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Carlier L, Samson D, Khemtemourian L, Joliot A, Fuchs PFJ, Lequin O. Anionic lipids induce a fold-unfold transition in the membrane-translocating Engrailed homeodomain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184030. [PMID: 35988722 DOI: 10.1016/j.bbamem.2022.184030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/17/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Homeoprotein transcription factors have the property of interacting with membranes through their DNA-binding homeodomain, which is involved in unconventional internalization and secretion. Both processes depend on membrane-translocating events but their detailed molecular mechanisms are still poorly understood. We have previously characterized the conformational properties of Engrailed 2 homeodomain (EnHD) in aqueous solution and in micelles as membrane-mimetic environments. In the present study, we used small isotropic lipid bicelles as a more relevant membrane-mimetic model to characterize the membrane-bound state of EnHD. We show that lipid bicelles, in contrast to micelles, adequately reproduce the requirement of anionic lipids in the membrane binding and conformational transition of EnHD. The fold-unfold transition of EnHD induced by anionic lipids was characterized by NMR using 1H, 13C, 15N chemical shifts, nuclear Overhauser effects, residual dipolar couplings, intramolecular and intermolecular paramagnetic relaxation enhancements induced by site-directed spin-label or paramagnetic lipid probe, respectively. A global unpacking of EnHD helices is observed leading to a loss of the native fold. However, near-native propensities of EnHD backbone conformation are maintained in membrane environment, including not only the three helices but also the turn connecting helices H2 and H3. NMR and coarse-grained molecular dynamics simulations reveal that the EnHD adopts a shallow insertion in the membrane, with the three helices oriented parallel to the membrane. EnHD explores extended conformations and closed U-shaped conformations, which are stabilized by anionic lipid recruitment.
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Affiliation(s)
- Ludovic Carlier
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France.
| | - Damien Samson
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France
| | - Lucie Khemtemourian
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France
| | - Alain Joliot
- INSERM U932, Institut Curie Centre de Recherche, PSL University, France
| | - Patrick F J Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France; Université Paris Cité, UFR Sciences du Vivant, F-75013 Paris, France
| | - Olivier Lequin
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, F-75005 Paris, France.
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2
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Yu L, Li DW, Brüschweiler R. Balanced Amino-Acid-Specific Molecular Dynamics Force Field for the Realistic Simulation of Both Folded and Disordered Proteins. J Chem Theory Comput 2019; 16:1311-1318. [DOI: 10.1021/acs.jctc.9b01062] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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3
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Nguyen C, Young JT, Slade GG, Oliveira RJ, McCully ME. A Dynamic Hydrophobic Core and Surface Salt Bridges Thermostabilize a Designed Three-Helix Bundle. Biophys J 2019; 116:621-632. [PMID: 30704856 PMCID: PMC6382955 DOI: 10.1016/j.bpj.2019.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/18/2018] [Accepted: 01/02/2019] [Indexed: 11/24/2022] Open
Abstract
Thermostable proteins are advantageous in industrial applications, as pharmaceuticals or biosensors, and as templates for directed evolution. As protein-design methodologies improve, bioengineers are able to design proteins to perform a desired function. Although many rationally designed proteins end up being thermostable, how to intentionally design de novo, thermostable proteins is less clear. UVF is a de novo-designed protein based on the backbone structure of the Engrailed homeodomain (EnHD) and is highly thermostable (Tm > 99°C vs. 52°C for EnHD). Although most proteins generally have polar amino acids on their surfaces and hydrophobic amino acids buried in their cores, protein engineers followed this rule exactly when designing UVF. To investigate the contributions of the fully hydrophobic core versus the fully polar surface to UVF’s thermostability, we built two hybrid, chimeric proteins combining the sets of buried and surface residues from UVF and EnHD. Here, we determined a structural, dynamic, and thermodynamic explanation for UVF’s thermostability by performing 4 μs of all-atom, explicit-solvent molecular dynamics simulations at 25 and 100°C, Tanford-Kirkwood solvent accessibility Monte Carlo electrostatic calculations, and a thermodynamic analysis of 40 temperature runs by the weighted-histogram analysis method of heavy-atom, structure-based models of UVF, EnHD, and both chimeric proteins. Our models showed that UVF was highly dynamic because of its fully hydrophobic core, leading to a smaller loss of entropy upon folding. The charged residues on its surface made favorable electrostatic interactions that contributed enthalpically to its thermostability. In the chimeric proteins, both the hydrophobic core and charged surface independently imparted thermostability.
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Affiliation(s)
- Catrina Nguyen
- Department of Biology, Santa Clara University, Santa Clara, California
| | - Jennifer T Young
- Department of Biology, Santa Clara University, Santa Clara, California
| | - Gabriel G Slade
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Ronaldo J Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
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4
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Childers MC, Daggett V. Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles. J Phys Chem B 2018; 122:6673-6689. [PMID: 29864281 DOI: 10.1021/acs.jpcb.8b02144] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Far from the static, idealized conformations deposited into structural databases, proteins are highly dynamic molecules that undergo conformational changes on temporal and spatial scales that may span several orders of magnitude. These conformational changes, often intimately connected to the functional roles that proteins play, may be obscured by traditional biophysical techniques. Over the past 40 years, molecular dynamics (MD) simulations have complemented these techniques by providing the "hidden" atomistic details that underlie protein dynamics. However, there are limitations of the degree to which molecular simulations accurately and quantitatively describe protein motions. Here we show that although four molecular dynamics simulation packages (AMBER, GROMACS, NAMD, and ilmm) reproduced a variety of experimental observables for two different proteins (engrailed homeodomain and RNase H) equally well overall at room temperature, there were subtle differences in the underlying conformational distributions and the extent of conformational sampling obtained. This leads to ambiguity about which results are correct, as experiment cannot always provide the necessary detailed information to distinguish between the underlying conformational ensembles. However, the results with different packages diverged more when considering larger amplitude motion, for example, the thermal unfolding process and conformational states sampled, with some packages failing to allow the protein to unfold at high temperature or providing results at odds with experiment. While most differences between MD simulations performed with different packages are attributed to the force fields themselves, there are many other factors that influence the outcome, including the water model, algorithms that constrain motion, how atomic interactions are handled, and the simulation ensemble employed. Here four different MD packages were tested each using best practices as established by the developers, utilizing three different protein force fields and three different water models. Differences between the simulated protein behavior using two different packages but the same force field, as well as two different packages with different force fields but the same water models and approaches to restraining motion, show how other factors can influence the behavior, and it is incorrect to place all the blame for deviations and errors on force fields or to expect improvements in force fields alone to solve such problems.
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Affiliation(s)
- Matthew Carter Childers
- Department of Bioengineering , University of Washington , Seattle , Washington 98195-5013 , United States
| | - Valerie Daggett
- Department of Bioengineering , University of Washington , Seattle , Washington 98195-5013 , United States
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5
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Gandhi NS, Blancafort P, Mancera RL. Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps). Oncotarget 2018; 9:22383-22397. [PMID: 29854286 PMCID: PMC5976472 DOI: 10.18632/oncotarget.25025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 03/15/2018] [Indexed: 12/21/2022] Open
Abstract
The neural-specific transcription factor Engrailed 1 - is overexpressed in basal-like breast tumours. Synthetic interference peptides - comprising a cell-penetrating peptide/nuclear localisation sequence and the Engrailed 1-specific sequence from the N-terminus have been engineered to produce a strong apoptotic response in tumour cells overexpressing EN1, with no toxicity to normal or non Engrailed 1-expressing cells. Here scaled molecular dynamics simulations were used to study the conformational dynamics of these interference peptides in aqueous solution to characterise their structure and dynamics. Transitions from disordered to α-helical conformation, stabilised by hydrogen bonds and proline-aromatic interactions, were observed throughout the simulations. The backbone of the wild-type peptide folds to a similar conformation as that found in ternary complexes of anterior Hox proteins with conserved hexapeptide motifs important for recognition of pre-B-cell leukemia Homeobox 1, indicating that the motif may possess an intrinsic preference for helical structure. The predicted NMR chemical shifts of these peptides are consistent with the Hox hexapeptides in solution and Engrailed 2 NMR data. These findings highlight the importance of aromatic residues in determining the structure of Engrailed 1 interference peptides, shedding light on the rational design strategy of molecules that could be adopted to inhibit other transcription factors overexpressed in other cancer types, potentially including other transcription factor families that require highly conserved and cooperative protein-protein partnerships for biological activity.
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Affiliation(s)
- Neha S Gandhi
- School of Mathematical Sciences and Institute for Health and Biomedical Innovation, Queensland University of Technology, Gardens Point Campus, Brisbane QLD 4000, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth WA 6845, Australia
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6
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Nasedkin A, Davidsson J, Niemi AJ, Peng X. Solution x-ray scattering and structure formation in protein dynamics. Phys Rev E 2018; 96:062405. [PMID: 29347365 DOI: 10.1103/physreve.96.062405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Indexed: 11/07/2022]
Abstract
We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jan Davidsson
- Department of Chemistry, Uppsala University, P. O. Box 803, S-75108, Uppsala, Sweden
| | - Antti J Niemi
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Nordita, Stockholm University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden.,Department of Physics and Astronomy, Uppsala University, P. O. Box 803, S-75108, Uppsala, Sweden.,Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours, France.,School of Physics, Beijing Institute of Technology, Beijing 100081, P.R. China.,Laboratory of Physics of Living Matter, School of Biomedicine, Far Eastern Federal University, Vladivostok 690090, Russia¶
| | - Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
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7
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Špačková N, Trošanová Z, Šebesta F, Jansen S, Burda JV, Srb P, Zachrdla M, Žídek L, Kozelka J. Protein environment affects the water–tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Phys Chem Chem Phys 2018; 20:12664-12677. [DOI: 10.1039/c7cp08623g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water molecules can interact with the π-face of tryptophan either forming an O–H⋯π hydrogen bond or by a lone-pair⋯π interaction. Surrounding amino acids can favor the one or the other interaction type.
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Affiliation(s)
- Nad'a Špačková
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
| | - Zuzana Trošanová
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
| | - Filip Šebesta
- Department of Chemical Physics and Optics
- Faculty of Mathematics and Physics
- Charles University
- 12116 Praha
- Czech Republic
| | - Séverine Jansen
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics and Optics
- Faculty of Mathematics and Physics
- Charles University
- 12116 Praha
- Czech Republic
| | - Pavel Srb
- National Centre for Biomolecular Research
- Faculty of Science
- Masaryk University
- 62500 Brno
- Czech Republic
| | - Milan Zachrdla
- National Centre for Biomolecular Research
- Faculty of Science
- Masaryk University
- 62500 Brno
- Czech Republic
| | - Lukáš Žídek
- National Centre for Biomolecular Research
- Faculty of Science
- Masaryk University
- 62500 Brno
- Czech Republic
| | - Jiří Kozelka
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
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8
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Nasedkin A, Marcellini M, Religa TL, Freund SM, Menzel A, Fersht AR, Jemth P, van der Spoel D, Davidsson J. Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation. PLoS One 2015; 10:e0125662. [PMID: 25946337 PMCID: PMC4422743 DOI: 10.1371/journal.pone.0125662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/11/2015] [Indexed: 12/30/2022] Open
Abstract
The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Chemistry-Ångström laboratory, Uppsala University, Box 523, SE-75110 Uppsala, Sweden
| | - Moreno Marcellini
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - Tomasz L. Religa
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Stefan M. Freund
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | | | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - Jan Davidsson
- Department of Chemistry-Ångström laboratory, Uppsala University, Box 523, SE-75110 Uppsala, Sweden
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9
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Bratholm LA, Christensen AS, Hamelryck T, Jensen JH. Bayesian inference of protein structure from chemical shift data. PeerJ 2015; 3:e861. [PMID: 25825683 PMCID: PMC4375973 DOI: 10.7717/peerj.861] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/06/2015] [Indexed: 12/15/2022] Open
Abstract
Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.
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Affiliation(s)
- Lars A. Bratholm
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | | | - Thomas Hamelryck
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan H. Jensen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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10
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Investigation of homeodomain membrane translocation properties: insights from the structure determination of engrailed-2 homeodomain in aqueous and membrane-mimetic environments. Biophys J 2014; 105:667-78. [PMID: 23931315 DOI: 10.1016/j.bpj.2013.06.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/02/2013] [Accepted: 06/07/2013] [Indexed: 11/21/2022] Open
Abstract
In addition to their well-known DNA-binding properties, homeodomains have the ability to efficiently translocate across biological membranes through still poorly-characterized mechanisms. To date, most biophysical studies addressing the mechanisms of internalization have focused on small synthetic peptides rather than full-length globular homeodomains. In this work, we characterized the conformational properties of chicken Engrailed 2 homeodomain (En2HD) in aqueous solution and in membrane mimetic environments using circular dichroism, Trp fluorescence, and NMR spectroscopy. En2HD adopts a well-defined three-helical bundle fold in aqueous solution. The Trp-48 residue, which is critical for internalization, is fully buried in the hydrophobic core. Circular dichroism and fluorescence reveal that a conformational transition occurs in anionic lipid vesicles and in micelles. En2HD loses its native three-dimensional structure in micellar environments but, remarkably, near-native helical secondary structures are maintained. Long-range interactions could be detected using site-directed spin labels, indicating that the three helices do not adopt extended orientations. Noncovalent paramagnetic probes yielded information about helix positioning and unveiled the burial of critical aromatic and basic residues within the micelles. Our results suggest that electrostatic interactions with membranes may be determinant in inducing a conformational change enabling Trp-48 to insert into membranes.
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11
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Abstract
Fast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well <1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even 'slow' folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.
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12
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Multimolecule test-tube simulations of protein unfolding and aggregation. Proc Natl Acad Sci U S A 2012; 109:17851-6. [PMID: 23091038 DOI: 10.1073/pnas.1201809109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations of protein folding or unfolding, unlike most in vitro experimental methods, are performed on a single molecule. The effects of neighboring molecules on the unfolding/folding pathway are largely ignored experimentally and simply not modeled computationally. Here, we present two all-atom, explicit solvent molecular dynamics simulations of 32 copies of the Engrailed homeodomain (EnHD), an ultrafast-folding and -unfolding protein for which the folding/unfolding pathway is well-characterized. These multimolecule simulations, in comparison with single-molecule simulations and experimental data, show that intermolecular interactions have little effect on the folding/unfolding pathway. EnHD unfolded by the same mechanism whether it was simulated in only water or also in the presence of other EnHD molecules. It populated the same native state, transition state, and folding intermediate in both simulation systems, and was in good agreement with experimental data available for each of the three states. Unfolding was slowed slightly by interactions with neighboring proteins, which were mostly hydrophobic in nature and ultimately caused the proteins to aggregate. Protein-water hydrogen bonds were also replaced with protein-protein hydrogen bonds, additionally contributing to aggregation. Despite the increase in protein-protein interactions, the protein aggregates formed in simulation did not do so at the total exclusion of water. These simulations support the use of single-molecule techniques to study protein unfolding and also provide insight into the types of interactions that occur as proteins aggregate at high temperature at an atomic level.
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13
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McCully ME, Beck DAC, Daggett V. Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. Protein Eng Des Sel 2012; 26:35-45. [PMID: 23012442 DOI: 10.1093/protein/gzs063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A thermostabilized variant (UVF) of the engrailed homeodomain (EnHD) was previously engineered by Mayo and co-workers. The melting temperature of the non-natural, designed protein is 50°C higher than the natural wild-type protein (>99 vs. 52°C), and the two proteins share 22% sequence identity. We have performed extensive (1 μs) all-atom, explicit solvent molecular dynamics simulations of the wild-type and engineered proteins to investigate their structural and dynamic properties at room temperature and at 100°C. Our simulations are in good agreement with nuclear magnetic resonance data available for the two proteins [nuclear Overhauser effect crosspeaks (NOEs), J-coupling constants and order parameters for EnHD; and NOEs for UVF], showing that we reproduce the backbone dynamics and side chain packing in the native state of both proteins. UVF was more dynamic at room temperature than EnHD, with respect to both its backbone and side chain motion. When the temperature was raised, the thermostable protein maintained this mobility while retaining its native conformation. EnHD, on the other hand, was unable to maintain its more rigid native structure at higher temperature and began to unfold. Heightened protein dynamics leading to promiscuous and dynamically interchangeable amino acid contacts makes UVF more tolerant to increasing temperature, providing a molecular explanation for heightened thermostability of this protein.
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Affiliation(s)
- Michelle E McCully
- Biomolecular Structure and Design Program, University of Washington, Seattle, WA 98195-5013, USA
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14
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McCully ME, Beck DAC, Fersht AR, Daggett V. Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate. Biophys J 2010; 99:1628-36. [PMID: 20816076 DOI: 10.1016/j.bpj.2010.06.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/14/2010] [Accepted: 06/22/2010] [Indexed: 11/15/2022] Open
Abstract
The ultrafast folding pathway of the engrailed homeodomain has been exceptionally well characterized by experiment and simulation. Helices II and III of the three-helix bundle protein form the native helix-turn-helix motif as an on-pathway intermediate within a few microseconds. The slow step is then the proper docking of the helices in approximately 15 mus. However, there is still the unexplained puzzle of why helix docking is relatively slow, which is part of the more general question as to why rearrangements of intermediates occur slowly. To address this problem, we performed 46 all-atom molecular dynamics refolding simulations in explicit water, for a total of 15 micros of simulation time. The simulations started from an intermediate state structure that was generated in an unfolding simulation at 498 K and was then quenched to folding-permissive temperatures. The protein refolded successfully in only one of the 46 simulations, and in that case the refolding pathway mirrored the unfolding pathway at high temperature. In the 45 simulations in which the protein did not fully fold, nonnative salt bridges trapped the protein, which explains why the protein folds relatively slowly from the intermediate state.
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Affiliation(s)
- Michelle E McCully
- Biomolecular Structure and Design Program, Department of Bioengineering, University of Washington, Seattle, Washington, USA
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15
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Hanson B, Bedrov D, Magda JJ, Smith GD. The effect of hydrogen bonding on oligoleucine structure in water: A molecular dynamics simulation study. Eur Polym J 2010. [DOI: 10.1016/j.eurpolymj.2010.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Isaksson J, Nyström S, Derbyshire D, Wallberg H, Agback T, Kovacs H, Bertini I, Giachetti A, Luchinat C. Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. J Med Chem 2009; 52:1712-22. [DOI: 10.1021/jm801388q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johan Isaksson
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Susanne Nyström
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Dean Derbyshire
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Hans Wallberg
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Tatiana Agback
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Helena Kovacs
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Ivano Bertini
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Andrea Giachetti
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Claudio Luchinat
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
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