1
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Garg A, González-Foutel NS, Gielnik MB, Kjaergaard M. Design of functional intrinsically disordered proteins. Protein Eng Des Sel 2024; 37:gzae004. [PMID: 38431892 DOI: 10.1093/protein/gzae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.
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Affiliation(s)
- Ankush Garg
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Maciej B Gielnik
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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2
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Chen SH, Weiss KL, Stanley C, Bhowmik D. Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing. Protein Sci 2023; 32:e4772. [PMID: 37646172 PMCID: PMC10503416 DOI: 10.1002/pro.4772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/22/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure-function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Lastly, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.
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Affiliation(s)
- Serena H. Chen
- Computational Sciences and Engineering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Kevin L. Weiss
- Neutron Scattering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Christopher Stanley
- Computational Sciences and Engineering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Debsindhu Bhowmik
- Computational Sciences and Engineering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
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3
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Saurabh A, Safar M, Fazel M, Sgouralis I, Pressé S. Single-photon smFRET: II. Application to continuous illumination. BIOPHYSICAL REPORTS 2022; 3:100087. [PMID: 36582656 PMCID: PMC9792399 DOI: 10.1016/j.bpr.2022.100087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/01/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
Here we adapt the Bayesian nonparametrics (BNP) framework presented in the first companion article to analyze kinetics from single-photon, single-molecule Förster resonance energy transfer (smFRET) traces generated under continuous illumination. Using our sampler, BNP-FRET, we learn the escape rates and the number of system states given a photon trace. We benchmark our method by analyzing a range of synthetic and experimental data. Particularly, we apply our method to simultaneously learn the number of system states and the corresponding kinetics for intrinsically disordered proteins using two-color FRET under varying chemical conditions. Moreover, using synthetic data, we show that our method can deduce the number of system states even when kinetics occur at timescales of interphoton intervals.
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Affiliation(s)
- Ayush Saurabh
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Matthew Safar
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Mathematics and Statistical Science, Arizona State University, Tempe, Arizona
| | - Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee Knoxville, Knoxville, Tennessee
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona,School of Molecular Sciences, Arizona State University, Tempe, Arizona,Corresponding author
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4
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Lenton S, Fagerberg E, Tully M, Skepö M. From dilute to concentrated solutions of intrinsically disordered proteins: Interpretation and analysis of collected data. Methods Enzymol 2022; 678:299-330. [PMID: 36641212 DOI: 10.1016/bs.mie.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) have a broad energy landscape and consequently sample many different conformations in solution. The innate flexibility of IDPs is exploited in their biological function, and in many instances allows a single IDP to regulate a range of processes in vivo. Due to their highly flexible nature, characterizing the structural properties of IDPs is not straightforward. Often solution-based methods such as Nuclear Magnetic Resonance (NMR), Förster Resonance Energy Transfer (FRET), and Small-Angle X-ray Scattering (SAXS) are used. SAXS is indeed a powerful technique to study the structural and conformational properties of IDPs in solution, and from the obtained SAXS spectra, information about the average size, shape, and extent of oligomerization can be determined. In this chapter, we will introduce model-free methods that can be used to interpret SAXS data and introduce methods that can be used to interpret SAXS data beyond analytical models, for example, by using atomistic and different levels of coarse-grained models in combination with molecular dynamics (MD) and Monte Carlo simulations.
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Affiliation(s)
- Samuel Lenton
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | - Eric Fagerberg
- Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | - Mark Tully
- BioSAXS beamline, BM29, European Synchrotron Radiation Facility, ESRF, Grenoble, France
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, Lund, Sweden; LINXS-Institute of Advanced Neutron and X-ray Science, Lund, Sweden.
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5
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Houser JR, Cho HW, Hayden CC, Yang NX, Wang L, Lafer EM, Thirumalai D, Stachowiak JC. Molecular mechanisms of steric pressure generation and membrane remodeling by disordered proteins. Biophys J 2022; 121:3320-3333. [PMID: 36016498 PMCID: PMC9515369 DOI: 10.1016/j.bpj.2022.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/18/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022] Open
Abstract
Cellular membranes, which are densely crowded by proteins, take on an elaborate array of highly curved shapes. Steric pressure generated by protein crowding plays a significant role in shaping membrane surfaces. It is increasingly clear that many proteins involved in membrane remodeling contain substantial regions of intrinsic disorder. These domains have large hydrodynamic radii, suggesting that they may contribute significantly to steric congestion on membrane surfaces. However, it has been unclear to what extent they are capable of generating steric pressure, owing to their conformational flexibility. To address this gap, we use a recently developed sensor based on Förster resonance energy transfer to measure steric pressure generated at membrane surfaces by the intrinsically disordered domain of the endocytic protein, AP180. We find that disordered domains generate substantial steric pressure that arises from both entropic and electrostatic components. Interestingly, this steric pressure is largely invariant with the molecular weight of the disordered domain, provided that coverage of the membrane surface is held constant. Moreover, equivalent levels of steric pressure result in equivalent degrees of membrane remodeling, regardless of protein molecular weight. This result, which is consistent with classical polymer scaling relationships for semi-dilute solutions, helps to explain the molecular and physical origins of steric pressure generation by intrinsically disordered domains. From a physiological perspective, these findings suggest that a broad range of membrane-associated disordered domains are likely to play a significant and previously unknown role in controlling membrane shape.
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Affiliation(s)
- Justin R Houser
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Hyun Woo Cho
- Department of Chemistry, Seoul National University of Science and Technology, Seoul, South Korea
| | - Carl C Hayden
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Noel X Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Liping Wang
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Eileen M Lafer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Dave Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas.
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6
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Gong Z, Yang J, Qin LY, Tang C, Jiang H, Ke Y, Dong X. Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders. J Phys Chem B 2022; 126:4840-4848. [PMID: 35731981 DOI: 10.1021/acs.jpcb.2c02713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The environmental condition is a critical regulation factor for protein behavior in solution. Several studies have shown that macromolecular crowders can modulate protein structures, interactions, and functions. Recent publications described the regulation of specific interaction by macromolecular crowders. However, the other category of protein-protein interaction, namely, the transient interaction, is rarely investigated, especially from the perspective of protein structure to study transient interactions between proteins. Here, we used nuclear magnetic resonance and small-angle X-ray/neutron scattering methods to structurally investigate the ensemble of the protein complex in dilute buffer and crowded environments. Histidine phosphocarrier protein (HPr) and the N-terminal domain of enzyme I (EIN) are the important components of the bacterial phosphotransfer system. Our results show that the addition of Ficoll-70 promotes HPr molecules to form the encounter complex with EIN maintained by long-range electrostatic interaction. However, when macromolecular crowder BSA is used, the soft interaction between BSA and HPr perturbs the active site of HPr, driving HPr to form an encounter complex with EIN at the weakly charged interface. Our results indicate that different macromolecular crowders could influence transient EIN-HPr interaction through different mechanisms and provide new insights into protein-protein interaction regulation in native environments.
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Affiliation(s)
- Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ju Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ling-Yun Qin
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hanqiu Jiang
- Spallation Neutron Source Science Center (SNSSC), Dalang, Dongguan 523803, China.,Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Yubin Ke
- Spallation Neutron Source Science Center (SNSSC), Dalang, Dongguan 523803, China.,Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xu Dong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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7
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Bazmi S, Wallin S. Crowding-induced protein destabilization in the absence of soft attractions. Biophys J 2022; 121:2503-2513. [PMID: 35672949 DOI: 10.1016/j.bpj.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, φc. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with φc. Hence, for all φc>0, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, Tm, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-φc conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at T<Tm, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at φc=0, but increasing monotonically with φc. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.
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Affiliation(s)
- Saman Bazmi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada.
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8
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Cubuk J, Soranno A. Macromolecular crowding and intrinsically disordered proteins: a polymer physics perspective. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202100051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Cubuk
- Washington University in St Louis Biochemistry and Molecular Biophysics UNITED STATES
| | - Andrea Soranno
- Washington University in St Louis Biochemistry and Molecular Biophysics 660 St Euclid Ave 63110 St Louis UNITED STATES
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9
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Rajendran D, Mitra S, Oikawa H, Madhurima K, Sekhar A, Takahashi S, Naganathan AN. Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein. J Phys Chem Lett 2022; 13:3112-3120. [PMID: 35357183 PMCID: PMC7612738 DOI: 10.1021/acs.jpclett.2c00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We investigate the conformational properties of the intrinsically disordered DNA-binding domain of CytR in the presence of the polymeric crowder polyethylene glycol (PEG). Integrating circular dichroism, nuclear magnetic resonance, and single-molecule Förster resonance energy transfer measurements, we demonstrate that disordered CytR populates a well-folded minor conformation in its native ensemble, while the unfolded ensemble collapses and folds with an increase in crowder density independent of the crowder size. Employing a statistical-mechanical model, the effective reduction in the accessible conformational space of a residue in the unfolded state is estimated to be 10% at 300 mg/mL PEG8000, relative to dilute conditions. The experimentally consistent PEG-temperature phase diagram thus constructed reveals that entropic effects can stabilize disordered CytR by 10 kJ mol-1, driving the equilibrium toward folded conformations under physiological conditions. Our work highlights the malleable conformational landscape of CytR, the presence of a folded conformation in the disordered ensemble, and proposes a scaling relation for quantifying excluded volume effects on protein stability.
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Affiliation(s)
- Divya Rajendran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Shrutarshi Mitra
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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10
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Mavani A, Ovung A, Luikham S, Suresh Kumar G, Das A, Ray D, Aswal VK, Bhattacharyya J. Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin. J Biomol Struct Dyn 2022; 41:3779-3790. [PMID: 35380096 DOI: 10.1080/07391102.2022.2057358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular mechanism of the heme protein, hemoglobin (Hb) interaction with sulfa molecule, sulfadiazine (SDZ) has been investigated through spectroscopic, neutron scattering and molecular modeling techniques. Absorption and emission spectroscopic studies showed that SDZ molecules were bound to Hb protein, non-cooperatively. The binding affinityof SDZ-Hb complex at standard experimental condition was evaluated to be around (4.2 ± 0.07) ×104, M-1with 1:1 stoichiometry. Drug induced structural perturbation of the 3 D protein moiety was confirmed through circular dichroism (CD), synchronous fluorescence and small angle neutron scattering methods. From the temperature dependent spectrofluorometric studies, the negative standard molar Gibbs energy change suggested the spontaneity of the reaction. The negative enthalpy and positive entropy change(s) indicated towards the involvement of both electrostatic and hydrophobic forces during the association process. Salt dependent fluorescence study revealed major contributions from non-poly-electrolytic forces. Molecular modeling studies determined the probable binding sites, types of interaction involved and the conformational alteration of the compactness of the Hb structure upon interaction with SDZ molecule. Overall, the study provides detailed insights into the binding mechanism of SDZ antibiotics to Hb protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A. Mavani
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Aben Ovung
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Abhi Das
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Debes Ray
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Vinod K. Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
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11
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Li L, Casalini T, Arosio P, Salvalaglio M. Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations. J Chem Theory Comput 2022; 18:1915-1928. [PMID: 35174713 PMCID: PMC9097291 DOI: 10.1021/acs.jctc.1c00889] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins play a key role in many biological processes, including the formation of biomolecular condensates within cells. A detailed characterization of their configurational ensemble and structure-function paradigm is crucial for understanding their biological activity and for exploiting them as building blocks in material sciences. In this work, we incorporate bias-exchange metadynamics and parallel-tempering well-tempered metadynamics with CHARMM36m and CHARMM22* to explore the structural and thermodynamic characteristics of a short archetypal disordered sequence derived from a DEAD-box protein. The conformational landscapes emerging from our simulations are largely congruent across methods and force fields. Nevertheless, differences in fine details emerge from varying combinations of force-fields and sampling methods. For this protein, our analysis identifies features that help to explain the low propensity of this sequence to undergo self-association in vitro, which are common to all force-field/sampling method combinations. Overall, our work demonstrates the importance of using multiple force-field and sampling method combinations for accurate structural and thermodynamic information in the study of disordered proteins.
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Affiliation(s)
- Lunna Li
- Thomas
Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K.
| | - Tommaso Casalini
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Matteo Salvalaglio
- Thomas
Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K.
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12
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From dilute to concentrated solutions of intrinsically disordered proteins: Sample preparation and data collection. Methods Enzymol 2022; 677:457-478. [DOI: 10.1016/bs.mie.2022.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Structural Refolding and Thermal Stability of Myoglobin in the Presence of Mixture of Crowders: Importance of Various Interactions for Protein Stabilization in Crowded Conditions. Molecules 2021; 26:molecules26092807. [PMID: 34068693 PMCID: PMC8126177 DOI: 10.3390/molecules26092807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
The intracellular environment is overcrowded with a range of molecules (small and large), all of which influence protein conformation. As a result, understanding how proteins fold and stay functional in such crowded conditions is essential. Several in vitro experiments have looked into the effects of macromolecular crowding on different proteins. However, there are hardly any reports regarding small molecular crowders used alone and in mixtures to observe their effects on the structure and stability of the proteins, which mimics of the cellular conditions. Here we investigate the effect of different mixtures of crowders, ethylene glycol (EG) and its polymer polyethylene glycol (PEG 400 Da) on the structural and thermal stability of myoglobin (Mb). Our results show that monomer (EG) has no significant effect on the structure of Mb, while the polymer disrupts its structure and decreases its stability. Conversely, the additive effect of crowders showed structural refolding of the protein to some extent. Moreover, the calorimetric binding studies of the protein showed very weak interactions with the mixture of crowders. Usually, we can assume that soft interactions induce structural perturbations while exclusion volume effects stabilize the protein structure; therefore, we hypothesize that under in vivo crowded conditions, both phenomena occur and maintain the stability and function of proteins.
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14
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Okuda A, Inoue R, Morishima K, Saio T, Yunoki Y, Yagi-Utsumi M, Yagi H, Shimizu M, Sato N, Urade R, Kato K, Sugiyama M. Deuteration Aiming for Neutron Scattering. Biophys Physicobiol 2021; 18:16-27. [PMID: 33954079 PMCID: PMC8049778 DOI: 10.2142/biophysico.bppb-v18.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/03/2021] [Indexed: 01/17/2023] Open
Abstract
The distinguished feature of neutron as a scattering probe is an isotope effect, especially the large difference in neutron scattering length between hydrogen and deuterium. The difference renders the different visibility between hydrogenated and deuterated proteins. Therefore, the combination of deuterated protein and neutron scattering enables the selective visualization of a target domain in the complex or a target protein in the multi-component system. Despite of this fascinating character, there exist several problems for the general use of this method: difficulty and high cost for protein deuteration, and control and determination of deuteration ratio of the sample. To resolve them, the protocol of protein deuteration techniques is presented in this report. It is strongly expected that this protocol will offer more opportunity for conducting the neutron scattering studies with deuterated proteins.
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Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Tomohide Saio
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Yasuhiro Yunoki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
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15
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Fagerberg E, Månsson LK, Lenton S, Skepö M. The Effects of Chain Length on the Structural Properties of Intrinsically Disordered Proteins in Concentrated Solutions. J Phys Chem B 2020; 124:11843-11853. [PMID: 33337879 PMCID: PMC7872433 DOI: 10.1021/acs.jpcb.0c09635] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Intrinsically disordered proteins (IDP) are proteins that sample
a heterogeneous ensemble of conformers in solution. An estimated 25–30%
of all eukaryotic proteins belong to this class. In vivo, IDPs function under conditions that are highly crowded by other
biological macromolecules. Previous research has highlighted that
the presence of crowding agents can influence the conformational ensemble
sampled by IDPs, resulting in either compaction or expansion. The
effects of self-crowding of the disordered protein Histatin 5 has,
in an earlier study, been found to have limited influence on the conformational
ensemble. In this study, it is examined whether the short chain length
of Histatin 5 can explain the limited effects of crowding observed,
by introducing (Histatin 5)2, a tandem repeat of Histatin
5. By utilizing small-angle X-ray scattering, it is shown that the
conformational ensemble is conserved at high protein concentrations,
in resemblance with Histatin 5, although with a lowered protein concentration
at which aggregation arises. Under dilute conditions, atomistic molecular
dynamics and coarse-grained Monte Carlo simulations, as well as an
established scaling law, predicted more extended conformations than
indicated by experimental data, hence implying that (Histatin 5)2 does not behave as a self-avoiding random walk.
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Affiliation(s)
- Eric Fagerberg
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden
| | - Linda K Månsson
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden
| | - Samuel Lenton
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden.,LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, P.O. Box 124, Lund SE-221 00, Sweden.,LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
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16
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Grosas AB, Rekas A, Mata JP, Thorn DC, Carver JA. The Aggregation of αB-Crystallin under Crowding Conditions Is Prevented by αA-Crystallin: Implications for α-Crystallin Stability and Lens Transparency. J Mol Biol 2020; 432:5593-5613. [PMID: 32827531 DOI: 10.1016/j.jmb.2020.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/08/2023]
Abstract
One of the most crowded biological environments is the eye lens which contains a high concentration of crystallin proteins. The molecular chaperones αB-crystallin (αBc) with its lens partner αA-crystallin (αAc) prevent deleterious crystallin aggregation and cataract formation. However, some forms of cataract are associated with structural alteration and dysfunction of αBc. While many studies have investigated the structure and function of αBc under dilute in vitro conditions, the effect of crowding on these aspects is not well understood despite its in vivo relevance. The structure and chaperone ability of αBc under conditions that mimic the crowded lens environment were investigated using the polysaccharide Ficoll 400 and bovine γ-crystallin as crowding agents and a variety of biophysical methods, principally contrast variation small-angle neutron scattering. Under crowding conditions, αBc unfolds, increases its size/oligomeric state, decreases its thermal stability and chaperone ability, and forms kinetically distinct amorphous and fibrillar aggregates. However, the presence of αAc stabilizes αBc against aggregation. These observations provide a rationale, at the molecular level, for the aggregation of αBc in the crowded lens, a process that exhibits structural and functional similarities to the aggregation of cataract-associated αBc mutants R120G and D109A under dilute conditions. Strategies that maintain or restore αBc stability, as αAc does, may provide therapeutic avenues for the treatment of cataract.
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Affiliation(s)
- Aidan B Grosas
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Agata Rekas
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia
| | - Jitendra P Mata
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia
| | - David C Thorn
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia.
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17
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Le Coeur C, Teixeira J, Longeville S. Comment on "Combining Diffusion NMR and Small-Angle Neutron Scattering Enables Precise Measurements of Polymer Chain Compression in a Crowded Environment". PHYSICAL REVIEW LETTERS 2019; 123:239801. [PMID: 31868507 DOI: 10.1103/physrevlett.123.239801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Indexed: 06/10/2023]
Affiliation(s)
- C Le Coeur
- Laboratoire Léon Brillouin, CEA-CNRS, Université de Paris-Saclay, CEA-Saclay, F91191 Gif-sur-Yvette, France
| | - J Teixeira
- Laboratoire Léon Brillouin, CEA-CNRS, Université de Paris-Saclay, CEA-Saclay, F91191 Gif-sur-Yvette, France
| | - S Longeville
- Laboratoire Léon Brillouin, CEA-CNRS, Université de Paris-Saclay, CEA-Saclay, F91191 Gif-sur-Yvette, France
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18
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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci U S A 2019; 116:20446-20452. [PMID: 31548393 DOI: 10.1073/pnas.1907251116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.
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19
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Chen PC, Shevchuk R, Strnad FM, Lorenz C, Karge L, Gilles R, Stadler AM, Hennig J, Hub JS. Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4687-4698. [DOI: 10.1021/acs.jctc.9b00292] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Roman Shevchuk
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Felix M. Strnad
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Charlotte Lorenz
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Lukas Karge
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Ralph Gilles
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
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20
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Blinov N, Wishart DS, Kovalenko A. Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation. J Phys Chem B 2019; 123:2491-2506. [PMID: 30811210 DOI: 10.1021/acs.jpcb.9b00480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural characterization of amyloid (A)β peptides implicated in Alzheimer's disease is a challenging problem due to their intrinsically disordered nature and their high propensity for aggregation. Only limited information is currently available from experiments on conformational properties and aggregation pathways of the peptides in cellular environments. In silico modeling complements experimental information, providing atomistic insight into structure and dynamics of different Aβ species. All-atom explicit solvent molecular dynamics (MD) simulations with a properly selected force field can deliver reliable structural and dynamic information. In the case of intrinsically disordered Aβ peptides, enhanced sampling simulations beyond the nanosecond time scale are required to obtain statistically meaningful results even for simple solvent conditions. To overcome the challenges of conformational sampling in crowded cellular environments, alternative approaches have to be used, including postprocessing of MD data. In this study, we employ the statistical-mechanical, three-dimensional reference interaction site model with the Kovalenko-Hirata closure integral equation molecular theory of solvation to describe solvent composition effects on the conformational equilibrium in a structural ensemble of the Aβ42 (covering residues 1-42) monomer based on a statistical reweighting technique. The methodology enables a computationally efficient prediction on how different factors in the cellular environment, such as solvent composition, nonpolar solvation, and macromolecular crowding, affect the structural properties of the monomer. Similarities have been identified between changes in the structural ensemble caused by nonpolar solvation and crowded environments modeled by ionic solution with large negative ions. In particular, both solvent conditions reduce the random coil content and enhance the helical structure content of the monomer. In contrast to the previous studies, which reported increased α-helical content of peptides in crowded environments, this work attributes these structural features to the difference in solvent exposure of hydrophilic residues of the monomer for different secondary structure elements, rather than to (entropic) excluded volume effects.
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Affiliation(s)
- Nikolay Blinov
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
| | - David S Wishart
- Departments of Computing Science and Biological Sciences , University of Alberta , Edmonton , Alberta T6G 2E8 , Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
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21
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Fonin AV, Darling AL, Kuznetsova IM, Turoverov KK, Uversky VN. Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo. Cell Mol Life Sci 2018; 75:3907-3929. [PMID: 30066087 PMCID: PMC11105604 DOI: 10.1007/s00018-018-2894-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/18/2022]
Abstract
Effects of macromolecular crowding on structural and functional properties of ordered proteins, their folding, interactability, and aggregation are well documented. Much less is known about how macromolecular crowding might affect structural and functional behaviour of intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDPRs). To fill this gap, this review represents a systematic analysis of the available literature data on the behaviour of IDPs/IDPRs in crowded environment. Although it was hypothesized that, due to the excluded-volume effects present in crowded environments, IDPs/IDPRs would invariantly fold in the presence of high concentrations of crowding agents or in the crowded cellular environment, accumulated data indicate that, based on their response to the presence of crowders, IDPs/IDPRs can be grouped into three major categories, foldable, non-foldable, and unfoldable. This is because natural cellular environment is not simply characterized by the presence of high concentration of "inert" macromolecules, but represents an active milieu, components of which are engaged in direct physical interactions and soft interactions with target proteins. Some of these interactions with cellular components can cause (local) unfolding of query proteins. In other words, since crowding can cause both folding and unfolding of an IDP or its regions, the outputs of the placing of a query protein to the crowded environment would depend on the balance between these two processes. As a result, and because of the spatio-temporal heterogeneity in structural organization of IDPs, macromolecular crowding can differently affect structures of different IDPs. Recent studies indicate that some IDPs are able to undergo liquid-liquid-phase transitions leading to the formation of various proteinaceous membrane-less organelles (PMLOs). Although interiors of such PMLOs are self-crowded, being characterized by locally increased concentrations of phase-separating IDPs, these IDPs are minimally foldable or even non-foldable at all (at least within the physiologically safe time-frame of normal PMLO existence).
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Affiliation(s)
- Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
- St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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22
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Sparks S, Temel DB, Rout MP, Cowburn D. Deciphering the "Fuzzy" Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering. Structure 2018; 26:477-484.e4. [PMID: 29429880 PMCID: PMC5929991 DOI: 10.1016/j.str.2018.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 10/27/2017] [Accepted: 01/12/2018] [Indexed: 11/16/2022]
Abstract
The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism that enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformational transitions upon interacting with TFs. To selectively characterize conformational changes in FG Nups induced by TFs we performed small-angle neutron scattering (SANS) with contrast matching. Conformational-ensembles derived from SANS data indicated an increase in the overall size of FG Nups is associated with TF interaction. Moreover, the organization of the FG motif in the interacting state is consistent with prior experimental analyses defining that FG motifs undergo conformational restriction upon interacting with TFs. These results provide structural insights into a highly dynamic interaction and illustrate how functional disorder imparts rapid and selective FG Nup-TF interactions.
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Affiliation(s)
- Samuel Sparks
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deniz B Temel
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY, USA
| | - David Cowburn
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA.
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23
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González-Burgos M, Arbe A, Moreno AJ, Pomposo JA, Radulescu A, Colmenero J. Crowding the Environment of Single-Chain Nanoparticles: A Combined Study by SANS and Simulations. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02438] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marina González-Burgos
- Materials
Physics Center (MPC), Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Arantxa Arbe
- Materials
Physics Center (MPC), Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Angel J. Moreno
- Materials
Physics Center (MPC), Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - José A. Pomposo
- Materials
Physics Center (MPC), Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- IKERBASQUE
- Basque
Foundation for Science, María
Díaz de Haro 3, 48013 Bilbao, Spain
- Departamento
de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain
| | - Aurel Radulescu
- Jülich
Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation
at Heinz Maier-Leibnitz Zentrum, Lichtenbergstr.1, 85747 Garching, Germany
| | - Juan Colmenero
- Materials
Physics Center (MPC), Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Departamento
de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain
- Donostia International
Physics Center, Paseo Manuel de Lardizabal
4, 20018 San Sebastián, Spain
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24
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Palit S, He L, Hamilton WA, Yethiraj A, Yethiraj A. Combining Diffusion NMR and Small-Angle Neutron Scattering Enables Precise Measurements of Polymer Chain Compression in a Crowded Environment. PHYSICAL REVIEW LETTERS 2017; 118:097801. [PMID: 28306301 DOI: 10.1103/physrevlett.118.097801] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Indexed: 06/06/2023]
Abstract
The effect of particles on the behavior of polymers in solution is important in a number of important phenomena such as the effect of "crowding" proteins in cells, colloid-polymer mixtures, and nanoparticle "fillers" in polymer solutions and melts. In this Letter, we study the effect of spherical inert nanoparticles (which we refer to as "crowders") on the diffusion coefficient and radius of gyration of polymers in solution using pulsed-field-gradient NMR and small-angle neutron scattering (SANS), respectively. The diffusion coefficients exhibit a plateau below a characteristic polymer concentration, which we identify as the overlap threshold concentration c^{⋆}. Above c^{⋆}, in a crossover region between the dilute and semidilute regimes, the (long-time) self-diffusion coefficients are found, universally, to decrease exponentially with polymer concentration at all crowder packing fractions, consistent with a structural basis for the long-time dynamics. The radius of gyration obtained from SANS in the crossover regime changes linearly with an increase in polymer concentration, and must be extrapolated to c^{⋆} in order to obtain the radius of gyration of an individual polymer chain. When the polymer radius of gyration and crowder size are comparable, the polymer size is very weakly affected by the presence of crowders, consistent with recent computer simulations. There is significant chain compression, however, when the crowder size is much smaller than the polymer radius gyration.
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Affiliation(s)
- Swomitra Palit
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland A1B3X7, Canada
| | - Lilin He
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - William A Hamilton
- Instrument and Source Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland A1B3X7, Canada
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25
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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The Differential Response of Proteins to Macromolecular Crowding. PLoS Comput Biol 2016; 12:e1005040. [PMID: 27471851 PMCID: PMC4966950 DOI: 10.1371/journal.pcbi.1005040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/27/2016] [Indexed: 12/02/2022] Open
Abstract
The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins. Most in vitro and in silico biophysical experiments generally study proteins in an isolated environment, overlooking that their natural environment—the cell cytoplasm—is a solution that is highly populated by proteins. To address this knowledge gap, here we explored how a crowded environment alters the conformational sampling of three proteins, each with a different degree of disorder and flexibility. We simulated a crowded system composed by the three proteins and reaching a cell-like concentration and compared the protein behavior observed with that induced by PEG500, a synthetic crowding agent. Despite some similarities between the environments, protein crowders showed a number of characteristics that raise concerns about the use of diluted solutions or synthetic agents when studying protein behavior.
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27
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Balu R, Mata JP, Knott R, Elvin CM, Hill AJ, Choudhury NR, Dutta NK. Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation. J Phys Chem B 2016; 120:6490-503. [PMID: 27281267 DOI: 10.1021/acs.jpcb.6b02475] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, we explore the overall structural ensembles and transitions of a biomimetic, multi-stimuli-responsive, intrinsically disordered protein (IDP), Rec1-resilin. The structural transition of Rec1-resilin with change in molecular crowding and environment is evaluated using small-angle neutron scattering and small-angle X-ray scattering. The quantitative analyses of the experimental scattering data using a combination of computational models allowed comprehensive description of the structural evolution, organization, and conformational ensembles of Rec1-resilin in response to the changes in concentration, pH, and temperature. Rec1-resilin in uncrowded solutions demonstrates the equilibrium intrinsic structure quality of an IDP with radius of gyration Rg ∼ 5 nm, and a scattering function for the triaxial ellipsoidal model best fit the experimental dataset. On crowding (increase in concentration >10 wt %), Rec1-resilin molecules exert intermolecular repulsive force of interaction, the Rg value reduces with a progressive increase in concentration, and molecular chains transform from a Gaussian coil to a fully swollen coil. It is also revealed that the structural organization of Rec1-resilin dynamically transforms from a rod (pH 2) to coil (pH 4.8) and to globular (pH 12) as a function of pH. The findings further support the temperature-triggered dual-phase-transition behavior of Rec1-resilin, exhibiting rod-shaped structural organization below the upper critical solution temperature (∼4 °C) and a large but compact structure above the lower critical solution temperature (∼75 °C). This work attempted to correlate unusual responsiveness of Rec1-resilin to the evolution of conformational ensembles.
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Affiliation(s)
- Rajkamal Balu
- Future Industries Institute, University of South Australia , Mawson Lakes, SA 5095, Australia
| | - Jitendra P Mata
- Bragg Institute, ANSTO , Private Mail Bag, Kirrawee, NSW 2232, Australia
| | - Robert Knott
- Bragg Institute, ANSTO , Private Mail Bag, Kirrawee, NSW 2232, Australia
| | - Christopher M Elvin
- CSIRO Agriculture, Level 6, Queensland Bioscience Precinct , St Lucia, QLD 4067, Australia
| | - Anita J Hill
- CSIRO Manufacturing , Bayview Avenue, Clayton, VIC 3168, Australia
| | - Namita R Choudhury
- School of Chemical Engineering, The University of Adelaide , Adelaide, SA 5005, Australia.,Future Industries Institute, University of South Australia , Mawson Lakes, SA 5095, Australia
| | - Naba K Dutta
- School of Chemical Engineering, The University of Adelaide , Adelaide, SA 5005, Australia.,Future Industries Institute, University of South Australia , Mawson Lakes, SA 5095, Australia
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28
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Schuler B, Soranno A, Hofmann H, Nettels D. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Annu Rev Biophys 2016; 45:207-31. [PMID: 27145874 DOI: 10.1146/annurev-biophys-062215-010915] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
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29
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Urbanowicz A, Lewandowski D, Szpotkowski K, Figlerowicz M. Tick receptor for outer surface protein A from Ixodes ricinus - the first intrinsically disordered protein involved in vector-microbe recognition. Sci Rep 2016; 6:25205. [PMID: 27112540 PMCID: PMC4844993 DOI: 10.1038/srep25205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/12/2016] [Indexed: 01/02/2023] Open
Abstract
The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.
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Affiliation(s)
- Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Dominik Lewandowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Kamil Szpotkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland.,Institute of Computing Science, University of Technology, Poznan, 60-965, Poland
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30
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Moreno AJ, Lo Verso F, Arbe A, Pomposo JA, Colmenero J. Concentrated Solutions of Single-Chain Nanoparticles: A Simple Model for Intrinsically Disordered Proteins under Crowding Conditions. J Phys Chem Lett 2016; 7:838-844. [PMID: 26894933 DOI: 10.1021/acs.jpclett.6b00144] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
By means of large-scale computer simulations and small-angle neutron scattering (SANS), we investigate solutions of single-chain nanoparticles (SCNPs), covering the whole concentration range from infinite dilution to melt density. The analysis of the conformational properties of the SCNPs reveals that these synthetic nano-objects share basic ingredients with intrinsically disordered proteins (IDPs), as topological polydispersity, generally sparse conformations, and locally compact domains. We investigate the role of the architecture of the SCNPs in their collapse behavior under macromolecular crowding. Unlike in the case of linear macromolecules, which experience the usual transition from self-avoiding to Gaussian random-walk conformations, crowding leads to collapsed conformations of SCNPs resembling those of crumpled globules. This behavior is already found at volume fractions (about 30%) that are characteristic of crowding in cellular environments. The simulation results are confirmed by the SANS experiments. Our results for SCNPs--a model system free of specific interactions--propose a general scenario for the effect of steric crowding on IDPs: collapse from sparse conformations at high dilution to crumpled globular conformations in cell environments.
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Affiliation(s)
- Angel J Moreno
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain
| | - Federica Lo Verso
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - José A Pomposo
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Departamento de Física de Materiales, Universidad del País Vasco (UPV/EHU) , Apartado 1072, E-20800 San Sebastián, Spain
- IKERBASQUE - Basque Foundation for Science, Alameda Urquijo 36, E-48011 Bilbao, Spain
| | - Juan Colmenero
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain
- Departamento de Física de Materiales, Universidad del País Vasco (UPV/EHU) , Apartado 1072, E-20800 San Sebastián, Spain
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31
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Burchard W, Schweins R, Werner M. Branched conformational properties of macromolecules in close relation to chemical synthesis. II. Influence of excluded volume interactions. J Chem Phys 2015; 143:114907. [DOI: 10.1063/1.4928963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Mikaelsson T, Ådén J, Wittung-Stafshede P, Johansson LBÅ. Macromolecular crowding effects on two homologs of ribosomal protein s16: protein-dependent structural changes and local interactions. Biophys J 2015; 107:401-410. [PMID: 25028882 DOI: 10.1016/j.bpj.2014.05.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/30/2022] Open
Abstract
Proteins function in cellular environments that are crowded with biomolecules, and in this reduced available space, their biophysical properties may differ from those observed in dilute solutions in vitro. Here, we investigated the effects of a synthetic macromolecular crowding agent, dextran 20, on the folded states of hyperthermophilic (S16Thermo) and mesophilic (S16Meso) homologs of the ribosomal protein S16. As expected for an excluded-volume effect, the resistance of the mesophilic protein to heat-induced unfolding increased in the presence of dextran 20, and chemical denaturation experiments at different fixed temperatures showed the macromolecular crowding effect to be temperature-independent. Förster resonance energy transfer experiments show that intramolecular distances between an intrinsic Trp residue and BODIPY-labeled S16Meso depend on the level of the crowding agent. The BODIPY group was attached at three specific positions in S16Meso, allowing measurements of three intraprotein distances. All S16Meso variants exhibited a decrease in the average Trp-BODIPY distance at up to 100 mg/mL dextran 20, whereas the changes in distance became anisotropic (one distance increased, two distances decreased) at higher dextran concentrations. In contrast, the two S16Thermo mutants did not show any changes in Trp-BODIPY distances upon increase of dextran 20 concentrations. It should be noted that the fluorescence quantum yields and lifetimes of BODIPY attached to the two S16 homologs decreased gradually in the presence of dextran 20. To investigate the origin of this decrease, we studied the BODIPY quantum yield in three protein variants in the presence of a tyrosine-labeled dextran. The experiments revealed distinct tyrosine quenching behaviors of BODIPY in the three variants, suggesting a dynamic local interaction between dextran and one particular S16 variant.
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Affiliation(s)
| | - Jörgen Ådén
- Department of Chemistry, Umeå University, Umeå, Sweden
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Knowles DB, Shkel IA, Phan NM, Sternke M, Lingeman E, Cheng X, Cheng L, O'Connor K, Record MT. Chemical Interactions of Polyethylene Glycols (PEGs) and Glycerol with Protein Functional Groups: Applications to Effects of PEG and Glycerol on Protein Processes. Biochemistry 2015; 54:3528-42. [PMID: 25962980 DOI: 10.1021/acs.biochem.5b00246] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, we obtain the data needed to predict chemical interactions of polyethylene glycols (PEGs) and glycerol with proteins and related organic compounds and thereby interpret or predict chemical effects of PEGs on protein processes. To accomplish this, we determine interactions of glycerol and tetraEG with >30 model compounds displaying the major C, N, and O functional groups of proteins. Analysis of these data yields coefficients (α values) that quantify interactions of glycerol, tetraEG, and PEG end (-CH2OH) and interior (-CH2OCH2-) groups with these groups, relative to interactions with water. TetraEG (strongly) and glycerol (weakly) interact favorably with aromatic C, amide N, and cationic N, but unfavorably with amide O, carboxylate O, and salt ions. Strongly unfavorable O and salt anion interactions help make both small and large PEGs effective protein precipitants. Interactions of tetraEG and PEG interior groups with aliphatic C are quite favorable, while interactions of glycerol and PEG end groups with aliphatic C are not. Hence, tetraEG and PEG300 favor unfolding of the DNA-binding domain of lac repressor (lacDBD), while glycerol and di- and monoethylene glycol are stabilizers. Favorable interactions with aromatic and aliphatic C explain why PEG400 greatly increases the solubility of aromatic hydrocarbons and steroids. PEG400-steroid interactions are unusually favorable, presumably because of simultaneous interactions of multiple PEG interior groups with the fused ring system of the steroid. Using α values reported here, chemical contributions to PEG m-values can be predicted or interpreted in terms of changes in water-accessible surface area (ΔASA) and separated from excluded volume effects.
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Affiliation(s)
- D B Knowles
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Noel M Phan
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Matt Sternke
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Emily Lingeman
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Xian Cheng
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Lixue Cheng
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Kevin O'Connor
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - M Thomas Record
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
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Stadler AM, Koza MM, Fitter J. Determination of Conformational Entropy of Fully and Partially Folded Conformations of Holo- and Apomyoglobin. J Phys Chem B 2014; 119:72-82. [DOI: 10.1021/jp509732q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andreas M. Stadler
- Jülich
Centre for Neutron Science JCNS and Institute for Complex Systems
ICS, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | | | - Jörg Fitter
- Institute
of Complex Systems (ICS-5): Molecular Biophysics, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- I.
Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse
14, 52074 Aachen, Germany
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35
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What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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36
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Goldenberg DP, Argyle B. Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study. Biophys J 2014; 106:905-14. [PMID: 24559993 DOI: 10.1016/j.bpj.2013.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 01/04/2023] Open
Abstract
Small-angle neutron scattering was used to study the effects of macromolecular crowding by two globular proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an intrinsically disordered protein, the N protein of bacteriophage λ. The λ N protein was uniformly labeled with (2)H, and the concentrations of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples containing up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded protein was estimated to be 30 Å and was found to be remarkably insensitive to the presence of crowders, varying by <2 Å for the highest crowder concentrations. The scattering profiles were also used to estimate the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examined. These results are contrary to the predictions of theoretical treatments and previous experimental studies demonstrating compaction of unfolded proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective volumes of disordered proteins and the variation of these volumes within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding proteins, which may compensate for the effects of steric exclusion.
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Affiliation(s)
| | - Brian Argyle
- Department of Biology, University of Utah, Salt Lake City, Utah
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37
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Goldenberg DP, Argyle B. Self crowding of globular proteins studied by small-angle x-ray scattering. Biophys J 2014; 106:895-904. [PMID: 24559992 DOI: 10.1016/j.bpj.2013.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/26/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022] Open
Abstract
Small-angle x-ray scattering (SAXS) was used to study the behavior of equine metmyoglobin (Mb) and bovine pancreatic trypsin inhibitor (BPTI) at concentrations up to 0.4 and 0.15 g/mL, respectively, in solutions also containing 50% D2O and 1 M urea. For both proteins, significant effects because of interference between x-rays scattered by different molecules (interparticle interference) were observed, indicating nonideal behavior at high concentrations. The experimental data were analyzed by comparison of the observed scattering profiles with those predicted by crystal structures of the proteins and a hard-sphere fluid model used to represent steric exclusion effects. The Mb scattering data were well fit by the hard-sphere model using a sphere radius of 18 Å, only slightly smaller than that estimated from the three-dimensional structure (20 Å). In contrast, the scattering profiles for BPTI in phosphate buffer displayed substantially less pronounced interparticle interference than predicted by the hard-sphere model and the radius estimated from the known structure of the protein (15 Å). Replacing the phosphate buffer with 3-(N-morpolino)propane sulfonic acid (MOPS) led to increased interparticle interference, consistent with a larger effective radius and suggesting that phosphate ions may mediate attractive intermolecular interactions, as observed in some BPTI crystal structures, without the formation of stable oligomers. The scattering data were also used to estimate second virial coefficients for the two proteins: 2.0 ×10(-4) cm(3)mol/g(2) for Mb in phosphate buffer, 1.6 ×10(-4) cm(3)mol/g(2) for BPTI in phosphate buffer and 9.2 ×10(-4) cm(3)mol/g(2) for BPTI in MOPS. The results indicate that the behavior of Mb, which is nearly isoelectric under the conditions used, is well described by the hard-sphere model, but that of BPTI is considerably more complex and is likely influenced by both repulsive and attractive electrostatic interactions. The hard-sphere model may be a generally useful tool for the analysis of small-angle scattering data from concentrated macromolecular solutions.
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Affiliation(s)
| | - Brian Argyle
- Department of Biology, University of Utah, Salt Lake City, Utah
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38
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Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI. SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res 2014; 43:D357-63. [PMID: 25352555 PMCID: PMC4383894 DOI: 10.1093/nar/gku1047] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Small-angle X-ray and neutron scattering (SAXS and SANS) are fundamental tools used to study the global shapes of proteins, nucleic acids, macromolecular complexes and assemblies in solution. Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically. The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf). The small-angle scattering biological data bank (SASBDB) www.sasbdb.org has been designed in accordance with the plans of the SAStf as part of a future federated system of databases for biological SAXS and SANS. SASBDB is a comprehensive repository of freely accessible and fully searchable SAS experimental data and models that are deposited together with the relevant experimental conditions, sample details and instrument characteristics. At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.
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Affiliation(s)
- Erica Valentini
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Gianpietro Previtali
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
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Smith WW, Ho PY, O'Hern CS. Calibrated Langevin-dynamics simulations of intrinsically disordered proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:042709. [PMID: 25375525 DOI: 10.1103/physreve.90.042709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 06/04/2023]
Abstract
We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the interresidue separations for 36 pairs of residues in five IDPs: α-, β-, and γ-synuclein, the microtubule-associated protein τ, and prothymosin α. We find that our CG model is able to recapitulate the average interresidue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein.
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Affiliation(s)
- W Wendell Smith
- Department of Physics, Yale University, New Haven, Connecticut 06520-8120, USA and Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520-8114, USA
| | - Po-Yi Ho
- Department of Physics, Yale University, New Haven, Connecticut 06520-8120, USA
| | - Corey S O'Hern
- Department of Physics, Yale University, New Haven, Connecticut 06520-8120, USA and Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520-8114, USA and Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520-8286, USA and Department of Applied Physics, Yale University, New Haven, Connecticut 06520-8267, USA and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
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40
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Hennig J, Sattler M. The dynamic duo: combining NMR and small angle scattering in structural biology. Protein Sci 2014; 23:669-82. [PMID: 24687405 DOI: 10.1002/pro.2467] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 12/12/2022]
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of complementary aspects provided by different structural biology techniques. Although X-ray crystallography remains the method of choice for structural analysis of large complexes, crystallization of flexible systems is often difficult and does typically not provide insights into conformational dynamics present in solution. Nuclear magnetic resonance spectroscopy (NMR) is well-suited to study dynamics at picosecond to second time scales, and to map binding interfaces even of large systems at residue resolution but suffers from poor sensitivity with increasing molecular weight. Small angle scattering (SAS) methods provide low resolution information in solution and can characterize dynamics and conformational equilibria complementary to crystallography and NMR. The combination of NMR, crystallography, and SAS is, thus, very useful for analysis of the structure and conformational dynamics of (large) protein complexes in solution. In high molecular weight systems, where NMR data are often sparse, SAS provides additional structural information and can differentiate between NMR-derived models. Scattering data can also validate the solution conformation of a crystal structure and indicate the presence of conformational equilibria. Here, we review current state-of-the-art approaches for combining NMR, crystallography, and SAS data to characterize protein complexes in solution.
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Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr.1, D-85764, Neuherberg, Germany; Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747, Garching, Germany
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41
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Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. Proc Natl Acad Sci U S A 2014; 111:4874-9. [PMID: 24639500 DOI: 10.1073/pnas.1322611111] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [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 involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect of crowding as mimicked by commonly used biocompatible polymers. We observe a compaction of IDPs not only with increasing concentration, but also with increasing size of the crowding agents, at variance with the predictions from scaled-particle theory, the prevalent paradigm in the field. However, the observed behavior can be explained quantitatively if the polymeric nature of both the IDPs and the crowding molecules is taken into account explicitly. Our results suggest that excluded volume interactions between overlapping biopolymers and the resulting criticality of the system can be essential contributions to the physics governing the crowded cellular milieu.
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42
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Denatured state structural property determines protein stabilization by macromolecular crowding: a thermodynamic and structural approach. PLoS One 2013; 8:e78936. [PMID: 24265729 PMCID: PMC3827121 DOI: 10.1371/journal.pone.0078936] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/26/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding of protein structure and stability gained to date has been acquired through investigations made under dilute conditions where total macromolecular concentration never surpasses 10 g l−1. However, biological macromolecules are known to evolve and function under crowded intracellular environments that comprises of proteins, nucleic acids, ribosomes and carbohydrates etc. Crowded environment is known to result in altered biological properties including thermodynamic, structural and functional aspect of macromolecules as compared to the macromolecules present in our commonly used experimental dilute buffers (for example, Tris HCl or phosphate buffer). In this study, we have investigated the thermodynamic and structural consequences of synthetic crowding agent (Ficoll 70) on three different proteins (Ribonuclease-A, lysozyme and holo α-lactalbumin) at different pH values. We report here that the effect of crowding is protein dependent in terms of protein thermal stability and structure. We also observed that the structural characteristics of the denatured state determines if crowding will have an effect or not on the protein stability.
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43
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The transcriptional repressor domain of Gli3 is intrinsically disordered. PLoS One 2013; 8:e76972. [PMID: 24146948 PMCID: PMC3798401 DOI: 10.1371/journal.pone.0076972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/26/2013] [Indexed: 01/03/2023] Open
Abstract
The transcription factor Gli3 is acting mainly as a transcriptional repressor in the Sonic hedgehog signal transduction pathway. Gli3 contains a repressor domain in its N-terminus from residue G106 to E236. In this study we have characterized the intracellular structure of the Gli3 repressor domain using a combined bioinformatics and experimental approach. According to our findings the Gli3 repressor domain while being intrinsically disordered contains predicted anchor sites for partner interactions. The obvious interaction partners to test were Ski and DNA; however, with both of these the structure of Gli3 repressor domain remained disordered. To locate residues important for the repressor function we mutated several residues within the Gli3 repressor domain. Two of these, H141A and H157N, targeting predicted helical regions, significantly decreased transcriptional repression and thus identify important functional parts of the domain.
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44
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Qin S, Zhou HX. Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins. J Phys Chem Lett 2013; 4:10.1021/jz401817x. [PMID: 24312701 PMCID: PMC3846091 DOI: 10.1021/jz401817x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Due to their conformational malleability, intrinsically disordered proteins (IDPs) are particularly susceptible to influences of crowded cellular environments. Here we report a computational study of the effects of macromolecular crowding on the conformational ensemble of a coarse-grained IDP model, by using two approaches. In one, the IDP is simulated along with the crowders; in the other, crowder-free simulations are postprocessed to predict the conformational ensembles under crowding. We found significant decreases in the radius of gyration of the IDP under crowding, and suggest repulsive interactions with crowders as a common cause for chain compaction in a number of experimental studies. The postprocessing approach accurately reproduced the conformational ensembles of the IDP in the direct simulations here, and holds enormous potential for realistic modeling of IDPs under crowding, by permitting thorough conformation sampling for the proteins even when they and the crowders are both represented at the all-atom level.
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Affiliation(s)
| | - Huan-Xiang Zhou
- Correspondence information: phone, (850) 645-1336; fax, (850) 644-7244; e-mail,
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45
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Lee V, Hawa T. Investigation of the effect of bilayer membrane structures and fluctuation amplitudes on SANS/SAXS profile for short membrane wavelength. J Chem Phys 2013; 139:124905. [DOI: 10.1063/1.4821816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Kosol S, Contreras-Martos S, Cedeño C, Tompa P. Structural characterization of intrinsically disordered proteins by NMR spectroscopy. Molecules 2013; 18:10802-28. [PMID: 24008243 PMCID: PMC6269831 DOI: 10.3390/molecules180910802] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/19/2013] [Accepted: 08/30/2013] [Indexed: 01/25/2023] Open
Abstract
Recent advances in NMR methodology and techniques allow the structural investigation of biomolecules of increasing size with atomic resolution. NMR spectroscopy is especially well-suited for the study of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) which are in general highly flexible and do not have a well-defined secondary or tertiary structure under functional conditions. In the last decade, the important role of IDPs in many essential cellular processes has become more evident as the lack of a stable tertiary structure of many protagonists in signal transduction, transcription regulation and cell-cycle regulation has been discovered. The growing demand for structural data of IDPs required the development and adaption of methods such as 13C-direct detected experiments, paramagnetic relaxation enhancements (PREs) or residual dipolar couplings (RDCs) for the study of ‘unstructured’ molecules in vitro and in-cell. The information obtained by NMR can be processed with novel computational tools to generate conformational ensembles that visualize the conformations IDPs sample under functional conditions. Here, we address NMR experiments and strategies that enable the generation of detailed structural models of IDPs.
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Affiliation(s)
- Simone Kosol
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
- Authors to whom correspondence should be addressed; E-Mails: (S.K.); (P.T.)
| | - Sara Contreras-Martos
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
| | - Cesyen Cedeño
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium; E-Mails: (S.C.M.); (C.C.)
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest 1518, Hungary
- Authors to whom correspondence should be addressed; E-Mails: (S.K.); (P.T.)
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47
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Qin S, Zhou HX. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders. J Chem Theory Comput 2013; 9. [PMID: 24187527 DOI: 10.1021/ct4005195] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
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48
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Direct observation of protein unfolded state compaction in the presence of macromolecular crowding. Biophys J 2013; 104:694-704. [PMID: 23442920 DOI: 10.1016/j.bpj.2012.12.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/20/2012] [Accepted: 12/06/2012] [Indexed: 11/22/2022] Open
Abstract
Proteins fold and function in cellular environments that are crowded with other macromolecules. As a consequence of excluded volume effects, compact folded states of proteins should be indirectly stabilized due to destabilization of extended unfolded conformations. Here, we assess the role of excluded volume in terms of protein stability, structural dimensions and folding dynamics using a sugar-based crowding agent, dextran 20, and the small ribosomal protein S16 as a model system. To specifically address dimensions, we labeled the protein with BODIPY at two positions and measured Trp-BODIPY distances under different conditions. As expected, we found that dextran 20 (200 mg/ml) stabilized the variants against urea-induced unfolding. At conditions where the protein is unfolded, Förster resonance energy transfer measurements reveal that in the presence of dextran, the unfolded ensemble is more compact and there is residual structure left as probed by far-ultraviolet circular dichroism. In the presence of a crowding agent, folding rates are faster in the two-state regime, and at low denaturant concentrations, a kinetic intermediate is favored. Our study provides direct evidence for protein unfolded-state compaction in the presence of macromolecular crowding along with its energetic and kinetic consequences.
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49
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Sotomayor-Pérez AC, Subrini O, Hessel A, Ladant D, Chenal A. Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State and the Folded Calcium-Bound State of a Repeat in Toxin (RTX) Protein. J Am Chem Soc 2013; 135:11929-34. [DOI: 10.1021/ja404790f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana-Cristina Sotomayor-Pérez
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Orso Subrini
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Audrey Hessel
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Daniel Ladant
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
| | - Alexandre Chenal
- Unité
de Biochimie des Interactions Macromoléculaires, CNRS UMR 3528,
Département de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex
15, France
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50
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Christiansen A, Wang Q, Cheung MS, Wittung-Stafshede P. Effects of macromolecular crowding agents on protein folding in vitro and in silico. Biophys Rev 2013; 5:137-145. [PMID: 28510156 DOI: 10.1007/s12551-013-0108-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/31/2013] [Indexed: 01/24/2023] Open
Abstract
Proteins fold and function inside cells which are environments very different from that of dilute buffer solutions most often used in traditional experiments. The crowded milieu results in excluded-volume effects, increased bulk viscosity and amplified chances for inter-molecular interactions. These environmental factors have not been accounted for in most mechanistic studies of protein folding executed during the last decades. The question thus arises as to how these effects-present when polypeptides normally fold in vivo-modulate protein biophysics. To address excluded volume effects, we use synthetic macromolecular crowding agents, which take up significant volume but do not interact with proteins, in combination with strategically selected proteins and a range of equilibrium and time-resolved biophysical (spectroscopic and computational) methods. In this review, we describe key observations on macromolecular crowding effects on protein stability, folding and structure drawn from combined in vitro and in silico studies. As expected based on Minton's early predictions, many proteins (apoflavodoxin, VlsE, cytochrome c, and S16) became more thermodynamically stable (magnitude depends inversely on protein stability in buffer) and, unexpectedly, for apoflavodoxin and VlsE, the folded states changed both secondary structure content and, for VlsE, overall shape in the presence of macromolecular crowding. For apoflavodoxin and cytochrome c, which have complex kinetic folding mechanisms, excluded volume effects made the folding energy landscapes smoother (i.e., less misfolding and/or kinetic heterogeneity) than in buffer.
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Affiliation(s)
| | - Qian Wang
- Department of Physics, University of Houston, Houston, TX, 77204, USA
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX, 77204, USA
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