | - Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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95
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Rogers JM, Oleinikovas V, Shammas SL, Wong CT, De Sancho D, Baker CM, Clarke J. Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. Proc Natl Acad Sci U S A 2014; 111:15420-5. [PMID: 25313042 PMCID: PMC4217413 DOI: 10.1073/pnas.1409122111] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here we examine a typical system, where a small disordered protein (PUMA, p53 upregulated modulator of apoptosis) folds to an α-helix when bound to a groove on the surface of a folded protein (MCL-1, induced myeloid leukemia cell differentiation protein). We follow the association of these proteins using rapid-mixing stopped flow, and examine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations. We demonstrate the utility of methods developed for the study of monomeric protein folding, including β-Tanford values, Leffler α, Φ-value analysis, and coarse-grained simulations, and propose a self-consistent mechanism for binding. Folding of the disordered protein before binding does not appear to be required and few, if any, specific interactions are required to commit to association. The majority of PUMA folding occurs after the transition state, in the presence of MCL-1. We also examine the role of the side chains of folded MCL-1 that make up the binding groove and find that many favor equilibrium binding but, surprisingly, inhibit the association process.
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Affiliation(s)
- Joseph M Rogers
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | | | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Chi T Wong
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M Baker
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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96
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Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants. J Phys Chem B 2014; 119:896-905. [PMID: 25231121 DOI: 10.1021/jp505902m] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Vasopressin and oxytocin are intrinsically disordered cyclic nonapeptides belonging to a family of neurohypophysial hormones. Although unique in their functions, these peptides differ only by two residues and both feature a tocin ring formed by the disulfide bridge between first and sixth cysteine residues. This sequence and structural similarity are experimentally linked to oxytocin agonism at vasopressin receptors and vasopressin antagonism at oxytocin receptors. Yet single- or double-residue mutations in both peptides have been shown to have drastic impacts on their activities at either receptor, and possibly the ability to bind to their neurophysin carrier protein. In this study we perform molecular dynamics simulations of the unbound native and mutant sequences of the oxytocin and vasopressin hormones to characterize their structural ensembles. We classify the subpopulations of these structural ensembles on the basis of the distributions of radius of gyration and secondary structure and hydrogen-bonding features of the canonical tocin ring and disordered tail region. We then relate the structural changes observed in the unbound form of the different hormone sequences to experimental information about peptide receptor binding, and more indirectly, carrier protein binding affinity, receptor activity, and protease degradation. This study supports the hypothesis that the structural characteristics of the unbound form of an IDP can be used to predict structural or functional preferences of its functional bound form.
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Affiliation(s)
- Eugene Yedvabny
- Department of Chemistry, ‡Department of Bioengineering, and §Department of Chemical and Biomolecular Engineering, University of California , Berkeley, California 94720-3220, United States
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