1
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Nelmark CE, Serrano AL. A Simple Doublet Lens Design for Mid-Infrared Imaging. APPLIED SPECTROSCOPY 2024:37028241250030. [PMID: 38693755 DOI: 10.1177/00037028241250030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Wide-field mid-infrared (MIR) hyperspectral imaging offers a promising approach for studying heterogeneous chemical systems due to its ability to independently characterize the molecular properties of different regions of a sample. However, applications of wide-field MIR microscopy are limited to spatial resolutions no better than ∼1 μm. While methods exist to overcome the classical diffraction limit of ∼λ/2, chromatic aberration from transmissive imaging reduces the achievable resolution. Here we describe the design and implementation of a simple MIR achromatic lens combination that we believe will aid in the development of resolution-enhanced wide-field MIR hyperspectral optical and chemical absorption imaging. We also examine the use of this doublet lens to image through polystyrene microspheres, an emerging and simple means for enhancing spatial resolution.
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Affiliation(s)
- Claire E Nelmark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Arnaldo L Serrano
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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2
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Li S, Zhang Y, Chen J. Backbone interactions and secondary structures in phase separation of disordered proteins. Biochem Soc Trans 2024; 52:319-329. [PMID: 38348795 DOI: 10.1042/bst20230618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/29/2024]
Abstract
Intrinsically disordered proteins (IDPs) are one of the major drivers behind the formation and characteristics of biomolecular condensates. Due to their inherent flexibility, the backbones of IDPs are significantly exposed, rendering them highly influential and susceptible to biomolecular phase separation. In densely packed condensates, exposed backbones have a heightened capacity to interact with neighboring protein chains, which might lead to strong coupling between the secondary structures and phase separation and further modulate the subsequent transitions of the condensates, such as aging and fibrillization. In this mini-review, we provide an overview of backbone-mediated interactions and secondary structures within biomolecular condensates to underscore the importance of protein backbones in phase separation. We further focus on recent advances in experimental techniques and molecular dynamics simulation methods for probing and exploring the roles of backbone interactions and secondary structures in biomolecular phase separation involving IDPs.
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Affiliation(s)
- Shanlong Li
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
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3
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Zhang Y, Li S, Gong X, Chen J. Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation. J Am Chem Soc 2024; 146:342-357. [PMID: 38112495 PMCID: PMC10842759 DOI: 10.1021/jacs.3c09195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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4
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Lorenz-Ochoa KA, Baiz CR. Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates. J Am Chem Soc 2023; 145:27800-27809. [PMID: 38061016 DOI: 10.1021/jacs.3c10862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.
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Affiliation(s)
- Keegan A Lorenz-Ochoa
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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5
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Krevert C, Chavez D, Chatterjee S, Stelzl LS, Pütz S, Roeters SJ, Rudzinski JF, Fawzi NL, Girard M, Parekh SH, Hunger J. Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics. J Phys Chem Lett 2023; 14:11224-11234. [PMID: 38056002 PMCID: PMC10726384 DOI: 10.1021/acs.jpclett.3c02790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.
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Affiliation(s)
- Carola
S. Krevert
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Chavez
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sayantan Chatterjee
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Lukas S. Stelzl
- KOMET 1,
Institute of Physics, Johannes Gutenberg
University, Staudingerweg 7, 55099 Mainz, Germany
- Faculty of
Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), Ackermannweg 2, 55128 Mainz, Germany
| | - Sabine Pütz
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Steven J. Roeters
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department
of Anatomy and Neurosciences, Amsterdam
UMC, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Joseph F. Rudzinski
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- IRIS
Adlershof, Humboldt-Universität zu
Berlin, Zum Großen
Windkanal 2, 12489 Berlin, Germany
| | - Nicolas L. Fawzi
- Department
of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
| | - Martin Girard
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Johannes Hunger
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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6
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Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554378. [PMID: 37662293 PMCID: PMC10473686 DOI: 10.1101/2023.08.22.554378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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7
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Sinha NJ, Cunha KC, Murphy R, Hawker CJ, Shea JE, Helgeson ME. Competition between β-Sheet and Coacervate Domains Yields Diverse Morphologies in Mixtures of Oppositely Charged Homochiral Polypeptides. Biomacromolecules 2023; 24:3580-3588. [PMID: 37486022 DOI: 10.1021/acs.biomac.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Biomolecular assembly processes involving competition between specific intermolecular interactions and thermodynamic phase instability have been implicated in a number of pathological states and technological applications of biomaterials. As a model for such processes, aqueous mixtures of oppositely charged homochiral polypeptides such as poly-l-lysine and poly-l-glutamic acid have been reported to form either β-sheet-rich solid-like precipitates or liquid-like coacervate droplets depending on competing hydrogen bonding interactions. Herein, we report studies of polypeptide mixtures that reveal unexpectedly diverse morphologies ranging from partially coalescing and aggregated droplets to bulk precipitates, as well as a previously unreported re-entrant liquid-liquid phase separation at high polypeptide concentration and ionic strength. Combining our experimental results with all-atom molecular dynamics simulations of folded polypeptide complexes reveals a concentration dependence of β-sheet-rich secondary structure, whose relative composition correlates with the observed macroscale morphologies of the mixtures. These results elucidate a crucial balance of interactions that are important for controlling morphology during coacervation in these and potentially similar biologically relevant systems.
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Affiliation(s)
- Nairiti J Sinha
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Materials Department and Materials Research Laboratory, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Keila Cristina Cunha
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Robert Murphy
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Craig J Hawker
- Materials Department and Materials Research Laboratory, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Matthew E Helgeson
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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8
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Choi S, Chun SY, Kwak K, Cho M. Micro-Raman spectroscopic analysis of liquid-liquid phase separation. Phys Chem Chem Phys 2023; 25:9051-9060. [PMID: 36843414 DOI: 10.1039/d2cp05115j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Liquid-liquid phase separation (LLPS) plays a significant role in various biological processes, including the formation of membraneless organelles and pathological protein aggregation. Although many studies have found various factors that modulate the LLPS process or the liquid-to-solid phase transition (LSPT) using microscopy or fluorescence-based methods, the molecular mechanistic details underlying LLPS and protein aggregation within liquid droplets remain uncharacterized. Therefore, structural information on proteins inside liquid droplets is required to understand the mechanistic link to amyloid formation. In the present study, we monitored droplet formation related to protein fibrillation using micro-Raman spectroscopy in combination with differential interference contrast (DIC) microscopy to study the conformational change in proteins and the hydrogen-bonding (H-bonding) structure of water during LLPS. Interestingly, we found that the O-D stretching band for water (HOD in H2O) inside the droplets exhibited a distinct Raman spectrum from that of the bulk water, suggesting that the time-dependent change in the hydration environment in the protein droplets during the process of LLPS can be studied. These results demonstrate that the superior spatial resolution of micro-Raman spectroscopy offers significant advantages in investigating the molecular mechanisms of LLPS and following LSPT processes.
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Affiliation(s)
- Suin Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - So Yeon Chun
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
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9
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Abstract
Phenol soluble modulins (PSMs) are an important class of peptides secreted by Staphylococcus aureus bacteria. The toxicity to human cells and unique ability of one such peptide, PSMα3, to aggregate into an α-helical amyloid-like structure may hold a key to a better understanding of the virulence of dangerous pathogens such as methicillin resistant S. aureus. In reporting a detailed two-dimensional infrared (2DIR) analysis of PSMα3, we found direct evidence of multiple aggregate architectures existing in equilibrium with one another. We also discovered a unique and characteristic 2DIR spectroscopic signature that unambiguously reports on the presence of the unusual and highly cytotoxic cross-α amyloid structure. The formation of ordered cross-β amyloid protein aggregates is associated with a variety of human disorders. While conventional infrared methods serve as sensitive reporters of the presence of these amyloids, the recently discovered amyloid secondary structure of cross-α fibrils presents new questions and challenges. Herein, we report results using Fourier transform infrared spectroscopy and two-dimensional infrared spectroscopy to monitor the aggregation of one such cross-α–forming peptide, phenol soluble modulin alpha 3 (PSMα3). Phenol soluble modulins (PSMs) are involved in the formation and stabilization of Staphylococcus aureus biofilms, making sensitive methods of detecting and characterizing these fibrils a pressing need. Our experimental data coupled with spectroscopic simulations reveals the simultaneous presence of cross-α and cross-β polymorphs within samples of PSMα3 fibrils. We also report a new spectroscopic feature indicative of cross-α fibrils.
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10
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Hydrogen Bond Arrangement Is Shown to Differ in Coexisting Phases of Aqueous Two-Phase Systems. Biomolecules 2021; 11:biom11121787. [PMID: 34944431 PMCID: PMC8698934 DOI: 10.3390/biom11121787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 12/25/2022] Open
Abstract
Analysis by attenuated total reflection–Fourier transform infrared spectroscopy shows that each coexisting phase in aqueous two-phase systems has a different arrangement of hydrogen bonds. Specific arrangements vary for systems formed by different solutes. The hydrogen bond arrangement is shown to correlate with differences in hydrophobic and electrostatic properties of the different phases of five specific systems, four formed by two polymers and one by a single polymer and salt. The results presented here suggest that the arrangement of hydrogen bonds may be an important factor in phase separation.
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11
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Chen C, Yamanaka Y, Ueda K, Li P, Miyagi T, Harada Y, Tezuka S, Narumi S, Sugimoto M, Kuroda M, Hayamizu Y, Kanekura K. Phase separation and toxicity of C9orf72 poly(PR) depends on alternate distribution of arginine. J Cell Biol 2021; 220:212626. [PMID: 34499080 PMCID: PMC8438627 DOI: 10.1083/jcb.202103160] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022] Open
Abstract
Arg (R)-rich dipeptide repeat proteins (DPRs; poly(PR): Pro-Arg and poly(GR): Gly-Arg), encoded by a hexanucleotide expansion in the C9ORF72 gene, induce neurodegeneration in amyotrophic lateral sclerosis (ALS). Although R-rich DPRs undergo liquid-liquid phase separation (LLPS), which affects multiple biological processes, mechanisms underlying LLPS of DPRs remain elusive. Here, using in silico, in vitro, and in cellulo methods, we determined that the distribution of charged Arg residues regulates the complex coacervation with anionic peptides and nucleic acids. Proteomic analyses revealed that alternate Arg distribution in poly(PR) facilitates entrapment of proteins with acidic motifs via LLPS. Transcription, translation, and diffusion of nucleolar nucleophosmin (NPM1) were impaired by poly(PR) with an alternate charge distribution but not by poly(PR) variants with a consecutive charge distribution. We propose that the pathogenicity of R-rich DPRs is mediated by disturbance of proteins through entrapment in the phase-separated droplets via sequence-controlled multivalent protein-protein interactions.
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Affiliation(s)
- Chen Chen
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yoshiaki Yamanaka
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Peiying Li
- Center for Biosystems Dynamics Research, RIKEN, Kanagawa, Japan
| | - Tamami Miyagi
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Yuichiro Harada
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Sayaka Tezuka
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, Tokyo, Japan
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kohsuke Kanekura
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
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12
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Fawzi NL, Parekh SH, Mittal J. Biophysical studies of phase separation integrating experimental and computational methods. Curr Opin Struct Biol 2021; 70:78-86. [PMID: 34144468 PMCID: PMC8530909 DOI: 10.1016/j.sbi.2021.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/10/2021] [Indexed: 11/18/2022]
Abstract
Biomolecular phase separation that contributes to the formation of membraneless organelles and biomolecular condensates has recently gained tremendous attention because of the importance of these assemblies in physiology, disease, and engineering applications. Understanding and directing biomolecular phase separation requires a multiscale view of the biophysical properties of these phases. Yet, many classic tools to characterize biomolecular properties do not apply in these condensed phases. Here, we discuss insights obtained from spectroscopic methods, in particular nuclear magnetic resonance and optical spectroscopy, in understanding the molecular and atomic interactions that underlie the formation of protein-rich condensates. We also review approaches closely coupling nuclear magnetic resonance data with computational methods especially coarse-grained and all-atom molecular simulations, which provide insight into molecular features of phase separation. Finally, we point to future methodolical developments, particularly visualizing biophysical properties of condensates in cells.
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Affiliation(s)
- Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, United States.
| | - Sapun H Parekh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Drive, Bethlehem, PA, 18015, United States
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13
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Powers ET, Gierasch LM. The Proteome Folding Problem and Cellular Proteostasis. J Mol Biol 2021; 433:167197. [PMID: 34391802 DOI: 10.1016/j.jmb.2021.167197] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022]
Abstract
Stunning advances have been achieved in addressing the protein folding problem, providing deeper understanding of the mechanisms by which proteins navigate energy landscapes to reach their native states and enabling powerful algorithms to connect sequence to structure. However, the realities of the in vivo protein folding problem remain a challenge to reckon with. Here, we discuss the concept of the "proteome folding problem"-the problem of how organisms build and maintain a functional proteome-by admitting that folding energy landscapes are characterized by many misfolded states and that cells must deploy a network of chaperones and degradation enzymes to minimize deleterious impacts of these off-pathway species. The resulting proteostasis network is an inextricable part of in vivo protein folding and must be understood in detail if we are to solve the proteome folding problem. We discuss how the development of computational models for the proteostasis network's actions and the relationship to the biophysical properties of the proteome has begun to offer new insights and capabilities.
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Affiliation(s)
- Evan T Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Lila M Gierasch
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003, USA.
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14
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Choi S, Park J, Kwak K, Cho M. Substituent Effects on the Vibrational Properties of the CN Stretch Mode of Aromatic Nitriles: IR Probes Useful for Time-resolved IR Spectroscopy. Chem Asian J 2021; 16:2626-2632. [PMID: 34288497 DOI: 10.1002/asia.202100657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/19/2021] [Indexed: 11/10/2022]
Abstract
Developing ideal IR probes is essential to understand the structure and dynamics of biomolecules with time-resolved IR spectroscopies and imaging techniques. Especially, nitrile (CN) group has recently been proposed to serve as IR probes of the local environment of proteins. Herein, we investigated the effect of a substituent on the vibrational properties of the benzonitrile. The electron-donating and withdrawing character of p-substituent on benzonitrile are expected to modulate the vibrational frequency, molar extinction coefficient, and vibrational lifetime of CN probe. FT-IR revealed the positive correlation between electron-donating character and the molar extinction coefficient of CN stretch mode. Infrared pump-probe (IR-PP) measurements showed that the vibrational lifetime of CN stretch mode exhibits a relatively weak correlation with the electron-donating strength. Among the investigated samples, 4-dimethylamino benzonitrile with the strongest electron-donating strength shows enhanced absorption and extended vibrational lifetime. Utilizing substituent effects will be a practical strategy to improve the performance of the IR probe.
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Affiliation(s)
- Suin Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Junyoung Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
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