1
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Shang J, Li H, Liu X, Sun S, Huan S, Xiong B. Single-particle rotational sensing for analyzing the neutralization activity of antiviral antibodies. Talanta 2024; 279:126606. [PMID: 39089080 DOI: 10.1016/j.talanta.2024.126606] [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: 03/30/2024] [Revised: 07/13/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024]
Abstract
Due to the pathogen-specific targeting, neutralization capabilities, and enduring efficacy, neutralizing antibodies (NAs) have received widespread attentions as a critical immunotherapeutic strategy against infectious viruses. However, because of the high variability and complexity of pathogens, rapid determination of neutralization activity of antiviral antibodies remains a challenge. Here, we report a new method, named as out-of-plane polarization imaging based single-particle rotational sensing, for rapid analysis of neutralization activity of antiviral antibody against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using the spike protein functionalized gold nanorods (AuNRs) and angiotensin-converting enzyme 2 (ACE2) coated gold nanoparticles (AuNPs) as the rotational sensors and chaperone probes, we demonstrated the single-particle rotational sensing strategy for the measurement of rotational diffusion coefficient of the chaperone-bound rotational sensors caused by the specific spike protein-ACE2 interactions. This enables us to measure the neutralizing activity of neutralizing antibody from the analysis of dose-dependent changes in rotational diffusion coefficient (Dr) of the rotational sensors upon the treatment of SARS-CoV-2 antibody. With this technique, we achieved the quantitative determination of neutralization activity of a commercially available SARS-CoV-2 antibody (IC50, 294.1 ng/mL) with satisfying accuracy and anti-interference ability. This simple and robust method holds the potential for rapid and accurate evaluation of neutralization activity against different pathogenic viruses.
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Affiliation(s)
- Jinhui Shang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Huiwen Li
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xixuan Liu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Shijie Sun
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Shuangyan Huan
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Bin Xiong
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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2
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Joshi K, Bhuyan AK. Glycerol-slaved 1H- 1H NMR cross-relaxation in quasi-native lysozyme. Biophys Chem 2024; 312:107286. [PMID: 38964115 DOI: 10.1016/j.bpc.2024.107286] [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: 05/11/2024] [Revised: 06/14/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
1H-1H nuclear cross-relaxation experiments have been carried out with lysozyme in variable glycerol viscosity to study intramolecular motion, self-diffusion, and isotropic rigid-body rotational tumbling at 298 K, pH 3.8. Dynamics of intramolecular 1H-1H cross-relaxation rates, the increase in internuclear spatial distances, and lateral and rotational diffusion coefficients all show fractional viscosity dependence with a power law exponent κ in the 0.17-0.83 range. The diffusion coefficient of glycerol Ds with the bulk viscosity itself is non-Stokesian, having a fractional viscosity dependence on the medium viscosity (Ds ∼ η-κ, κ ≈ 0.71). The concurrence and close similarity of the fractional viscosity dependence of glycerol diffusion on the one hand, and diffusion and intramolecular cross-relaxation rates of the protein on the other lead to infer that relaxation of glycerol slaves protein relaxations. Glycerol-transformed native lysozyme to a quasi-native state does not affect the conclusion that both global and internal fluctuations are slaved to glycerol relaxation.
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Affiliation(s)
- Kirthi Joshi
- School of Chemistry, University of Hyderabad, Hyderabad 50046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 50046, India.
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3
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Shang J, Ma Y, Liu X, Sun S, Pang X, Zhou R, Huan S, He Y, Xiong B, Zhang XB. Single-particle rotational microrheology enables pathological staging of macrophage foaming and antiatherosclerotic studies. Proc Natl Acad Sci U S A 2024; 121:e2403740121. [PMID: 39102540 PMCID: PMC11331104 DOI: 10.1073/pnas.2403740121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
The formation of macrophage-derived foam cells has been recognized as the pathological hallmark of atherosclerotic diseases. However, the pathological evolution dynamics and underlying regulatory mechanisms remain largely unknown. Herein, we introduce a single-particle rotational microrheology method for pathological staging of macrophage foaming and antiatherosclerotic explorations by probing the dynamic changes of lysosomal viscous feature over the pathological evolution progression. The principle of this method involves continuous monitoring of out-of-plane rotation-caused scattering brightness fluctuations of the gold nanorod (AuNR) probe-based microrheometer and subsequent determination of rotational relaxation time to analyze the viscous feature in macrophage lysosomes. With this method, we demonstrated the lysosomal viscous feature as a robust pathological reporter and uncovered three distinct pathological stages underlying the evolution dynamics, which are highly correlated with a pathological stage-dependent activation of the NLRP3 inflammasome-involved positive feedback loop. We also validated the potential of this positive feedback loop as a promising therapeutic target and revealed the time window-dependent efficacy of NLRP3 inflammasome-targeted drugs against atherosclerotic diseases. To our knowledge, the pathological staging of macrophage foaming and the pathological stage-dependent activation of the NLRP3 inflammasome-involved positive feedback mechanism have not yet been reported. These findings provide insights into in-depth understanding of evolutionary features and regulatory mechanisms of macrophage foaming, which can benefit the analysis of effective therapeutical drugs as well as the time window of drug treatment against atherosclerotic diseases in preclinical studies.
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Affiliation(s)
- Jinhui Shang
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Yuan Ma
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Xixuan Liu
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Shijie Sun
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Xiayun Pang
- State Key Laboratory of Research and Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi University of Chinese Medicine, Xianyang712083, China
| | - Rui Zhou
- State Key Laboratory of Research and Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi University of Chinese Medicine, Xianyang712083, China
| | - Shuangyan Huan
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Yan He
- Department of Chemistry, Tsinghua University, Beijing100084, China
| | - Bin Xiong
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Xiao-Bing Zhang
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
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4
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Nüesch MF, Pietrek L, Holmstrom ED, Nettels D, von Roten V, Kronenberg-Tenga R, Medalia O, Hummer G, Schuler B. Nanosecond chain dynamics of single-stranded nucleic acids. Nat Commun 2024; 15:6010. [PMID: 39019880 PMCID: PMC11255343 DOI: 10.1038/s41467-024-50092-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and nanophotonic enhancement to determine the conformational ensembles and rapid chain dynamics of short single-stranded nucleic acids in solution. To interpret the experimental results in terms of end-to-end distance dynamics, we utilize the hierarchical chain growth approach, simple polymer models, and refinement with Bayesian inference to generate structural ensembles that closely align with the experimental data. The resulting chain reconfiguration times are exceedingly rapid, in the 10-ns range. Solvent viscosity-dependent measurements indicate that these dynamics of single-stranded nucleic acids exhibit negligible internal friction and are thus dominated by solvent friction. Our results provide a detailed view of the conformational distributions and rapid dynamics of single-stranded nucleic acids.
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Affiliation(s)
- Mark F Nüesch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lisa Pietrek
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Erik D Holmstrom
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA.
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Valentin von Roten
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Rafael Kronenberg-Tenga
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany.
- Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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5
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Gomes I, Martins GF, Galamba N. Essential dynamics of ubiquitin in water and in a natural deep eutectic solvent. Phys Chem Chem Phys 2024; 26:18244-18255. [PMID: 38904333 DOI: 10.1039/d4cp01773k] [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: 06/22/2024]
Abstract
Natural deep eutectic solvents (NADESs) comprised of osmolytes are of interest as potential biomolecular (cryo)protectants. However, the way these solvents influence the structure and dynamics of biomolecules as well as the role of water remains poorly understood. We carried out principal component analysis of various secondary structure elements of ubiquitin in water and a betaine : glycerol : water (1 : 2 : ζ; ζ = 0, 1, 2, 5, 10, 20, 45) NADES, from molecular dynamics trajectories, to gain insight into the protein dynamics as it undergoes a transition from a highly viscous anhydrous to an aqueous environment. A crossover of the protein's essential dynamics at ζ ∼ 5, induced by solvent-shell coupled fluctuations, is observed, indicating that ubiquitin might (re)fold in the NADES upon water addition at ζ > ∼5. Further, in contrast to water, the anhydrous NADES preserves ubiquitin's essential modes at high temperatures explaining the protein's seemingly enhanced thermal stability.
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Affiliation(s)
- Inês Gomes
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal.
| | - Gabriel F Martins
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal.
| | - Nuno Galamba
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal.
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6
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Dalton BA, Kiefer H, Netz RR. The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media. Nat Commun 2024; 15:3761. [PMID: 38704367 PMCID: PMC11069540 DOI: 10.1038/s41467-024-48016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
Molecular isomerization kinetics in liquid solvent depends on a complex interplay between the solvent friction acting on the molecule, internal dissipation effects (also known as internal friction), the viscosity of the solvent, and the dihedral free energy profile. Due to the absence of accurate techniques to directly evaluate isomerization friction, it has not been possible to explore these relationships in full. By combining extensive molecular dynamics simulations with friction memory-kernel extraction techniques we consider a variety of small, isomerising molecules under a range of different viscogenic conditions and directly evaluate the viscosity dependence of the friction acting on a rotating dihedral. We reveal that the influence of different viscogenic media on isomerization kinetics can be dramatically different, even when measured at the same viscosity. This is due to the dynamic solute-solvent coupling, mediated by time-dependent friction memory kernels. We also show that deviations from the linear dependence of isomerization rates on solvent viscosity, which are often simply attributed to internal friction effects, are due to the simultaneous violation of two fundamental relationships: the Stokes-Einstein relation and the overdamped Kramers prediction for the barrier-crossing rate, both of which require explicit knowledge of friction.
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Affiliation(s)
| | - Henrik Kiefer
- Freie Universität Berlin, Fachbereich Physik, Berlin, Germany
| | - Roland R Netz
- Freie Universität Berlin, Fachbereich Physik, Berlin, Germany.
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7
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Zamanos A, Ioannakis G, Emiris IZ. HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures. J Chem Inf Model 2024; 64:2594-2611. [PMID: 38552195 PMCID: PMC11005053 DOI: 10.1021/acs.jcim.3c01559] [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: 09/28/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 04/09/2024]
Abstract
Water molecules are integral to the structural stability of proteins and vital for facilitating molecular interactions. However, accurately predicting their precise position around protein structures remains a significant challenge, making it a vibrant research area. In this paper, we introduce HydraProt (deep Hydration of Proteins), a novel methodology for predicting precise positions of water molecule oxygen atoms around protein structures, leveraging two interconnected deep learning architectures: a 3D U-net and a Multi-Layer Perceptron (MLP). Our approach starts by introducing a coarse voxel-based representation of the protein, which allows for rapid sampling of candidate water positions via the 3D U-net. These water positions are then assessed by embedding the water-protein relationship in the Euclidean space by means of an MLP. Finally, a postprocessing step is applied to further refine the MLP predictions. HydraProt surpasses existing state-of-the-art approaches in terms of precision and recall and has been validated on large data sets of protein structures. Notably, our method offers rapid inference runtime and should constitute the method of choice for protein structure studies and drug discovery applications. Our pretrained models, data, and the source code required to reproduce these results are accessible at https://github.com/azamanos/HydraProt.
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Affiliation(s)
- Andreas Zamanos
- Archimedes, Athena Research Center, Marousi 15125, Greece
- Department
of Informatics and Telecommunications, National
and Kapodistrian University of Athens, Athens 16122, Greece
| | - George Ioannakis
- Institute
for Language and Speech Processing, Athena
Research Center, Xanthi 67100, Greece
| | - Ioannis Z. Emiris
- Department
of Informatics and Telecommunications, National
and Kapodistrian University of Athens, Athens 16122, Greece
- Athena
Research Center, Marousi 15125, Greece
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8
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Min D. Folding speeds of helical membrane proteins. Biochem Soc Trans 2024; 52:491-501. [PMID: 38385525 PMCID: PMC10903471 DOI: 10.1042/bst20231315] [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: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
Membrane proteins play key roles in human health, contributing to cellular signaling, ATP synthesis, immunity, and metabolite transport. Protein folding is the pivotal early step for their proper functioning. Understanding how this class of proteins adopts their native folds could potentially aid in drug design and therapeutic interventions for misfolding diseases. It is an essential piece in the whole puzzle to untangle their kinetic complexities, such as how rapid membrane proteins fold, how their folding speeds are influenced by changing conditions, and what mechanisms are at play. This review explores the folding speed aspect of multipass α-helical membrane proteins, encompassing plausible folding scenarios based on the timing and stability of helix packing interactions, methods for characterizing the folding time scales, relevant folding steps and caveats for interpretation, and potential implications. The review also highlights the recent estimation of the so-called folding speed limit of helical membrane proteins and discusses its consequent impact on the current picture of folding energy landscapes.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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9
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Li MG, Hu M, Fan LM, Bao JD, Li PC. Quantifying the energy landscape in weakly and strongly disordered frictional media. J Chem Phys 2024; 160:024903. [PMID: 38189619 DOI: 10.1063/5.0178092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
We investigate the "roughness" of the energy landscape of a system that diffuses in a heterogeneous medium with a random position-dependent friction coefficient α(x). This random friction acting on the system stems from spatial inhomogeneity in the surrounding medium and is modeled using the generalized Caldira-Leggett model. For a weakly disordered medium exhibiting a Gaussian random diffusivity D(x) = kBT/α(x) characterized by its average value ⟨D(x)⟩ and a pair-correlation function ⟨D(x1)D(x2)⟩, we find that the renormalized intrinsic diffusion coefficient is lower than the average one due to the fluctuations in diffusivity. The induced weak internal friction leads to increased roughness in the energy landscape. When applying this idea to diffusive motion in liquid water, the dissociation energy for a hydrogen bond gradually approaches experimental findings as fluctuation parameters increase. Conversely, for a strongly disordered medium (i.e., ultrafast-folding proteins), the energy landscape ranges from a few to a few kcal/mol, depending on the strength of the disorder. By fitting protein folding dynamics to the escape process from a metastable potential, the decreased escape rate conceptualizes the role of strong internal friction. Studying the energy landscape in complex systems is helpful because it has implications for the dynamics of biological, soft, and active matter systems.
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Affiliation(s)
- Ming-Gen Li
- Department of Physics, Shantou University, Shantou, Guangdong 515063, China
| | - Meng Hu
- Department of Mathematics and Physics, North China Electric Power University, Baoding 071003, China
| | - Li-Ming Fan
- College of Physical Science and Technology, Shenyang Normal University, Shenyang 110034, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing 100048, China
| | - Peng-Cheng Li
- Department of Physics, Shantou University, Shantou, Guangdong 515063, China
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10
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Vancraenenbroeck R, Hofmann H. Electrostatics and hydrophobicity in the dynamics of intrinsically disordered proteins. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:133. [PMID: 38127117 PMCID: PMC10739388 DOI: 10.1140/epje/s10189-023-00383-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
Internal friction is a major contribution to the dynamics of intrinsically disordered proteins (IDPs). Yet, the molecular origin of internal friction has so far been elusive. Here, we investigate whether attractive electrostatic interactions in IDPs modulate internal friction differently than the hydrophobic effect. To this end, we used nanosecond fluorescence correlation spectroscopy (nsFCS) and single-molecule Förster resonance energy transfer (FRET) to quantify the conformation and dynamics of the disordered DNA-binding domains Myc, Max and Mad at different salt concentrations. We find that internal friction effects are stronger when the chain is compacted by electrostatic attractions compared to the hydrophobic effect. Although the effect is moderate, the results show that the heteropolymeric nature of IDPs is reflected in their dynamics.
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Affiliation(s)
- Renee Vancraenenbroeck
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel
- Present Address: Department of Structural and Molecular Biology, University College London, Darwin Building, 107 Gower Street, London, WC1E 6BT, UK
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel.
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11
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Gomes I, Galamba N. Protein stability in a natural deep eutectic solvent: Preferential hydration or solvent slaving? J Chem Phys 2023; 159:235101. [PMID: 38099555 DOI: 10.1063/5.0177095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Deep eutectic solvents (DESs) emerged as potential alternative solvent media in multiple areas, including biomolecular (cryo)preservation. Herein, we studied the stability of a small protein (ubiquitin) in water and a betaine-glycerol-water (B:G:W) (1:2:ζ; ζ = 0, 1, 2, 5, 10) DES, through molecular dynamics. An AMBER-based model that accurately describes the density and shear viscosity of the DES is proposed. We find that water molecules are largely trapped in the solvent, precluding the formation of a full hydration layer, seemingly opposite to osmolytes' preferential exclusion/preferential hydration mechanism. Although the protein is stable in the DES, structural fluctuations are largely suppressed and only recovered upon sufficient hydration. This is explained by a solvent-slaving mechanism where β-fluctuations are key, with the non-monotonic hydration of some amino acids with the water content providing an explanation to the non-monotonic folding of some proteins in aqueous DESs. A major thermal stability enhancement in the DES is also observed, caused by a similar slowdown of the backbone torsional dynamics. Our results support a kinetic stabilization of the protein in the DES, whereas a possible thermodynamic stabilization does not follow a preferential hydration or water entrapment mechanism.
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Affiliation(s)
- Inês Gomes
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Nuno Galamba
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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12
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Lupi L, Gallo P. Glassy dynamics of water in TIP4P/Ice aqueous solutions of trehalose in comparison with the bulk phase. J Chem Phys 2023; 159:154504. [PMID: 37850697 DOI: 10.1063/5.0168933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
We perform molecular dynamics simulations of TIP4P/Ice water in solution with trehalose for 3.65 and 18.57 wt. % concentrations and of bulk TIP4P/Ice water at ambient pressure, to characterize the structure and dynamics of water in a sugar aqueous solution in the supercooled region. We find here that TIP4P/Ice water in solution with trehalose molecules follows the Mode Coupling Theory and undergoes a fragile to strong transition up to the highest concentration investigated, similar to the bulk. Moreover, we perform a Mode Coupling Theory test, showing that the Time Temperature Superposition principle holds for both bulk TIP4P/Ice water and for TIP4P/Ice water in the solutions and we calculate the exponents of the theory. The direct comparison of the dynamical results for bulk water and water in the solutions shows upon cooling along the isobar a fastening of water dynamics for lower temperatures, T < 240 K. We found that the counter-intuitive behavior for the low temperature solutions can be explained with the diffusion anomaly of water leading us to the conclusion that the fastening observed below T = 240 K in water dynamics is only fictitious, due to the fact that the density of water molecules in the solutions is higher than the density of the bulk at the same temperature and pressure. This result should be taken into account in experimental investigations which are often carried out at constant pressure.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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13
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Guevara L, Gouge M, Ohler A, Hill SG, Patel S, Offenbacher AR. Effect of solvent viscosity on the activation barrier of hydrogen tunneling in the lipoxygenase reaction. Arch Biochem Biophys 2023; 747:109740. [PMID: 37678425 DOI: 10.1016/j.abb.2023.109740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Hydrogen tunneling in enzyme reactions has played an important role in linking protein thermal motions to the chemical steps of catalysis. Lipoxygenases (LOXs) have served as model systems for such reactions, showcasing deep hydrogen tunneling mechanisms associated with enzymatic C-H bond cleavage from polyunsaturated fatty acids. Here, we examined the effect of solvent viscosity on the protein thermal motions associated with LOX catalysis using trehalose and glucose as viscogens. Kinetic analysis of the reaction of the paradigm plant orthologue, soybean lipoxygenase (SLO), with linoleic acid revealed no effect on the first-order rate constants, kcat, or activation energy, Ea. Further studies of SLO active site mutants displaying varying Eas, which have been used to probe catalytically relevant motions, likewise provided no evidence for viscogen-dependent motions. Kinetic analyses were extended to a representative fungal LOX from M. oryzae, MoLOX, and a human LOX, 15-LOX-2. While MoLOX behaved similarly to SLO, we show that viscogens inhibit 15-LOX-2 activity. The latter implicates viscogen sensitive, conformational motions in animal LOX reactions. The data provide insight into the role of water hydration layers in facilitating hydrogen (quantum) tunneling in LOX.
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Affiliation(s)
- Luis Guevara
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Melissa Gouge
- Department of Chemistry and Biochemistry, Ohio Northern University, Ada, OH, 45810, USA
| | - Amanda Ohler
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - S Gage Hill
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Soham Patel
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA.
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14
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Khandave NP, Sekhar A, Vallurupalli P. Studying micro to millisecond protein dynamics using simple amide 15N CEST experiments supplemented with major-state R 2 and visible peak-position constraints. JOURNAL OF BIOMOLECULAR NMR 2023; 77:165-181. [PMID: 37300639 PMCID: PMC7615914 DOI: 10.1007/s10858-023-00419-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/10/2023] [Indexed: 06/12/2023]
Abstract
Over the last decade amide 15N CEST experiments have emerged as a popular tool to study protein dynamics that involves exchange between a 'visible' major state and sparsely populated 'invisible' minor states. Although initially introduced to study exchange between states that are in slow exchange with each other (typical exchange rates of, 10 to 400 s-1), they are now used to study interconversion between states on the intermediate to fast exchange timescale while still using low to moderate (5 to 350 Hz) 'saturating' B1 fields. The 15N CEST experiment is very sensitive to exchange as the exchange delay TEX can be quite long (~0.5 s) allowing for a large number of exchange events to occur making it a very powerful tool to detect minor sates populated ([Formula: see text]) to as low as 1%. When systems are in fast exchange and the 15N CEST data has to be described using a model that contains exchange, the exchange parameters are often poorly defined because the [Formula: see text] versus [Formula: see text] and [Formula: see text] versus exchange rate ([Formula: see text]) plots can be quite flat with shallow or no minima and the analysis of such 15N CEST data can lead to wrong estimates of the exchange parameters due to the presence of 'spurious' minima. Here we show that the inclusion of experimentally derived constraints on the intrinsic transverse relaxation rates and the inclusion of visible state peak-positions during the analysis of amide 15N CEST data acquired with moderate B1 values (~50 to ~350 Hz) results in convincing minima in the [Formula: see text] versus [Formula: see text] and the [Formula: see text] versus [Formula: see text] plots even when exchange occurs on the 100 μs timescale. The utility of this strategy is demonstrated on the fast-folding Bacillus stearothermophilus peripheral subunit binding domain that folds with a rate constant ~104 s-1. Here the analysis of 15N CEST data alone results in [Formula: see text] versus [Formula: see text] and [Formula: see text] versus [Formula: see text] plots that contain shallow minima, but the inclusion of visible-state peak positions and restraints on the intrinsic transverse relaxation rates of both states during the analysis of the 15N CEST data results in pronounced minima in the [Formula: see text] versus [Formula: see text] and [Formula: see text] versus [Formula: see text] plots and precise exchange parameters even in the fast exchange regime ([Formula: see text]~5). Using this strategy we find that the folding rate constant of PSBD is invariant (~10,500 s-1) from 33.2 to 42.9 °C while the unfolding rates (~70 to ~500 s-1) and unfolded state populations (~0.7 to ~4.3%) increase with temperature. The results presented here show that protein dynamics occurring on the 10 to 104 s-1 timescale can be studied using amide 15N CEST experiments.
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Affiliation(s)
- Nihar Pradeep Khandave
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Pramodh Vallurupalli
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, India.
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15
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Simongini M, Puglisi A, Genovese F, Hochkoeppler A. Trehalose counteracts the dissociation of tetrameric rabbit lactate dehydrogenase induced by acidic pH conditions. Arch Biochem Biophys 2023; 740:109584. [PMID: 37001749 DOI: 10.1016/j.abb.2023.109584] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/19/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023]
Abstract
The lactate dehydrogenase from rabbit skeletal muscle (rbLDH) is a tetrameric enzyme, known to undergo dissociation when exposed to acidic pH conditions. Moreover, it should be mentioned that this dissociation translates into a pronounced loss of enzyme activity. Notably, among the compounds able to stabilize proteins and enzymes, the disaccharide trehalose represents an outperformer. In particular, trehalose was shown to efficiently counteract quite a number of physical and chemical agents inducing protein denaturation. However, no information is available on the effect, if any, exerted by trehalose against the dissociation of protein oligomers. Accordingly, we thought it of interest to investigate whether this disaccharide is competent in preventing the dissociation of rbLDH induced by acidic pH conditions. Further, we compared the action of trehalose with the effects triggered by maltose and cellobiose. Surprisingly, both these disaccharides enhanced the dissociation of rbLDH, with maltose being responsible for a major effect when compared to cellobiose. On the contrary, trehalose was effective in preventing enzyme dissociation, as revealed by activity assays and by Dynamic Light Scattering (DLS) experiments. Moreover, we detected a significant decrease of both K0.5 and Vmax when the rbLDH activity was tested (at pH 7.5 and 6.5) as a function of pyruvate concentration in the presence of trehalose. Further, we found that trehalose induces a remarkable increase of Vmax when the enzyme is exposed to pH 5. Overall, our observations suggest that trehalose triggers conformational rearrangements of tetrameric rbLDH mirrored by resistance to dissociation and peculiar catalytic features.
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Affiliation(s)
- Michelangelo Simongini
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Andrea Puglisi
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Filippo Genovese
- CIGS, University of Modena and Reggio Emilia, Via Campi 213/A, 41125, Modena, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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16
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Zhu P, Ma C, Fan J, Yang Y, Liu X, Bian X, Ren L, Xu Y, Yu D, Liu L, Fu Y, Gao J, Zhang N. The interaction of trehalose and molten globule state soybean 11S globulin and its impact on foaming capacities. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1194-1204. [PMID: 36088619 DOI: 10.1002/jsfa.12214] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/04/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Soybean 11S globulin has good functional properties, which are widely used in the field of food. However, natural soybean 11S globulin (N-11S) has low flexibility and is easy to aggregate, impacting its foaming process. Studies have shown that soybean 11S globulin in molten globule state (MG-11S) has better molecular flexibility than N-11S, and trehalose has been shown to improve the properties of proteins. Therefore, this study investigated the interaction mechanism between trehalose and MG-11S, and its impact on rheological and foaming properties of MG-11S. RESULTS The molecular docking and intrinsic fluorescence results showed that hydrogen bonding was the main interaction force at lower than 0.5 mol L-1 trehalose added. Meanwhile, rheology and foaming showed that the MG-11S-trehalose complexes had better viscoelasticity, foaming ability (66.67-86.67%) and foaming stability (75.00-89.29%) than N-11S (16.67% foaming ability and 40.00% foaming stability); however, when the trehalose was higher than 0.5 mol L-1 , molecular crowding occurred and H-bonds were weakened, resulting in reduction of foaming capacities. Microstructure determination showed that trehalose attached to the surface of foam membrane; meanwhile, the foaming structure of the complex with 0.5 mol L-1 trehalose had a thicker liquid film with decreased drainage rate, less agglomeration and disproportionation of foam, illustrating the best foaming ability and foaming stability. CONCLUSION The results suggested that trehalose at different concentrations can interact with MG-11S through different mechanisms, and improve the foaming capacity of MS-11S. This provided a reference for the application of MS-11S in foaming food. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Pengyu Zhu
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Chunmin Ma
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Jing Fan
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Yang Yang
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Xiaofei Liu
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Xin Bian
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Likun Ren
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Yue Xu
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Dehui Yu
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Linlin Liu
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Yu Fu
- College of Food Science, Southwest University, Chongqing, China
| | - Jian Gao
- College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Na Zhang
- College of Food Engineering, Harbin University of Commerce, Harbin, China
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17
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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18
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Das D, Mukhopadhyay S. Molecular Origin of Internal Friction in Intrinsically Disordered Proteins. Acc Chem Res 2022; 55:3470-3480. [PMID: 36346711 DOI: 10.1021/acs.accounts.2c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein folding and dynamics are controlled by an interplay of thermal and viscosity effects. The effect of viscous drag through the solvent molecules is described by the classic Kramers theory in the high friction limit, which considers the dampening of the reactant molecules in the solution and quantifies the dependence of the reaction rate on the frictional drag. In addition to the external energy dissipation originating from the surrounding solvent molecules, there is an additional mode of internal energy dissipative force operative within the polypeptide chain reflecting the internal resistance of the chain to its conformational alterations. This dry, solvent-independent intrinsic frictional drag is termed internal friction. In the case of natively folded proteins, the physical origin of internal friction is primarily attributed to the intrachain interactions or other nonnative interactions in their compact states. However, the molecular origin of internal friction in intrinsically disordered proteins (IDPs) remains elusive.In this Account, we address this fundamental issue: what are the principal drivers of viscosity-independent (dry) friction in highly solvated, expanded, conformationally flexible, rapidly fluctuating IDPs that do not possess persistent intrachain interactions? IDPs exhibit diffusive conformational dynamics that is predominantly dominated by the segmental motion of the backbone arising due to the dihedral rotations in the Ramachandran Φ-Ψ space. The physical origin of friction in a complex biopolymeric system such as IDPs can be described by classic polymer models, namely, Rouse/Zimm models with internal friction. These one-dimensional models do not invoke torsional fluctuation components. Kuhn's classic description includes the connection between internal friction and microscopic dihedral hopping. Based on our time-resolved fluorescence anisotropy results, we describe that the sequence-dependent, collective, short-range backbone dihedral rotations govern localized internal friction in an archetypal IDP, namely, α-synuclein. The highly sensitive, residue-specific fluorescence depolarization kinetics offers a potent methodology to characterize and quantify the directional decorrelation engendered due to the short-range dihedral relaxation of the polypeptide backbone in the dihedral space. We utilized this characteristic relaxation time scale as our dynamic readout to quantify the site-specific frictional component. Our linear viscosity-dependent model of torsional relaxation time scale furnished a finite nonzero time constant at the zero solvent viscosity representing the solvent-independent internal friction. These results unveil the effect of the degree of dihedral restraining parameter on the internal friction component by showing that a restrained proline residue imparts higher torsional stiffness in the chain segments and, therefore, exhibits higher internal friction. This Account sheds light on the molecular underpinning of the sequence-specific internal friction in IDPs and will be of interest to unmask the role of internal friction in a diverse range of biomolecular processes involving binding-induced folding, allosteric interaction, protein misfolding and aggregation, and biomolecular condensation via phase separation.
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Affiliation(s)
- Debapriya Das
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Punjab 140306, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Punjab 140306, India
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19
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Chen A, Tapia H, Goddard JM, Gibney PA. Trehalose and its applications in the food industry. Compr Rev Food Sci Food Saf 2022; 21:5004-5037. [PMID: 36201393 DOI: 10.1111/1541-4337.13048] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/29/2022] [Accepted: 08/31/2022] [Indexed: 01/28/2023]
Abstract
Trehalose is a nonreducing disaccharide composed of two glucose molecules linked by α, α-1,1-glycosidic bond. It is present in a wide variety of organisms, including bacteria, fungi, insects, plants, and invertebrate animals. Trehalose has distinct physical and chemical properties that have been investigated for their biological importance in a range of prokaryotic and eukaryotic species. Emerging research on trehalose has identified untapped opportunities for its application in the food, medical, pharmaceutical, and cosmetics industries. This review summarizes the chemical and biological properties of trehalose, its occurrence and metabolism in living organisms, its protective role in molecule stabilization, and natural and commercial production methods. Utilization of trehalose in the food industry, in particular how it stabilizes protein, fat, carbohydrate, and volatile compounds, is also discussed in depth. Challenges and opportunities of its application in specific applications (e.g., diagnostics, bioprocessing, ingredient technology) are described. We conclude with a discussion on the potential of leveraging the unique molecular properties of trehalose in molecular stabilization for improving the safety, quality, and sustainability of our food systems.
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Affiliation(s)
- Anqi Chen
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Hugo Tapia
- Biology Program, California State University - Channel Islands, Camarillo, California, USA
| | - Julie M Goddard
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, New York, USA
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20
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Song F, Ou X, Chou TY, Liu J, Gao H, Zhang R, Huang X, Zhao Z, Sun J, Chen S, Lam JWY, Tang BZ. Oxygen Quenching-Resistant Nanoaggregates with Aggregation-Induced Delayed Fluorescence for Time-Resolved Mapping of Intracellular Microviscosity. ACS NANO 2022; 16:6176-6184. [PMID: 35318852 DOI: 10.1021/acsnano.1c11661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microviscosity is a fundamental parameter in the biophysics of life science and governs numerous cellular processes. Thus, the development of real-time quantitative monitoring of microviscosity inside cells is important. The traditional probes for detecting microviscosity via time-resolved luminescence imaging (TRLI) are generally disturbed by autofluorescence or surrounding oxygen in cells. Herein, we developed loose packing nanoaggregates with aggregation-induced delayed fluorescence (FKP-POA and FKP-PTA) and free from the effect of oxygen and autofluorescence for viscosity mapping via TRLI. The feasibility of FKP-PTA nanoparticles (NPs) for microviscosity mapping through TRLI was demonstrated by monitoring the variation of microviscosity inside HepG2 cancer cells, which demonstrated a value change from 14.9 cP to 216.9 cP during the apoptosis. This indicates that FKP-PTA NP can be used as a probe for cellular microviscosity mapping to help people to understand the physiologically dynamic microenvironment. The present results are expected to promote the advancement of diagnostic and therapeutic methods to cope with related diseases.
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Affiliation(s)
- Fengyan Song
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- Department of Chemical Biology, School of Life Science and Chemistry, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Xinwen Ou
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Tsu Yu Chou
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong 999077, China
| | - Junkai Liu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Hui Gao
- School of Aeronautic Science and Engineering, Beihang University, Beijing 100191, China
| | - Ruoyao Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaolin Huang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Zujin Zhao
- State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Jianwei Sun
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong 999077, China
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
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21
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Mendive‐Tapia L, Mendive‐Tapia D, Zhao C, Gordon D, Benson S, Bromley MJ, Wang W, Wu J, Kopp A, Ackermann L, Vendrell M. Rationales Design von Phe-BODIPY-Aminosäuren als fluorogene Bausteine für den peptidbasierten Nachweis von Candida-Infektionen im Harntrakt. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202117218. [PMID: 38505242 PMCID: PMC10946803 DOI: 10.1002/ange.202117218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/08/2022]
Abstract
AbstractPilzinfektionen, die durch Candida‐Arten verursacht werden, gehören zu den häufigsten Infektionen bei Krankenhauspatienten. Die derzeitigen Methoden zum Nachweis von Candida‐Pilzzellen in klinischen Proben beruhen jedoch auf zeitaufwändigen Analysen, die eine schnelle und zuverlässige Diagnose erschweren. In diesem Beitrag beschreiben wir die rationale Entwicklung neuer Phe‐BODIPY‐Aminosäuren als kleine fluorogene Bausteine und ihre Anwendung zur Erzeugung fluoreszierender antimikrobieller Peptide für die schnelle Markierung von Candida‐Zellen im Urin. Mit Hilfe von computergestützten Berechnungen haben wir das fluorogene Verhalten von BODIPY‐substituierten aromatischen Aminosäuren analysiert und Bioaktivitäts‐ und konfokale Mikroskopieexperimente bei verschiedenen Stämmen durchgeführt, um den Nutzen und die Vielseitigkeit von Peptiden mit Phe‐BODIPYs zu bestätigen. Schließlich haben wir einen einfachen und sensitiven fluoreszensbasierten Test zum Nachweis von Candida albicans in menschlichen Urinproben entwickelt.
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Affiliation(s)
- Lorena Mendive‐Tapia
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - David Mendive‐Tapia
- Abteilung Theoretische ChemiePhysikalisch-Chemisches InstitutUniversität Heidelberg69120HeidelbergDeutschland
| | - Can Zhao
- Manchester Fungal Infection GroupAbteilung für EvolutionInfektion und GenomikM139NTManchesterGroßbritannien
| | - Doireann Gordon
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - Sam Benson
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
| | - Michael J. Bromley
- Manchester Fungal Infection GroupAbteilung für EvolutionInfektion und GenomikM139NTManchesterGroßbritannien
| | - Wei Wang
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Jun Wu
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Adelina Kopp
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenDeutschland
| | - Marc Vendrell
- Zentrum für EntzündungsforschungDie Universität von EdinburghEH16 4TJEdinburghGroßbritannien
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22
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Mendive‐Tapia L, Mendive‐Tapia D, Zhao C, Gordon D, Benson S, Bromley MJ, Wang W, Wu J, Kopp A, Ackermann L, Vendrell M. Rational Design of Phe-BODIPY Amino Acids as Fluorogenic Building Blocks for Peptide-Based Detection of Urinary Tract Candida Infections. Angew Chem Int Ed Engl 2022; 61:e202117218. [PMID: 35075763 PMCID: PMC9305947 DOI: 10.1002/anie.202117218] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 12/11/2022]
Abstract
Fungal infections caused by Candida species are among the most prevalent in hospitalized patients. However, current methods for the detection of Candida fungal cells in clinical samples rely on time-consuming assays that hamper rapid and reliable diagnosis. Herein, we describe the rational development of new Phe-BODIPY amino acids as small fluorogenic building blocks and their application to generate fluorescent antimicrobial peptides for rapid labelling of Candida cells in urine. We have used computational methods to analyse the fluorogenic behaviour of BODIPY-substituted aromatic amino acids and performed bioactivity and confocal microscopy experiments in different strains to confirm the utility and versatility of peptides incorporating Phe-BODIPYs. Finally, we have designed a simple and sensitive fluorescence-based assay for the detection of Candida albicans in human urine samples.
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Affiliation(s)
| | - David Mendive‐Tapia
- Department Theoretische ChemiePhysikalisch-Chemisches InstitutUniversität Heidelberg69120HeidelbergGermany
| | - Can Zhao
- Manchester Fungal Infection GroupDivision of EvolutionInfection and GenomicsUniversity of ManchesterM139NTManchesterUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Sam Benson
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Michael J. Bromley
- Manchester Fungal Infection GroupDivision of EvolutionInfection and GenomicsUniversity of ManchesterM139NTManchesterUK
| | - Wei Wang
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Jun Wu
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Adelina Kopp
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität37077GöttingenGermany
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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23
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Abstract
Proteins have dynamic structures that undergo chain motions on time scales spanning from picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential for gaining accurate insight into fundamental mechanistic aspects of the protein folding reaction. The use of high-resolution structural probes, sensitive to population distributions, has begun to enable the resolution of site-specific conformational heterogeneity at different stages of the folding reaction. Different states populated during protein folding, including the unfolded state, collapsed intermediate states, and even the native state, are found to possess significant conformational heterogeneity. Heterogeneity in protein folding and unfolding reactions originates from the reduced cooperativity of various kinds of physicochemical interactions between various structural elements of a protein, and between a protein and solvent. Heterogeneity may arise because of functional or evolutionary constraints. Conformational substates within the unfolded state and the collapsed intermediates that exchange at rates slower than the subsequent folding steps give rise to heterogeneity on the protein folding pathways. Multiple folding pathways are likely to represent distinct sequences of structure formation. Insight into the nature of the energy barriers separating different conformational states populated during (un)folding can also be obtained by resolving heterogeneity.
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Affiliation(s)
- Sandhya Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
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24
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Mukherjee S, Mondal S, Acharya S, Bagchi B. Tug-of-War between Internal and External Frictions and Viscosity Dependence of Rate in Biological Reactions. PHYSICAL REVIEW LETTERS 2022; 128:108101. [PMID: 35333093 DOI: 10.1103/physrevlett.128.108101] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/13/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The role of water in biological processes is studied in three reactions, namely, the Fe-CO bond rupture in myoglobin, GB1 unfolding, and insulin dimer dissociation. We compute both internal and external components of friction on relevant reaction coordinates. In all of the three cases, the cross-correlation between forces from protein and water is found to be large and negative that serves to reduce the total friction significantly, increase the calculated reaction rate, and weaken solvent viscosity dependence. The computed force spectrum reveals bimodal 1/f noise, suggesting the use of a non-Markovian rate theory.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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25
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Renner J, Schmidt M, Heras DDL. Shear and Bulk Acceleration Viscosities in Simple Fluids. PHYSICAL REVIEW LETTERS 2022; 128:094502. [PMID: 35302832 DOI: 10.1103/physrevlett.128.094502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Inhomogeneities in the velocity field of a moving fluid are dampened by the inherent viscous behavior of the system. Both bulk and shear effects, related to the divergence and the curl of the velocity field, are relevant. On molecular time scales, beyond the Navier-Stokes description, memory plays an important role. Using molecular and overdamped Brownian dynamics many-body simulations, we demonstrate that analogous viscous effects act on the acceleration field. This acceleration viscous behavior is associated with the divergence and the curl of the acceleration field, and it can be quantitatively described using simple exponentially decaying memory kernels. The simultaneous use of velocity and acceleration fields enables the description of fast dynamics on molecular scales.
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Affiliation(s)
- Johannes Renner
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Daniel de Las Heras
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
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26
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Das D, Arora L, Mukhopadhyay S. Short-Range Backbone Dihedral Rotations Modulate Internal Friction in Intrinsically Disordered Proteins. J Am Chem Soc 2022; 144:1739-1747. [DOI: 10.1021/jacs.1c11236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Debapriya Das
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Mohali, SAS Nagar, Punjab 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Mohali, SAS Nagar, Punjab 140306, India
| | - Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Mohali, SAS Nagar, Punjab 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Mohali, SAS Nagar, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Mohali, SAS Nagar, Punjab 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Mohali, SAS Nagar, Punjab 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Mohali, SAS Nagar, Punjab 140306, India
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27
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Eaton WA. Impact of Conformational Substates and Energy Landscapes on Understanding Hemoglobin Kinetics and Function. J Biol Phys 2021; 47:337-353. [PMID: 34762226 PMCID: PMC8603986 DOI: 10.1007/s10867-021-09588-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
Hans Frauenfelder's discovery of conformational substates in studies of myoglobin carbon monoxide geminate rebinding kinetics at cryogenic temperatures (Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, & Gunsalus IC (1975) Dynamics of Ligand Binding to Myoglobin. Biochemistry 14(24):5355-5373) followed by his introduction of energy landscape theory with Peter Wolynes (Frauenfelder H, Sligar SG, & Wolynes PG (1991) The Energy Landscapes and Motions of Proteins. Science 254(5038):1598-1603) marked the beginning of a new era in the physics and physical chemistry of proteins. Their work played a major role in demonstrating the power and importance of dynamics and of Kramers reaction rate theory for understanding protein function. The biggest impact of energy landscape theory has been in the protein folding field, which is well-known and has been documented in numerous articles and reviews, including a recent one of my own (Eaton WA (2021) Modern Kinetics and Mechanism of Protein Folding: a Retrospective. J. Phys. Chem. B. 125(14):3452-3467). Here I will describe the much less well-known impact of their modern view of proteins on both experimental and theoretical studies of hemoglobin kinetics and function. I will first describe how Frauenfelder's experiments motivated and influenced my own research on myoglobin, which were key ingredients to my work on understanding hemoglobin.
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Affiliation(s)
- William A Eaton
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5/104, Bethesda, MD, 20892-0520, United States.
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28
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Lee SJ, Talele S, King JT. Protein-Bath Coupling of an Internal Reaction Coordinate at Intermediate Time Scales. J Phys Chem Lett 2021; 12:10942-10946. [PMID: 34734731 DOI: 10.1021/acs.jpclett.1c02537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Thermally activated barrier-crossing processes are central to protein reaction kinetics. A determining factor for such kinetics is the extent to which the protein's motions are coupled to the surrounding bath. It is understood that slow large-scale conformational motions are strongly coupled to the environment, while fast librational motions are uncoupled. However, less is known about protein-bath coupling of reaction coordinates located on the interior of a protein and with dynamics on intermediate time scales. In this work, we use single molecule 2D fluorescence lifetime correlation spectroscopy to study the microsecond chemical reaction occurring in the chromophore pocket of eGFP. The equilibrium reaction involves a dihedral rotation of a glutamic acid residue and a rearrangement of the local hydrogen-bonding network surrounding the endogenous chromophore, with no accompanying large-scale conformational changes. We observe that the internal chemical reaction is coupled to the solvent viscosity, though the scaling deviates from Kramers' behavior. We attribute this deviation to the internal friction of the protein, which weakens the protein-solvent coupling at high viscosity and intermediate time scales.
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Affiliation(s)
- Seung Jae Lee
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Saurabh Talele
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - John T King
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea
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29
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Jas GS, Childs EW, Middaugh CR, Kuczera K. Probing the Internal Dynamics and Shape of Simple Peptides in Urea, Guanidinium Hydrochloride, and Proline Solutions with Time-Resolved Fluorescence Anisotropy and Atomistic Cosolvent Simulations. J Phys Chem B 2021; 125:10972-10984. [PMID: 34559968 DOI: 10.1021/acs.jpcb.1c06838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Picosecond time-resolved fluorescence anisotropy was used to measure the effect of denaturants and osmolytes on the reorientation dynamics of the simplest dipeptide. The solvent denaturants guanidinium hydrochloride (gdm), urea, and the osmolyte proline were used at several concentrations. Analysis of the concentration dependence of denaturants at a fixed temperature showed faster and slower reorientation time in two different denaturants at a nearly identical solvent viscosity (η). The reorientation time τ significantly deviates from Kramers' theory (τ ∝ η1) in the high friction limit for guanidinium and urea with r ≈ 0.4 and r ≈ 0.6 at pH 7.2, respectively. In proline, τ is nearly proportional to η. Atomistic molecular dynamics simulations of the dipeptide in identical cosolvents showed excellent agreement with the measured rotational orientation time. The dipeptide dihedral (ϕ, ψ) isomerization times in water and 6 M urea are almost identical and significantly slower in guanidinium. If a faster and slower reorientation time can be associated with the compact and expanded shapes, the fractional viscosity dependence for guanidinium and urea may result from the fact that internal dynamics of peptides in these cosolvents involve higher and lower internal friction within the dynamic elements.
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Affiliation(s)
- Gouri S Jas
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Ed W Childs
- Department of Surgery, Morehouse School of Medicine, Atlanta, Georgia 30310, United States
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Krzysztof Kuczera
- Department of Chemistry and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66045, United States
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30
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Zhao X, Meng X, Ragauskas AJ, Lai C, Ling Z, Huang C, Yong Q. Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques. Biotechnol Adv 2021; 54:107830. [PMID: 34480987 DOI: 10.1016/j.biotechadv.2021.107830] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/07/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.
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Affiliation(s)
- Xiaoxue Zhao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA; Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chenhuan Lai
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ling
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Yong
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
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31
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Kailasham R, Chakrabarti R, Prakash JR. How important are fluctuations in the treatment of internal friction in polymers? SOFT MATTER 2021; 17:7133-7157. [PMID: 34259278 DOI: 10.1039/d1sm00613d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an approximate treatment that is based on preaveraging internal friction. By comparison with Brownian dynamics simulations of an exact coarse-grained model that incorporates fluctuations in internal friction, the accuracy of the preaveraged model predictions is examined both at and away from equilibrium. While the two models predict intrachain autocorrelations that approach each other for long enough chain segments, they differ in their predictions for shorter segments. Furthermore, the two models differ qualitatively in their predictions for the chain extension and viscosity in shear flow, which is taken to represent a prototypical out-of-equilibrium condition.
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Affiliation(s)
- R Kailasham
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai, Maharashtra - 400076, India and Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra - 400076, India. and Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra - 400076, India.
| | - J Ravi Prakash
- Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia.
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32
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Abstract
The thermal motion of charged proteins causes randomly fluctuating electric fields inside cells. According to the fluctuation-dissipation theorem, there is an additional friction force associated with such fluctuations. However, the impact of these fluctuations on the diffusion and dynamics of proteins in the cytoplasm is unclear. Here, we provide an order-of-magnitude estimate of this effect by treating electric field fluctuations within a generalized Langevin equation model with a time-dependent friction memory kernel. We find that electric friction is generally negligible compared to solvent friction. However, a significant slowdown of protein diffusion and dynamics is expected for biomolecules with high net charges such as intrinsically disordered proteins and RNA. The results show that direct contacts between biomolecules in a cell are not necessarily required to alter their dynamics.
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Affiliation(s)
- Dmitrii E Makarov
- Department of Chemistry and Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
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33
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Singh D, Mondal K, Chaudhury S. Effect of Memory and Inertial Contribution on Transition-Time Distributions: Theory and Simulations. J Phys Chem B 2021; 125:4536-4545. [PMID: 33900087 DOI: 10.1021/acs.jpcb.1c00173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Transition paths refer to the time taken by molecules to cross a barrier separating two molecular conformations. In this work, we study how memory, as well as inertial contribution in the dynamics along a reaction coordinate, can affect the distribution of the transition-path time. We use a simple model of dynamics governed by a generalized Langevin equation with a power-law memory along with the inertial term, which was neglected in previous studies, where memory effects were explored only in the overdamped limit. We derive an approximate expression for the transit-time distribution and discuss our results for the short- and long-time limits and also compare it with known results in the high friction (overdamped) limit as well as in the Markovian limit. We have developed a numerical algorithm to test our theoretical results against extensive numerical simulations.
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Affiliation(s)
- Divya Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Kinjal Mondal
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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34
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Abstract
Modern experimental kinetics of protein folding began in the early 1990s with the introduction of nanosecond laser pulses to trigger the folding reaction, providing an almost 106-fold improvement in time resolution over the stopped-flow method being employed at the time. These experiments marked the beginning of the "fast-folding" subfield that enabled investigation of the kinetics of formation of secondary structural elements and disordered loops for the first time, as well as the fastest folding proteins. When I started to work on this subject, a fast folding protein was one that folded in milliseconds. There were, moreover, no analytical theoretical models and no atomistic or coarse-grained molecular dynamics simulations to describe the mechanism. Two of the most important discoveries from my lab since then are a protein that folds in hundreds of nanoseconds, as determined from nanosecond laser temperature experiments, and the discovery that the theoretically predicted barrier crossing time is about the same for proteins that differ in folding rates by 104-fold, as determined from single molecule fluorescence measurements. We also developed what has been called the "Hückel model" of protein folding, which quantitatively explains a wide range of equilibrium and kinetic measurements. This retrospective traces the history of contributions to the "fast folding" subfield from my lab until about 3 years ago, when I left protein folding to spend the rest of my research career trying to discover an inexpensive drug for treating sickle cell disease.
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Affiliation(s)
- William A Eaton
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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35
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Xia C, Kang W, Wang J, Wang W. Temperature Dependence of Internal Friction of Peptides. J Phys Chem B 2021; 125:2821-2832. [PMID: 33689339 DOI: 10.1021/acs.jpcb.0c09056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Internal friction is a valuable concept to describe the kinetics of proteins. As is well known, internal friction can be modulated by solvent features (such as viscosity). How can internal friction be affected by environmental temperature? The answer to this question is not evident. In the present work, we approach this problem with simulations on two model peptides. The thermodynamics and relaxation kinetics are characterized through long molecular dynamics simulations, with the viscosity modulated by varying the mass of solvent molecules. Based on the extrapolation to zero viscosity together with scaling of the relaxation time scales, we discover that internal friction is almost invariant at various temperatures. Controlled simulations further support the idea that internal friction is independent of environmental temperature. Comparisons between the two model peptides help us to understand the diverse phenomena in experiments.
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Affiliation(s)
- Chenliang Xia
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
| | - Wenbin Kang
- School of Public Health and Management, Hubei University of Medicine, Shiyan 442000, P.R. China
| | - Jun Wang
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
| | - Wei Wang
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
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36
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Lindorff-Larsen K, Teilum K. Linking thermodynamics and measurements of protein stability. Protein Eng Des Sel 2021; 34:6173616. [PMID: 33724431 DOI: 10.1093/protein/gzab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/21/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible folding/unfolding transitions and the experimental methods that are available for extracting thermodynamic parameters. We highlight the importance of modelling both how the folding equilibrium depends on a perturbing variable such as temperature or denaturant concentration, and the importance of modelling the baselines in the experimental observables.
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Affiliation(s)
- Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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37
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Yamaguchi T. Molecular dynamics simulation study on the isomerization reaction in a solvent with slow structural relaxation. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2020.111056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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38
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Moon S, Kim H, Kim D, Lee JB. Viscosity-Regulated Control of RNA Microstructure Fabrication. Polymers (Basel) 2021; 13:454. [PMID: 33572561 PMCID: PMC7866859 DOI: 10.3390/polym13030454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 01/20/2023] Open
Abstract
The development of RNA self-assemblies offers a powerful platform for a wide range of biomedical applications. The fabrication process has become more elaborate in order to achieve functional structures with maximized potential. As a facile means to control the structure, here, we report a new approach to manipulate the polymerization rate and subsequent self-assembly process through regulation of the reaction viscosity. As the RNA polymerization rate has a dependence on solution viscosity, the resulting assembly, crystallization, and overall sizes of the product could be manipulated. The simple and precise control of RNA polymerization and self-assembly by reaction viscosity will provide a way to widen the utility of RNA-based materials.
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Affiliation(s)
| | | | | | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Korea; (S.M.); (H.K.); (D.K.)
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39
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Abstract
Classical enzyme kinetic theories are summarized and linked with modern discoveries here. The sequential catalytic events along time axis by enzyme are analyzed at the molecular level, and by using master equations, this writing tries to connect the microscopic molecular behavior of enzyme to kinetic data (like velocity and catalytic coefficient k) obtained in experiment: 1/k = t equals to the sum of the times taken by the constituent individual steps. The relationships between catalytic coefficient k, catalytic rate or velocity, the amount of time taken by each step and physical or biochemical conditions of the system are discussed, and the perspective and hypothetic equations proposed here regarding diffusion, conformational change, chemical conversion, product release steps and the whole catalytic cycle provide an interpretation of previous experimental observations and can be testified by future experiments.
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40
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Fischer J, Radulescu A, Falus P, Richter D, Biehl R. Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model. J Phys Chem B 2021; 125:780-788. [PMID: 33470118 DOI: 10.1021/acs.jpcb.0c09476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Disordered regions as found in intrinsically disordered proteins (IDP) or during protein folding define response time to stimuli and protein folding times. Neutron spin-echo spectroscopy is a powerful tool to directly access the collective motions of the unfolded chain to enlighten the physical origin of basic conformational relaxation. During the thermal unfolding of native ribonuclease A, we examine the structure and dynamics of the disordered state within a two-state transition model using polymer models, including internal friction, to describe the chain dynamics. The presence of four disulfide bonds alters the disordered configuration to a more compact configuration compared to a Gaussian chain that is defined by the additional links, as demonstrated by coarse-grained simulation. The dynamics of the disordered chain is described by Zimm dynamics with internal friction (ZIF) between neighboring amino acids. Relaxation times are dominated by mode-independent internal friction. Internal friction relaxation times show an Arrhenius-like behavior with an activation energy of 33 kJ/mol. The Zimm dynamics is dominated by internal friction and suggest that the characteristic motions correspond to overdamped elastic modes similar to the motions observed for folded proteins but within a pool of disordered configurations spanning the configurational space. For IDP, internal friction dominates while solvent friction and hydrodynamic interactions are smaller corrections.
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Affiliation(s)
- Jennifer Fischer
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, 85748 Garching, Germany
| | - Peter Falus
- Institut Laue-Langevin (ILL), 71 rue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Dieter Richter
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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41
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Subramanian S, Golla H, Divakar K, Kannan A, de Sancho D, Naganathan AN. Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? J Phys Chem B 2020; 124:8973-8983. [PMID: 32955882 PMCID: PMC7659034 DOI: 10.1021/acs.jpcb.0c05976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The rate at which a protein molecule
folds is determined by opposing
energetic and entropic contributions to the free energy that shape
the folding landscape. Delineating the extent to which they impact
the diffusional barrier-crossing events, including the magnitude of
internal friction and barrier height, has largely been a challenging
task. In this work, we extract the underlying thermodynamic and dynamic
contributions to the folding rate of an unusually slow-folding helical
DNA-binding domain, PurR, which shares the characteristics of ultrafast
downhill-folding proteins but nonetheless appears to exhibit an apparent
two-state equilibrium. We combine equilibrium spectroscopy, temperature-viscosity-dependent
kinetics, statistical mechanical modeling, and coarse-grained simulations
to show that the conformational behavior of PurR is highly heterogeneous
characterized by a large spread in melting temperatures, marginal
thermodynamic barriers, and populated partially structured states.
PurR appears to be at the threshold of disorder arising from frustrated
electrostatics and weak packing that in turn slows down folding due
to a shallow, bumpy landscape and not due to large thermodynamic barriers
or strong internal friction. Our work highlights how a strong temperature
dependence on the pre-exponential could signal a shallow landscape
and not necessarily a slow-folding diffusion coefficient, thus determining
the folding timescales of even millisecond folding proteins and hints
at possible structural origins for the shallow landscape.
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Affiliation(s)
- Sandhyaa Subramanian
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Hemashree Golla
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Kalivarathan Divakar
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India
| | - Adithi Kannan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David de Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Donostia-San Sebastián 20080, Spain.,Donostia International Physics Center (DIPC), PK 1072, Donostia-San Sebastián 20080, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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42
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Liu F, Zhang J. Nano-second protein dynamics of key residue at Position 38 in catechol-O-methyltransferase system: a time-resolved fluorescence study. J Biochem 2020; 168:417-425. [DOI: 10.1093/jb/mvaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 02/02/2023] Open
Abstract
AbstractHuman catechol-O-methyltransferase, a key enzyme related to neurotransmitter metabolism, catalyses a methyl transfer from S-adenosylmethionine to catechol. Although extensive studies aim to understand the enzyme mechanisms, the connection of protein dynamics and enzyme catalysis is still not clear. Here, W38in (Trp143Phe) and W38in/Y68A (Trp143Phe with Tyr68Ala) mutants were carried out to study the relationship of dynamics and catalysis in nano-second timescale using time-resolved fluorescence lifetimes and Stokes shifts in various solvents. The comprehensive data implied the mutant W38in/Y68A with lower activity is more rigid than the ‘WT’−W38in, suggesting the importance of flexibility at residue 38 to maintain the optimal catalysis.
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Affiliation(s)
- Fan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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43
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Choi S, Moon S, Park Y. Spectroscopic Investigation of Entropic Canopy-Canopy Interactions of Nanoparticle Organic Hybrid Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9626-9633. [PMID: 32683866 DOI: 10.1021/acs.langmuir.0c01784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanoparticle organic hybrid materials (NOHMs) are self-suspended liquid-like nanoparticle-based functional materials consisting of a surface-functionalized inorganic nanocore and oligomeric or polymeric chains. They often exhibit complex intermolecular and intramolecular interactions among their constituents, resulting in versatile physicochemical characteristics that range from glassy solids to solvent-free nanoparticle fluids. A variety of applications involving NOHMs have been investigated thus far, including thermal management fluids, lubricants, magnetic fluids, nanocomposites, electrolytes, water treatment and biomass pretreatment chemicals, and CO2 capture solvents. In particular, NOHMs have recently been recognized as a promising CO2 capture and utilization medium. To capture CO2 more effectively, a variety of specific functional groups of strong chemical affinity to CO2 can be added to the polymeric canopy (enthalpic contribution), and various steric considerations induced by attractive/repulsive interactions among the nanocores and canopies can be introduced (entropic contribution). These occur while maintaining negligible vapor pressure and enhanced thermal stability. Here, we investigated the canopy dynamics of NOHMs with different-sized SiO2 nanocores, aiming to reveal the hidden nature of the entropic interaction occurring in NOHMs. Pulse-field gradient nuclear magnetic resonance spectroscopy (with 1H) was employed to investigate the canopy dynamics of the NOHMs synthesized using 7, 12, and 22 nm SiO2 particles, and these results were compared with those from a ternary mix of all three sizes of SiO2 nanocores. The self-diffusion coefficient and thermal diffusivity were also evaluated.
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Affiliation(s)
- Soyoung Choi
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Seokyoon Moon
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Youngjune Park
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
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44
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Gaipov A, Utegulov Z, Bukasov R, Turebekov D, Tarlykov P, Markhametova Z, Nurekeyev Z, Kunushpayeva Z, Sultangaziyev A. Development and validation of hybrid Brillouin-Raman spectroscopy for non-contact assessment of mechano-chemical properties of urine proteins as biomarkers of kidney diseases. BMC Nephrol 2020; 21:229. [PMID: 32539773 PMCID: PMC7296939 DOI: 10.1186/s12882-020-01890-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Proteinuria is a major marker of chronic kidney disease (CKD) progression and the predictor of cardiovascular mortality. The rapid development of renal failure is expected in those patients who have higher level of proteinuria however, some patients may have slow decline of renal function despite lower level of urinary protein excretion. The different mechanical (visco-elastic) and chemical properties, as well as the proteome profiles of urinary proteins might explain their tubular toxicity mechanism. Brillouin light scattering (BLS) and surface enhanced Raman scattering (SERS) spectroscopies are non-contact, laser optical-based techniques providing visco-elastic and chemical property information of probed human biofluids. We proposed to study and compare these properties of urinary proteins using BLS and SERS spectroscopies in nephrotic patient and validate hybrid BLS-SERS spectroscopy in diagnostic of urinary proteins as well as their profiling. The project ultimately aims for the development of an optical spectroscopic sensor for rapid, non-contact monitoring of urine samples from patients in clinical settings. METHODS BLS and SERS spectroscopies will be used for non-contact assessment of urinary proteins in proteinuric patients and healthy subjects and will be cross-validated by Liquid Chromatography-Mass Spectrometry (LC-MS). Participants will be followed-up during the 1 year and all adverse events such as exacerbation of proteinuria, progression of CKD, complications of nephrotic syndrome, disease relapse rate and inefficacy of treatment regimen will be registered referencing incident dates. Associations between urinary protein profiles (obtained from BLS and SERS as well as LC-MS) and adverse outcomes will be evaluated to identify most unfavored protein profiles. DISCUSSION This prospective study is focused on the development of non-contact hybrid BLS - SERS sensing tool and its clinical deployment for diagnosis and prognosis of proteinuria. We will identify the most important types of urine proteins based on their visco-elasticity, amino-acid profile and molecular weight responsible for the most severe cases of proteinuria and progressive renal function decline. We will aim for the developed hybrid BLS - SERS sensor, as a new diagnostic & prognostic tool, to be transferred to other biomedical applications. TRIAL REGISTRATION The trial has been approved by ClinicalTrials.gov (Trial registration ID NCT04311684). The date of registration was March 17, 2020.
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Affiliation(s)
- Abduzhappar Gaipov
- Department of Clinical Sciences, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan, 010000.
| | - Zhandos Utegulov
- Department of Physics, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan, 010000
| | - Rostislav Bukasov
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan, 010000
| | - Duman Turebekov
- Department of Internal Medicine, Astana Medical University, Nur-Sultan, Kazakhstan, 010000
| | - Pavel Tarlykov
- Department of Proteomics and Mass Spectrometry, National Center for Biotechnology, Nur-Sultan, Kazakhstan, 010000
| | - Zhannur Markhametova
- Department of Clinical Sciences, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan, 010000
| | - Zhangatay Nurekeyev
- Department of Physics, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan, 010000
| | - Zhanar Kunushpayeva
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan, 010000
| | - Alisher Sultangaziyev
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan, 010000
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45
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Lee YR, Kwon S, Sung BJ. The non-classical kinetics and the mutual information of polymer loop formation. J Chem Phys 2020; 152:184905. [PMID: 32414275 DOI: 10.1063/5.0005453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The loop formation of a single polymer chain has served as a model system for various biological and chemical processes. Theories based on the Smoluchowski equation proposed that the rate constant (kloop) of the loop formation would be inversely proportional to viscosity (η), i.e., kloop ∼ η-1. Experiments and simulations showed, however, that kloop showed the fractional viscosity dependence of kloop ∼ η-β with β < 1 either in glasses or in low-viscosity solutions. The origin of the fractional viscosity dependence remains elusive and has been attributed to phenomenological aspects. In this paper, we illustrate that the well-known failure of classical kinetics of the loop formation results from the breakdown of the local thermal equilibrium (LTE) approximation and that the mutual information can quantify the breakdown of the LTE successfully.
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Affiliation(s)
- Young-Ro Lee
- Department of Chemistry, Sogang University, Seoul 04107, South Korea
| | - Seulki Kwon
- Department of Chemistry, Sogang University, Seoul 04107, South Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, South Korea
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46
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Luo J, Ye S, Ustriyana P, Wei B, Chen J, Raee E, Hu Y, Yang Y, Zhou Y, Wesdemiotis C, Sahai N, Liu T. Unraveling Chiral Selection in the Self-assembly of Chiral Fullerene Macroions: Effects of Small Chiral Components Including Counterions, Co-ions, or Neutral Molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4702-4710. [PMID: 32293900 DOI: 10.1021/acs.langmuir.0c00611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Lactic acid-functionalized chiral fullerene (C60) molecules are used as models to understand chiral selection in macroionic solutions involving chiral macroions, chiral counterions, and/or chiral co-ions. With the addition of Zn2+ cations, the C60 macroions exhibit slow self-assembly behavior into hollow, spherical, blackberry-type structures, as confirmed by laser light scattering (LLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) techniques. Chiral counterions with high charge density show no selection to the chirality of AC60 macroions (LAC60 and DAC60) during their self-assembly process, while obvious chiral discrimination between the assemblies of LAC60 and DAC60 is observed when chiral counterions with low charge density are present. Compared with chiral counterions, chiral co-ions show weaker effects on chiral selection with larger amounts needed to trigger the chiral discrimination between LAC60 and DAC60. However, they can induce a higher degree of discrimination when abundant chiral co-ions are present in solution. Furthermore, the self-assembly of chiral AC60 macroions is fully suppressed by adding significant amounts of neutral molecules with opposite chirality. Thermodynamic parameters from isothermal titration calorimetry (ITC) reveal that chiral selection is controlled by the ion pairing and the destruction of solvent shells between ions, and meanwhile originates from the delicate balance between electrostatic interaction and molecular chirality.
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Affiliation(s)
- Jiancheng Luo
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Songtao Ye
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Putu Ustriyana
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Benqian Wei
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Jiahui Chen
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Ehsan Raee
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Yinghe Hu
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Yuqing Yang
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Yifan Zhou
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Chrys Wesdemiotis
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
- Department of Chemistry, The University of Akron, Akron, Ohio 44325, United States
| | - Nita Sahai
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Tianbo Liu
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
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47
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Cohen NR, Kayatekin C, Zitzewitz JA, Bilsel O, Matthews CR. Friction-Limited Folding of Disulfide-Reduced Monomeric SOD1. Biophys J 2020; 118:1992-2000. [PMID: 32191862 DOI: 10.1016/j.bpj.2020.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/04/2020] [Accepted: 02/28/2020] [Indexed: 11/16/2022] Open
Abstract
The folding reaction of a stable monomeric variant of Cu/Zn superoxide dismutase (mSOD1), an enzyme responsible for the conversion of superoxide free radicals into hydrogen peroxide and oxygen, is known to be among the slowest folding processes that adhere to two-state behavior. The long lifetime, ∼10 s, of the unfolded state presents ample opportunities for the polypeptide chain to transiently sample nonnative structures before the formation of the productive folding transition state. We recently observed the formation of a nonnative structure in a peptide model of the C-terminus of SOD1, a sequence that might serve as a potential source of internal chain friction-limited folding. To test for friction-limited folding, we performed a comprehensive thermodynamic and kinetic analysis of the folding mechanism of mSOD1 in the presence of the viscogens glycerol and glucose. Using a, to our knowledge, novel analysis of the folding reactions, we found the disulfide-reduced form of the protein that exposes the C-terminal sequence, but not its disulfide-oxidized counterpart that protects it, experiences internal chain friction during folding. The sensitivity of the internal friction to the disulfide bond status suggests that one or both of the cross-linked regions play a critical role in driving the friction-limited folding. We speculate that the molecular mechanisms giving rise to the internal friction of disulfide-reduced mSOD1 might play a role in the amyotrophic lateral sclerosis-linked aggregation of SOD1.
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Affiliation(s)
- Noah R Cohen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Can Kayatekin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts; Rare and Neurological Therapeutic Area, Sanofi, Framingham, Massachusetts
| | - Jill A Zitzewitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - C R Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.
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48
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Tsuei M, Shivrayan M, Kim YK, Thayumanavan S, Abbott NL. Optical “Blinking” Triggered by Collisions of Single Supramolecular Assemblies of Amphiphilic Molecules with Interfaces of Liquid Crystals. J Am Chem Soc 2020; 142:6139-6148. [DOI: 10.1021/jacs.9b13360] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Michael Tsuei
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Manisha Shivrayan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Young-Ki Kim
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Nicholas L. Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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49
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Giordano D, Boubeta FM, di Prisco G, Estrin DA, Smulevich G, Viappiani C, Verde C. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins. Antioxid Redox Signal 2020; 32:396-411. [PMID: 31578873 DOI: 10.1089/ars.2019.7887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Temperature is one of the most important drivers in shaping protein adaptations. Many biochemical and physiological processes are influenced by temperature. Proteins and enzymes from organisms living at low temperature are less stable in comparison to high-temperature adapted proteins. The lower stability is generally due to greater conformational flexibility. Recent Advances: Adaptive changes in the structure of cold-adapted proteins may occur at subunit interfaces, distant from the active site, thus producing energy changes associated with conformational transitions transmitted to the active site by allosteric modulation, valid also for monomeric proteins in which tertiary structural changes may play an essential role. Critical Issues: Despite efforts, the current experimental and computational methods still fail to produce general principles on protein evolution, since many changes are protein and species dependent. Environmental constraints or other biological cellular signals may override the ancestral information included in the structure of the protein, thus introducing inaccuracy in estimates and predictions on the evolutionary adaptations of proteins in response to cold adaptation. Future Directions: In this review, we describe the studies and approaches used to investigate stability and flexibility in the cold-adapted globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. In fact, future research directions will be prescient on more detailed investigation of cold-adapted proteins and the role of fluctuations between different conformational states.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Fernando Martín Boubeta
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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50
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Coates C, Kerruth S, Helassa N, Török K. Kinetic Mechanisms of Fast Glutamate Sensing by Fluorescent Protein Probes. Biophys J 2019; 118:117-127. [PMID: 31787209 DOI: 10.1016/j.bpj.2019.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/01/2019] [Accepted: 11/11/2019] [Indexed: 01/18/2023] Open
Abstract
We have developed probes based on the bacterial periplasmic glutamate/aspartate binding protein with either an endogenously fluorescent protein or a synthetic fluorophore as the indicator of glutamate binding for studying the kinetic mechanism of glutamate binding. iGluSnFR variants termed iGluh, iGlum, and iGlul cover a broad range of Kd-s (5.8 μM and 2.1 and 50 mM, respectively), and a novel fluorescently labeled indicator, Fl-GluBP, has a Kd of 9.7 μM. The fluorescence response kinetics of all the probes are consistent with a two-step mechanism involving ligand binding and isomerization either of the apo or the ligand-bound binding protein. Although the previously characterized ultrafast indicators iGluu and iGluf had monophasic fluorescence enhancement that occurred in the rate limiting isomerization step, the sensors described here all have biphasic binding kinetics with fluorescence increases occurring both in the glutamate binding and the isomerization steps. For iGlum and iGlul, the data indicate prebinding conformational change followed by ligand binding. In contrast, for iGluh and Fl-GluBP, glutamate binding is followed by isomerization. Thus, the effects of structural heterogeneity introduced by single amino acid changes around the binding site on the kinetic path of interactions with glutamate are revealed. Remarkably, glutamate binding with a diffusion-limited rate constant to iGluh and Fl-GluBP is detected for the first time, hinting at the underlying mechanism of the supremely rapid activation of the highly homologous α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor by glutamate binding.
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Affiliation(s)
- Catherine Coates
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom
| | - Silke Kerruth
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom
| | - Nordine Helassa
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom
| | - Katalin Török
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom.
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