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Saikia B, Baruah A. Recent advances in de novo computational design and redesign of intrinsically disordered proteins and intrinsically disordered protein regions. Arch Biochem Biophys 2024; 752:109857. [PMID: 38097100 DOI: 10.1016/j.abb.2023.109857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
In the early 2000s, the concept of "unstructured biology" has emerged to be an important field in protein science by generating various new research directions. Many novel strategies and methods have been developed that are focused on effectively identifying/predicting intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs), identifying their potential functions, disorder based drug design etc. Due to the range of functions of IDPs/IDPRs and their involvement in various debilitating diseases they are of contemporary interest to the scientific community. Recent researches are focused on designing/redesigning specific IDPs/IDPRs de novo. These de novo design/redesigns of IDPs/IDPRs are carried out by altering compositional biases and specific sequence patterning parameters. The main focus of these researches is to influence specific molecular functions, phase behavior, cellular phenotypes etc. In this review, we first provide the differences of natively folded and natively unfolded or IDPs with respect to their potential energy landscapes. Here, we provide current understandings on the different computational design strategies and methods that have been utilized in de novo design and redesigns of IDPs and IDPRs. Finally, we conclude the review by discussing the challenges that have been faced during the computational design/design attempts of IDPs/IDPRs.
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Affiliation(s)
- Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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2
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Gerlach GJ, Carrock R, Stix R, Stollar EJ, Ball KA. A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway. PLoS Comput Biol 2020; 16:e1007815. [PMID: 32925900 PMCID: PMC7514057 DOI: 10.1371/journal.pcbi.1007815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/24/2020] [Accepted: 08/15/2020] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions are involved in a wide range of cellular processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains. However, the details of IDP binding pathways are hard to characterize using experimental approaches, which can rarely capture intermediate states present at low populations. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function. Molecular dynamics simulations were used to characterize the steps of binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 310 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations reveal that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long-range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting that segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs in general.
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Affiliation(s)
- Gabriella J. Gerlach
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Rachel Carrock
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Robyn Stix
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Elliott J. Stollar
- School of Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - K. Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
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3
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Zhao Y, Cortes-Huerto R, Kremer K, Rudzinski JF. Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model. J Phys Chem B 2020; 124:4097-4113. [PMID: 32345021 PMCID: PMC7246978 DOI: 10.1021/acs.jpcb.0c01949] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Intrinsically
disordered proteins (IDPs) play an important role
in an array of biological processes but present a number of fundamental
challenges for computational modeling. Recently, simple polymer models
have regained popularity for interpreting the experimental characterization
of IDPs. Homopolymer theory provides a strong foundation for understanding
generic features of phenomena ranging from single-chain conformational
dynamics to the properties of entangled polymer melts, but is difficult
to extend to the copolymer context. This challenge is magnified for
proteins due to the variety of competing interactions and large deviations
in side-chain properties. In this work, we apply a simple physics-based
coarse-grained model for describing largely disordered conformational
ensembles of peptides, based on the premise that sampling sterically
forbidden conformations can compromise the faithful description of
both static and dynamical properties. The Hamiltonian of the employed
model can be easily adjusted to investigate the impact of distinct
interactions and sequence specificity on the randomness of the resulting
conformational ensemble. In particular, starting with a bead–spring-like
model and then adding more detailed interactions one by one, we construct
a hierarchical set of models and perform a detailed comparison of
their properties. Our analysis clarifies the role of generic attractions,
electrostatics, and side-chain sterics, while providing a foundation
for developing efficient models for IDPs that retain an accurate description
of the hierarchy of conformational dynamics, which is nontrivially
influenced by interactions with surrounding proteins and solvent molecules.
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Affiliation(s)
- Yani Zhao
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Joseph F Rudzinski
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Wu H, Wolynes PG, Papoian GA. AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins. J Phys Chem B 2018; 122:11115-11125. [PMID: 30091924 PMCID: PMC6713210 DOI: 10.1021/acs.jpcb.8b05791] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The associative memory, water-mediated, structure and energy model (AWSEM) has been successfully used to study protein folding, binding, and aggregation problems. In this work, we introduce AWSEM-IDP, a new AWSEM branch for simulating intrinsically disordered proteins (IDPs), where the weights of the potentials determining secondary structure formation have been finely tuned, and a novel potential is introduced that helps to precisely control both the average extent of protein chain collapse and the chain's fluctuations in size. AWSEM-IDP can efficiently sample large conformational spaces, while retaining sufficient molecular accuracy to realistically model proteins. We applied this new model to two IDPs, demonstrating that AWSEM-IDP can reasonably well reproduce higher-resolution reference data, thus providing the foundation for a transferable IDP force field. Finally, we used thermodynamic perturbation theory to show that, in general, the conformational ensembles of IDPs are highly sensitive to fine-tuning of force field parameters.
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Affiliation(s)
- Hao Wu
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Peter G. Wolynes
- Departments of Chemistry and Physics and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Garegin A. Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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5
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Gibbs EB, Showalter SA. Quantification of Compactness and Local Order in the Ensemble of the Intrinsically Disordered Protein FCP1. J Phys Chem B 2016; 120:8960-9. [DOI: 10.1021/acs.jpcb.6b06934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Eric B. Gibbs
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Scott A. Showalter
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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6
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Assessing Coupled Protein Folding and Binding Through Temperature-Dependent Isothermal Titration Calorimetry. Methods Enzymol 2016; 567:23-45. [DOI: 10.1016/bs.mie.2015.07.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Rudzinski JF, Noid WG. Bottom-Up Coarse-Graining of Peptide Ensembles and Helix–Coil Transitions. J Chem Theory Comput 2015; 11:1278-91. [DOI: 10.1021/ct5009922] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph F. Rudzinski
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - William G. Noid
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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9
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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10
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Lawrence CW, Kumar S, Noid WG, Showalter SA. Role of Ordered Proteins in the Folding-Upon-Binding of Intrinsically Disordered Proteins. J Phys Chem Lett 2014; 5:833-838. [PMID: 26274075 DOI: 10.1021/jz402729x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, we quantitatively investigate the thermodynamic analogy between the folding of monomeric proteins and the interactions of intrinsically disordered proteins (IDPs). Motivated by the hypothesis that similar hydrophobic forces guide both globular protein folding and also IDP interactions, we present a unified experimental and computational investigation of the coupling between the folding and binding of the intrinsically disordered tail of FCP1 when interacting with the cooperatively folding winged-helix domain of Rap74. Our calorimetric measurements quantitatively demonstrate the significance of hydrophobic interactions for this binding event. Our computational studies indicate that IDPs relieve frustration at the surface of ordered proteins to generate a minimally frustrated complex that is strikingly similar to a globular monomeric protein. In summary, these results not only quantify the thermodynamic forces driving disordered protein interactions but also highlight the role of ordered proteins for IDP function.
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Affiliation(s)
- Chad W Lawrence
- §Department of Chemistry and †Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sushant Kumar
- §Department of Chemistry and †Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - William G Noid
- §Department of Chemistry and †Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Scott A Showalter
- §Department of Chemistry and †Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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11
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Sahu D, Bastidas M, Showalter SA. Generating NMR chemical shift assignments of intrinsically disordered proteins using carbon-detected NMR methods. Anal Biochem 2013; 449:17-25. [PMID: 24333248 DOI: 10.1016/j.ab.2013.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 10/25/2022]
Abstract
There is an extraordinary need to describe the structures of intrinsically disordered proteins (IDPs) due to their role in various biological processes involved in signaling and transcription. However, general study of IDPs by NMR spectroscopy is limited by the poor (1)H amide chemical shift dispersion typically observed in their spectra. Recently, (13)C direct-detected NMR spectroscopy has been recognized as enabling broad structural study of IDPs. Most notably, multidimensional experiments based on the (15)N,(13)C CON spectrum make complete chemical shift assignment feasible. Here we document a collection of NMR-based tools that efficiently lead to chemical shift assignment of IDPs, motivated by a case study of the C-terminal disordered region from the human pancreatic transcription factor Pdx1. Our strategy builds on the combination of two three-dimensional (3D) experiments, (HN-flip)N(CA)CON and 3D (HN-flip)N(CA)NCO, that enable daisy chain connections to be built along the IDP backbone, facilitated by acquisition of amino acid-specific (15)N,(13)C CON-detected experiments. Assignments are completed through carbon-detected, total correlation spectroscopy (TOCSY)-based side chain chemical shift measurement. Conducting our study required producing valuable modifications to many previously published pulse sequences, motivating us to announce the creation of a database of our pulse programs, which we make freely available through our website.
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Affiliation(s)
- Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Monique Bastidas
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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12
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Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein. Proc Natl Acad Sci U S A 2013; 110:E3743-52. [PMID: 24043820 DOI: 10.1073/pnas.1308381110] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding-binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between "downhill folding," "molten globule," and "intrinsic disorder" in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a "kinetic divide-and-conquer" strategy that confers them high specificity without high affinity.
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