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Nagy G, Hoffmann SV, Jones NC, Grubmüller H. Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models. APPLIED SPECTROSCOPY 2024; 78:897-911. [PMID: 38646777 PMCID: PMC11453034 DOI: 10.1177/00037028241239977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/15/2024] [Indexed: 04/23/2024]
Abstract
Circular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.
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Affiliation(s)
- Gabor Nagy
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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2
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Nde J, Zhang P, Waxham MN, Cheung MS. Experiment and Simulation Reveal Residue Details for How Target Binding Tunes Calmodulin's Calcium-Binding Properties. J Phys Chem B 2023; 127:2900-2908. [PMID: 36977372 DOI: 10.1021/acs.jpcb.2c08734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
We aim to elucidate the molecular mechanism of the reciprocal relation of calmodulin's (CaM) target binding and its affinity for calcium ions (Ca2+), which is central to decoding CaM-dependent Ca2+ signaling in a cell. We employed stopped-flow experiments and coarse-grained molecular simulations that learn the coordination chemistry of Ca2+ in CaM from first-principle calculations. The associative memories as part of the coarse-grained force fields built on known protein structures further influence CaM's selection of its polymorphic target peptides in the simulations. We modeled the peptides from the Ca2+/CaM-binding domain of Ca2+/CaM-dependent kinase II (CaMKII), CaMKIIp (293-310) and selected distinctive mutations at the N-terminus. Our stopped-flow experiments have shown that the CaM's affinity for Ca2+ in the bound complex of Ca2+/CaM/CaMKIIp decreased significantly when Ca2+/CaM bound to the mutant peptide (296-AAA-298) compared to that bound to the wild-type peptide (296-RRK-298). The coarse-grained molecular simulations revealed that the 296-AAA-298 mutant peptide destabilized the structures of Ca2+-binding loops at the C-domain of CaM (c-CaM) due to both loss of electrostatic interactions and differences in polymorphic structures. We have leveraged a powerful coarse-grained approach to advance a residue-level understanding of the reciprocal relation in CaM, that could not be possibly achieved by other computational approaches.
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Affiliation(s)
- Jules Nde
- Department of Physics, University of Washington, Seattle, Washington 98105, United States
| | - Pengzhi Zhang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Margaret S Cheung
- Department of Physics, University of Washington, Seattle, Washington 98105, United States
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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3
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Evans R, Ramisetty S, Kulkarni P, Weninger K. Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology. Biomolecules 2023; 13:124. [PMID: 36671509 PMCID: PMC9856150 DOI: 10.3390/biom13010124] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Intense study of intrinsically disordered proteins (IDPs) did not begin in earnest until the late 1990s when a few groups, working independently, convinced the community that these 'weird' proteins could have important functions. Over the past two decades, it has become clear that IDPs play critical roles in a multitude of biological phenomena with prominent examples including coordination in signaling hubs, enabling gene regulation, and regulating ion channels, just to name a few. One contributing factor that delayed appreciation of IDP functional significance is the experimental difficulty in characterizing their dynamic conformations. The combined application of multiple methods, termed integrative structural biology, has emerged as an essential approach to understanding IDP phenomena. Here, we review some of the recent applications of the integrative structural biology philosophy to study IDPs.
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Affiliation(s)
- Rachel Evans
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Sravani Ramisetty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
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4
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Macke AC, Kelly MS, Varikoti RA, Mullen S, Groves D, Forbes C, Dima RI. Microtubule Severing Enzymes Oligomerization and Allostery: A Tale of Two Domains. J Phys Chem B 2022; 126:10569-10586. [PMID: 36475672 DOI: 10.1021/acs.jpcb.2c05288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Severing proteins are nanomachines from the AAA+ (ATPases associated with various cellular activities) superfamily whose function is to remodel the largest cellular filaments, microtubules. The standard AAA+ machines adopt hexameric ring structures for functional reasons, while being primarily monomeric in the absence of the nucleotide. Both major severing proteins, katanin and spastin, are believed to follow this trend. However, studies proposed that they populate lower-order oligomers in the presence of cofactors, which are functionally relevant. Our simulations show that the preferred oligomeric assembly is dependent on the binding partners and on the type of severing protein. Essential dynamics analysis predicts that the stability of an oligomer is dependent on the strength of the interface between the helical bundle domain (HBD) of a monomer and the convex face of the nucleotide binding domain (NBD) of a neighboring monomer. Hot spots analysis found that the region consisting of the HBD tip and the C-terminal (CT) helix is the only common element between the allosteric networks responding to nucleotide, substrate, and intermonomer binding. Clustering analysis indicates the existence of multiple pathways for the transition between the secondary structure of the HBD tip in monomers and the structure(s) it adopts in oligomers.
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Affiliation(s)
- Amanda C Macke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Maria S Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Rohith Anand Varikoti
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Sarah Mullen
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Daniel Groves
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Clare Forbes
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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5
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Relationship between type II polyproline helix secondary structure and thermal hysteresis activity of short homopeptides. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Wang L, Zhang W, Shao Y, Zhang D, Guo G, Wang X. Analytical methods for obtaining binding parameters of drug–protein interactions: A review. Anal Chim Acta 2022; 1219:340012. [DOI: 10.1016/j.aca.2022.340012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
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Meng S, Wang Y, Mu J, Pang Z, Wang F, Liao Y. Biological preparation and characterization of surfactant‐like peptides. J SURFACTANTS DETERG 2022. [DOI: 10.1002/jsde.12590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shujuan Meng
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Yadong Wang
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Jing Mu
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Zhengjun Pang
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Fenghuan Wang
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Yonghong Liao
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
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8
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Piovesan D, Monzon AM, Quaglia F, Tosatto SCE. Databases for intrinsically disordered proteins. Acta Crystallogr D Struct Biol 2022; 78:144-151. [PMID: 35102880 PMCID: PMC8805306 DOI: 10.1107/s2059798321012109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/12/2021] [Indexed: 11/28/2022] Open
Abstract
Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. Only a small fraction of IDRs have been functionally characterized, with heterogeneous experimental evidence that is largely buried in the literature. Predictions of IDRs are still difficult to estimate and are poorly characterized. Here, an overview of the publicly available knowledge about IDRs is reported, including manually curated resources, deposition databases and prediction repositories. The types, scopes and availability of the various resources are analyzed, and their complementarity and overlap are highlighted. The volume of information included and the relevance to the field of structural biology are compared.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR–IBIOM), Bari, Italy
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9
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Gomes Ramalli S, John Miles A, Janes RW, Wallace BA. The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development. J Mol Biol 2022; 434:167441. [PMID: 34999124 DOI: 10.1016/j.jmb.2022.167441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/19/2021] [Accepted: 01/01/2022] [Indexed: 12/20/2022]
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and other metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB) and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included. The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes.
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Affiliation(s)
- Sergio Gomes Ramalli
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Andrew John Miles
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Robert W Janes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.
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10
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Helical Stabilization of Peptide Macrocycles by Stapled Architectures. Methods Mol Biol 2021. [PMID: 34596860 DOI: 10.1007/978-1-0716-1689-5_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Over the past two decades, significant efforts have invested in the development of strategies for the stabilization of macrocyclic peptides with α-helix structure by stapling their architectures. These strategies can be divided into two categories: side chain to side chain cross-linking and N-terminal helix nucleation. These stable macrocyclic peptides have been applied in PPI inhibitors and self-assembly materials. Compared with unmodified short peptides, stable α-helix macrocyclic polypeptides have better biophysical properties including higher serum stability, cell permeability, and higher target affinity. This chapter will systematically introduce approaches for helical stabilization of peptide macrocycles, such as ring-closing metathesis (RCM), lactamisation, cycloadditions, reversible reactions, thioether formation as well as newly found sulfonium center formation and the common use of helical stabilized macrocyclic peptides.
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11
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Couch T, Berger K, Kneisley DL, McCullock TW, Kammermeier P, Maclean DM. Topography and motion of acid-sensing ion channel intracellular domains. eLife 2021; 10:68955. [PMID: 34292153 PMCID: PMC8341984 DOI: 10.7554/elife.68955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/21/2021] [Indexed: 01/12/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are trimeric cation-selective channels activated by decreases in extracellular pH. The intracellular N and C terminal tails of ASIC1 influence channel gating, trafficking, and signaling in ischemic cell death. Despite several X-ray and cryo-EM structures of the extracellular and transmembrane segments of ASIC1, these important intracellular tails remain unresolved. Here, we describe the coarse topography of the chicken ASIC1 intracellular domains determined by fluorescence resonance energy transfer (FRET), measured using either fluorescent lifetime imaging or patch clamp fluorometry. We find the C terminal tail projects into the cytosol by approximately 35 Å and that the N and C tails from the same subunits are closer than adjacent subunits. Using pH-insensitive fluorescent proteins, we fail to detect any relative movement between the N and C tails upon extracellular acidification but do observe axial motions of the membrane proximal segments toward the plasma membrane. Taken together, our study furnishes a coarse topographic map of the ASIC intracellular domains while providing directionality and context to intracellular conformational changes induced by extracellular acidification.
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Affiliation(s)
- Tyler Couch
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, Reno, United States
| | - Kyle Berger
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - Dana L Kneisley
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - Tyler W McCullock
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, Reno, United States
| | - Paul Kammermeier
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
| | - David M Maclean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, United States
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12
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Spoel D, Zhang J, Zhang H. Quantitative predictions from molecular simulations using explicit or implicit interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1560] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- David Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology Uppsala University Uppsala Sweden
| | - Jin Zhang
- Department of Chemistry Southern University of Science and Technology Shenzhen China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering University of Science and Technology Beijing Beijing China
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13
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de Brevern AG. Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet. Biomolecules 2020; 10:biom10071080. [PMID: 32698546 PMCID: PMC7408373 DOI: 10.3390/biom10071080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
Intrinsically-disordered protein (IDP) characterization was an amazing change of paradigm in our classical sequence-structure-function theory. Moreover, IDPs are over-represented in major disease pathways and are now often targeted using small molecules for therapeutic purposes. This has had created a complex continuum from order-that encompasses rigid and flexible regions-to disorder regions; the latter being not accessible through classical crystallographic methodologies. In X-ray structures, the notion of order is dictated by access to resolved atom positions, providing rigidity and flexibility information with low and high experimental B-factors, while disorder is associated with the missing (non-resolved) residues. Nonetheless, some rigid regions can be found in disorder regions. Using ensembles of IDPs, their local conformations were analyzed in the light of a structural alphabet. An entropy index derived from this structural alphabet allowed us to propose a continuum of states from rigidity to flexibility and finally disorder. In this study, the analysis was extended to comparing these results to disorder predictions, underlying a limited correlation, and so opening new ideas to characterize and predict disorder.
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Affiliation(s)
- Alexandre G de Brevern
- INSERM, UMR_S 1134, DSIMB, Univ Paris, INTS, Laboratoire d'Excellence GR-Ex, 75015 Paris, France
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