1
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Skog AE, Paracini N, Gerelli Y, Skepö M. Translocation of Antimicrobial Peptides across Model Membranes: The Role of Peptide Chain Length. Mol Pharm 2024. [PMID: 38993084 DOI: 10.1021/acs.molpharmaceut.4c00450] [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: 07/13/2024]
Abstract
Cushioned lipid bilayers are structures consisting of a lipid bilayer supported on a solid substrate with an intervening layer of soft material. They offer possibilities for studying the behavior and interactions of biological membranes more accurately under physiological conditions. In this work, we continue our studies of cushion formation induced by histatin 5 (24Hst5), focusing on the effect of the length of the peptide chain. 24Hst5 is a short, positively charged, intrinsically disordered saliva peptide, and here, both a shorter (14Hst5) and a longer (48Hst5) peptide variant were evaluated. Experimental surface active techniques were combined with coarse-grained Monte Carlo simulations to obtain information about these peptides. Results show that at 10 mM NaCl, both the shorter and the longer peptide variants behave like 24Hst5 and a cushion below the bilayer is formed. At 150 mM NaCl, however, no interaction is observed for 24Hst5. On the contrary, a cushion is formed both in the case of 14Hst5 and 48Hst5, and in the latter, an additional thick, diffuse, and highly hydrated layer of peptide and lipid molecules is formed, on top of the bilayer. Similar trends were observed from the simulations, which allowed us to hypothesize that positively charged patches of the amino acids lysine and arginine in all three peptides are essential for them to interact with and translocate over the bilayer. We therefore hypothesize that electrostatic interactions are important for the interaction between the solid-supported lipid bilayers and the peptide depending on the linear charge density through the primary sequence and the positively charged patches in the sequence. The understanding of how, why, and when the cushion is formed opens up the possibility for this system to be used in the research and development of new drugs and pharmaceuticals.
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Affiliation(s)
- Amanda E Skog
- Division of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| | - Nicolò Paracini
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Yuri Gerelli
- Institute for Complex Systems - National Research Council (ISC-CNR), Piazzale Aldo Moro 2, 00185 Roma, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Marie Skepö
- Division of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
- NanoLund, Lund University, Box 118, 22100 Lund, Sweden
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2
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Patel KN, Chavda D, Manna M. Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies. Methods Mol Biol 2024; 2780:165-201. [PMID: 38987470 DOI: 10.1007/978-1-0716-3985-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very short period of time. These proteins are essentially characterized by their inherent structural disorder, encoded mainly by their amino acid sequences. The profound abundance of IDPs and intrinsically disordered regions (IDRs) in the biological world delineates their deep-rooted functionality. IDPs and IDRs convey such extensive functionality through their unique dynamic nature, which enables them to carry out huge number of multifaceted biomolecular interactions and make them "interaction hub" of the cellular systems. Additionally, with such widespread functions, their misfunctioning is also intimately associated with multiple diseases. Thus, understanding the dynamic heterogeneity of various IDPs along with their interactions with respective binding partners is an important field with immense potentials in biomolecular research. In this context, molecular docking-based computational approaches have proven to be remarkable in case of ordered proteins. Molecular docking methods essentially model the biomolecular interactions in both structural and energetic terms and use this information to characterize the putative interactions between the two participant molecules. However, direct applications of the conventional docking methods to study IDPs are largely limited by their structural heterogeneity and demands for unique IDP-centric strategies. Thus, in this chapter, we have presented an overview of current methodologies for successful docking operations involving IDPs and IDRs. These specialized methods majorly include the ensemble-based and fragment-based approaches with their own benefits and limitations. More recently, artificial intelligence and machine learning-assisted approaches are also used to significantly reduce the complexity and computational burden associated with various docking applications. Thus, this chapter aims to provide a comprehensive summary of major challenges and recent advancements of molecular docking approaches in the IDP field for their better utilization and greater applicability.Asp (D).
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Affiliation(s)
- Keyur N Patel
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Dhruvil Chavda
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Moutusi Manna
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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3
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Pesce F, Lindorff-Larsen K. Combining Experiments and Simulations to Examine the Temperature-Dependent Behavior of a Disordered Protein. J Phys Chem B 2023. [PMID: 37433228 DOI: 10.1021/acs.jpcb.3c01862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Intrinsically disordered proteins are a class of proteins that lack stable folded conformations and instead adopt a range of conformations that determine their biochemical functions. The temperature-dependent behavior of such disordered proteins is complex and can vary depending on the specific protein and environment. Here, we have used molecular dynamics simulations and previously published experimental data to investigate the temperature-dependent behavior of histatin 5, a 24-residue-long polypeptide. We examined the hypothesis that histatin 5 undergoes a loss of polyproline II (PPII) structure with increasing temperature, leading to more compact conformations. We found that the conformational ensembles generated by the simulations generally agree with small-angle X-ray scattering data for histatin 5, but show some discrepancies with the hydrodynamic radius as probed by pulsed-field gradient NMR spectroscopy, and with the secondary structure information derived from circular dichroism. We attempted to reconcile these differences by reweighting the conformational ensembles against the scattering and NMR data. By doing so, we were in part able to capture the temperature-dependent behavior of histatin 5 and to link the observed decrease in hydrodynamic radius with increasing temperature to a loss of PPII structure. We were, however, unable to achieve agreement with both the scattering and NMR data within experimental errors. We discuss different possible reasons for this including inaccuracies in the force field, differences in conditions of the NMR and scattering experiments, and issues related to the calculation of the hydrodynamic radius from conformational ensembles. Our study highlights the importance of integrating multiple types of experimental data when modeling conformational ensembles of disordered proteins and how environmental factors such as the temperature influence them.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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4
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Fagerberg E, Skepö M. Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining. J Chem Inf Model 2023. [PMID: 37339604 DOI: 10.1021/acs.jcim.3c00113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Coarse-graining is commonly used to decrease the computational cost of simulations. However, coarse-grained models are also considered to have lower transferability, with lower accuracy for systems outside the original scope of parametrization. Here, we benchmark a bead-necklace model and a modified Martini 2 model, both coarse-grained models, for a set of intrinsically disordered proteins, with the different models having different degrees of coarse-graining. The SOP-IDP model has earlier been used for this set of proteins; thus, those results are included in this study to compare how models with different levels of coarse-graining compare. The sometimes naive expectation of the least coarse-grained model performing best does not hold true for the experimental pool of proteins used here. Instead, it showed the least good agreement, indicating that one should not necessarily trust the otherwise intuitive notion of a more advanced model inherently being better in model choice.
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Affiliation(s)
- Eric Fagerberg
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
- LINXS - Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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5
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Lin TY, Ma YW, Tsai MY. Early-Stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-Disrupting Capacity by Proline Residues. J Phys Chem B 2023; 127:1074-1088. [PMID: 36705662 PMCID: PMC9924260 DOI: 10.1021/acs.jpcb.2c05463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/09/2022] [Indexed: 01/28/2023]
Abstract
Proline cis/trans isomerization governs protein local conformational changes via its local mechanical rigidity. The amyloid-disrupting capacity of proline is widely acknowledged; however, the molecular mechanism is still not clear. To understand how proline residues in polypeptide chains influence amyloid propensity, we study several truncated sequences of the TDP-43 C-terminal region (287-322) and their triple proline variants (308PPP310). We use coarse-grained molecular simulation to study the time evolution of the process of aggregation in the early stages in an effective high-concentration condition (∼25 mM). This ensures the long time scales for protein association at laboratory concentrations. We use several experimentally determined structure templates as initial structures of monomer conformations. We carry out oligomer size analysis and cluster analysis, along with several structural measures, to characterize the size distributions of oligomers and their morphological/structural properties. We show that average oligomer size is not a good indicator of amyloid propensity. Structural order and/or morphological properties are better alternatives. We show that proline variants can efficiently maintain the formation of large "ordered" oligomers of shorter truncated sequences, i.e., 307-322. This "order" maintenance is weakened when using longer truncated sequences (i.e., 287-322), leading to the formation of "disordered" oligomers. From an energy trade-off perspective, if the entropic effect is weak (short sequence length), the shape-complementarity of proline variants effectively guides the oligomerization process to form "ordered" oligomer intermediates. This leads to a distinct aggregation pathway that promotes amyloid formation (on-pathway). Strong entropic effects (long sequence length), however, would cause the formation of "disordered" oligomers. This in turn will suppress amyloid formation (off-pathway). The proline shape-complementary effects provide a guided morphological restraint to facilitate the pathways of amyloid formation. Our study supports the importance of structure-based kinetic heterogeneity of prion-like sequence fragments in driving different aggregation pathways. This work sheds light on the role of morphological and structural order of early-stage oligomeric species in regulating amyloid-disrupting capacity by prolines.
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Affiliation(s)
- Tong-You Lin
- Department of Chemistry, Tamkang
University, New Taipei
City, Taiwan251301
| | - Yuan-Wei Ma
- Department of Chemistry, Tamkang
University, New Taipei
City, Taiwan251301
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6
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Tesei G, Lindorff-Larsen K. Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range. OPEN RESEARCH EUROPE 2023; 2:94. [PMID: 37645312 PMCID: PMC10450847 DOI: 10.12688/openreseurope.14967.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 08/31/2023]
Abstract
The formation and viscoelastic properties of condensates of intrinsically disordered proteins (IDPs) is dictated by amino acid sequence and solution conditions. Because of the involvement of biomolecular condensates in cell physiology and disease, advancing our understanding of the relationship between protein sequence and phase separation (PS) may have important implications in the formulation of new therapeutic hypotheses. Here, we present CALVADOS 2, a coarse-grained model of IDPs that accurately predicts conformational properties and propensities to undergo PS for diverse sequences and solution conditions. In particular, we systematically study the effect of varying the range of the nonionic interactions and use our findings to improve the temperature scale of the model. We further optimize the residue-specific model parameters against experimental data on the conformational properties of 55 proteins, while also leveraging 70 hydrophobicity scales from the literature to avoid overfitting the training data. Extensive testing shows that the model accurately predicts chain compaction and PS propensity for sequences of diverse length and charge patterning, as well as at different temperatures and salt concentrations.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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7
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Tesei G, Lindorff-Larsen K. Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range. OPEN RESEARCH EUROPE 2023; 2:94. [PMID: 37645312 PMCID: PMC10450847 DOI: 10.12688/openreseurope.14967.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 02/13/2024]
Abstract
The formation and viscoelastic properties of condensates of intrinsically disordered proteins (IDPs) is dictated by amino acid sequence and solution conditions. Because of the involvement of biomolecular condensates in cell physiology and disease, advancing our understanding of the relationship between protein sequence and phase separation (PS) may have important implications in the formulation of new therapeutic hypotheses. Here, we present CALVADOS 2, a coarse-grained model of IDPs that accurately predicts conformational properties and propensities to undergo PS for diverse sequences and solution conditions. In particular, we systematically study the effect of varying the range of the nonionic interactions and use our findings to improve the temperature scale of the model. We further optimize the residue-specific model parameters against experimental data on the conformational properties of 55 proteins, while also leveraging 70 hydrophobicity scales from the literature to avoid overfitting the training data. Extensive testing shows that the model accurately predicts chain compaction and PS propensity for sequences of diverse length and charge patterning, as well as at different temperatures and salt concentrations.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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8
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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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9
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Arora L, Mukhopadhyay S. Conformational Characteristics and Phase Behavior of Intrinsically Disordered Proteins─Where Physical Chemistry Meets Biology. J Phys Chem B 2022; 126:5137-5139. [PMID: 35860904 DOI: 10.1021/acs.jpcb.2c04017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India
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10
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Thomasen FE, Pesce F, Roesgaard MA, Tesei G, Lindorff-Larsen K. Improving Martini 3 for Disordered and Multidomain Proteins. J Chem Theory Comput 2022; 18:2033-2041. [PMID: 35377637 DOI: 10.1021/acs.jctc.1c01042] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of proteins. Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of intrinsically disordered proteins (IDPs) and multidomain proteins when compared with small-angle X-ray scattering (SAXS) data and that increasing the strength of protein-water interactions favors more expanded conformations. We find that increasing the strength of interactions between protein and water by ca. 10% results in improved agreement with the SAXS data for IDPs and multidomain proteins. We also show that this correction results in a more accurate description of self-association of IDPs and folded proteins and better agreement with paramagnetic relaxation enhancement data for most IDPs. While simulations with this revised force field still show deviations to experiments for some systems, our results suggest that it is overall a substantial improvement for coarse-grained simulations of soluble proteins.
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Affiliation(s)
- F Emil Thomasen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Francesco Pesce
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Mette Ahrensback Roesgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Giulio Tesei
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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11
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Tesei G, Schulze TK, Crehuet R, Lindorff-Larsen K. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. Proc Natl Acad Sci U S A 2021; 118:2111696118. [PMID: 34716273 DOI: 10.1101/2021.06.23.449550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 05/25/2023] Open
Abstract
Many intrinsically disordered proteins (IDPs) may undergo liquid-liquid phase separation (LLPS) and participate in the formation of membraneless organelles in the cell, thereby contributing to the regulation and compartmentalization of intracellular biochemical reactions. The phase behavior of IDPs is sequence dependent, and its investigation through molecular simulations requires protein models that combine computational efficiency with an accurate description of intramolecular and intermolecular interactions. We developed a general coarse-grained model of IDPs, with residue-level detail, based on an extensive set of experimental data on single-chain properties. Ensemble-averaged experimental observables are predicted from molecular simulations, and a data-driven parameter-learning procedure is used to identify the residue-specific model parameters that minimize the discrepancy between predictions and experiments. The model accurately reproduces the experimentally observed conformational propensities of a set of IDPs. Through two-body as well as large-scale molecular simulations, we show that the optimization of the intramolecular interactions results in improved predictions of protein self-association and LLPS.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Thea K Schulze
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ramon Crehuet
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), E-08034 Barcelona, Spain
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
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12
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Tesei G, Schulze TK, Crehuet R, Lindorff-Larsen K. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. Proc Natl Acad Sci U S A 2021; 118:e2111696118. [PMID: 34716273 PMCID: PMC8612223 DOI: 10.1073/pnas.2111696118] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) may undergo liquid-liquid phase separation (LLPS) and participate in the formation of membraneless organelles in the cell, thereby contributing to the regulation and compartmentalization of intracellular biochemical reactions. The phase behavior of IDPs is sequence dependent, and its investigation through molecular simulations requires protein models that combine computational efficiency with an accurate description of intramolecular and intermolecular interactions. We developed a general coarse-grained model of IDPs, with residue-level detail, based on an extensive set of experimental data on single-chain properties. Ensemble-averaged experimental observables are predicted from molecular simulations, and a data-driven parameter-learning procedure is used to identify the residue-specific model parameters that minimize the discrepancy between predictions and experiments. The model accurately reproduces the experimentally observed conformational propensities of a set of IDPs. Through two-body as well as large-scale molecular simulations, we show that the optimization of the intramolecular interactions results in improved predictions of protein self-association and LLPS.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Thea K Schulze
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ramon Crehuet
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), E-08034 Barcelona, Spain
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
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13
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Jephthah S, Pesce F, Lindorff-Larsen K, Skepö M. Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. J Chem Theory Comput 2021; 17:6634-6646. [PMID: 34524800 PMCID: PMC8515809 DOI: 10.1021/acs.jctc.1c00408] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Five peptides previously suggested to possess polyproline II (PPII) structure have here been investigated by using atomistic molecular dynamics simulations to compare how well four different force fields known for simulating intrinsically disordered proteins relatively well (Amber ff99SB-disp, Amber ff99SB-ILDN, CHARM36IDPSFF, and CHARMM36m) can capture this secondary structure element. The results revealed that all force fields sample PPII structures but to different extents and with different propensities toward other secondary structure elements, in particular, the β-sheet and "random coils". A cluster analysis of the simulations of histatin 5 also revealed that the conformational ensembles of the force fields are quite different. We compared the simulations to circular dichroism and nuclear magnetic resonance spectroscopy experiments and conclude that further experiments and methods for interpreting them are needed to assess the accuracy of force fields in determining PPII structure.
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Affiliation(s)
- Stéphanie Jephthah
- Division of Theoretical Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Francesco Pesce
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, SE-221 00 Lund, Sweden
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14
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Khandia R, Alqahtani T, Alqahtani AM. Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage. Biomedicines 2021; 9:biomedicines9081001. [PMID: 34440205 PMCID: PMC8391990 DOI: 10.3390/biomedicines9081001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/20/2022] Open
Abstract
Primary immunodeficiencies (PIDs) are disorders of the immune system that involve faulty cellular, humoral, or both cellular and humoral functions. PIDs are present at the crossroad between infections, immune dysregulation, and cancers. A panel encompassing 42 genes involved in both PIDs and cancer has been investigated for the genes’ compositional properties, codon usage patterns, various forces affecting codon choice, protein properties, and gene expression profiles. In the present study, the codon choice of genes was found to be dependent upon the richness of the nucleotide; the viz AT nucleotide rich genome preferred AT ending codons. The dinucleotide TpA adversely affected protein expression, while CpG did not. The CTG codon was the most overrepresented codon in 80.95% of genes. Analysis of various protein properties, including GRAVY, AROMA, isoelectric point, aliphatic index, hydrophobicity, instability index, and numbers of acidic, basic, and neutral amino acid residues revealed that the hydrophobicity index, instability index, and numbers of acidic and basic amino acid residues are the factors affecting gene expression. Based on neutrality analysis, parity analysis, ENc-GC3 analysis, and regression analysis of nucleotides present at the first and third positions of the codon, it was determined that selection pressure, mutation pressure, and compositional constraints all participated in shaping codon usage. The study will help determine the various evolutionary forces acting on genes common to both PIDs and cancer. Codon usage analysis might be helpful in the future to augment both diseases simultaneously. The research also indicates a peculiar pattern adapted by a set of genes involved in any disease.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, India
- Correspondence:
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia; (T.A.); (A.M.A.)
| | - Ali M. Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia; (T.A.); (A.M.A.)
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15
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Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. J Chem Theory Comput 2021; 17:2014-2021. [PMID: 33725442 DOI: 10.1021/acs.jctc.1c00014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Ensemble Optimization Method (EOM) is a popular approach to describe small-angle X-ray scattering (SAXS) data from highly disordered proteins. The EOM algorithm selects subensembles of coexisting states from large pools of randomized conformations to fit the SAXS data. Based on the unphysical bimodal radius of gyration (Rg) distribution of conformations resulting from the EOM analysis, a recent article (Fagerberg et al. J. Chem. Theory Comput. 2019, 15 (12), 6968-6983) concluded that this approach inadequately described the SAXS data measured for human Histatin 5 (Hst5), a peptide with antifungal properties. Using extensive experimental and synthetic data, we explored the origin of this observation. We found that the one-bead-per-residue coarse-grained representation with averaged scattering form factors (provided in the EOM as an add-on to represent disordered missing loops or domains) may not be appropriate for EOM analyses of scattering data from short (below 50 residues) proteins/peptides. The method of choice for these proteins is to employ atomistic models (e.g., from molecular dynamics simulations) to sample the protein conformational landscape. As a convenient alternative, we have also improved the coarse-grained approach by introducing amino acid specific form factors in the calculations. We also found that, for small proteins, the search for relatively large subensembles of 20-50 conformers (as implemented in the original EOM version) more adequately describes the conformational space sampled in solution than the procedures optimizing the ensemble size. Our observations have been added as recommendations into the information for EOM users to promote the proper utilization of the program for ensemble-based modeling of SAXS data for all types of disordered systems.
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Affiliation(s)
- Amin Sagar
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maxim V Petoukhov
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, 119333 Moscow, Russia
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
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16
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Lenton S, Hervø-Hansen S, Popov AM, Tully MD, Lund M, Skepö M. Impact of Arginine-Phosphate Interactions on the Reentrant Condensation of Disordered Proteins. Biomacromolecules 2021; 22:1532-1544. [PMID: 33730849 PMCID: PMC8045028 DOI: 10.1021/acs.biomac.0c01765] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Re-entrant condensation results in the formation of a condensed protein regime between two critical ion concentrations. The process is driven by neutralization and inversion of the protein charge by oppositely charged ions. Re-entrant condensation of cationic proteins by the polyvalent anions, pyrophosphate and tripolyphosphate, has previously been observed, but not for citrate, which has similar charge and size compared to the polyphosphates. Therefore, besides electrostatic interactions, other specific interactions between the polyphosphate ions and proteins must contribute. Here, we show that additional attractive interactions between arginine and tripolyphosphate determine the re-entrant condensation and decondensation boundaries of the cationic, intrinsically disordered saliva protein, histatin 5. Furthermore, we show by small-angle X-ray scattering (SAXS) that polyvalent anions cause compaction of histatin 5, as would be expected based solely on electrostatic interactions. Hence, we conclude that arginine-phosphate-specific interactions not only regulate solution properties but also influence the conformational ensemble of histatin 5, which is shown to vary with the number of arginine residues. Together, the results presented here provide further insight into an organizational mechanism that can be used to tune protein interactions in solution of both naturally occurring and synthetic proteins.
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Affiliation(s)
- Samuel Lenton
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Stefan Hervø-Hansen
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Anton M Popov
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mark D Tully
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mikael Lund
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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