1
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Fischer MS, Rogers HT, Chapman EA, Chan HJ, Krichel B, Gao Z, Larson EJ, Ge Y. Online Mixed-Bed Ion Exchange Chromatography for Native Top-Down Proteomics of Complex Mixtures. J Proteome Res 2024; 23:2315-2322. [PMID: 38913967 PMCID: PMC11344481 DOI: 10.1021/acs.jproteome.4c00430] [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] [Indexed: 06/26/2024]
Abstract
Native top-down mass spectrometry (nTDMS) allows characterization of protein structure and noncovalent interactions with simultaneous sequence mapping and proteoform characterization. The majority of nTDMS studies utilize purified recombinant proteins, with significant challenges hindering application to endogenous systems. To perform native top-down proteomics (nTDP), where endogenous proteins from complex biological systems are analyzed by nTDMS, it is essential to separate proteins under nondenaturing conditions. However, it remains difficult to achieve high resolution with MS-compatible online chromatography while preserving protein tertiary structure and noncovalent interactions. Herein, we report the use of online mixed-bed ion exchange chromatography (IEC) to enable separation of endogenous proteins from complex mixtures under nondenaturing conditions, preserving noncovalent interactions for nTDP analysis. We have successfully detected large proteins (>146 kDa) and identified endogenous metal-binding and oligomeric protein complexes in human heart tissue lysate. The use of a mixed-bed stationary phase allowed retention and elution of proteins over a wide range of isoelectric points without altering the sample or mobile phase pH. Overall, our method provides a simple online IEC-MS platform that can effectively separate proteins from complex mixtures under nondenaturing conditions and preserve higher-order structure for nTDP applications.
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Affiliation(s)
- Matthew S. Fischer
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave, Madison, WI, USA 53706
| | - Holden T. Rogers
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave, Madison, WI, USA 53706
| | - Emily A. Chapman
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave, Madison, WI, USA 53706
| | - Hsin-Ju Chan
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave, Madison, WI, USA 53706
| | - Boris Krichel
- Department of Cell and Regenerative Biology, University of Wisconsin - Madison, 1111 Highland Ave., Madison, WI, USA 53705
- School of Life Sciences, University of Siegen, Adolf-Reichwein Str. 2a, Siegen, Germany, 57076
| | - Zhan Gao
- Department of Cell and Regenerative Biology, University of Wisconsin - Madison, 1111 Highland Ave., Madison, WI, USA 53705
| | - Eli J. Larson
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave, Madison, WI, USA 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave, Madison, WI, USA 53706
- Department of Cell and Regenerative Biology, University of Wisconsin - Madison, 1111 Highland Ave., Madison, WI, USA 53705
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin - 1111 Highland Ave., Madison, WI, USA 53705
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2
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Schanda P, Haran G. NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. Annu Rev Biophys 2024; 53:247-273. [PMID: 38346243 DOI: 10.1146/annurev-biophys-070323-022428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.
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Affiliation(s)
- Paul Schanda
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria;
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel;
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3
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Firouzbakht A, Haider A, Gaalswyk K, Alaeen S, Ghosh K, Gruebele M. HYPK: A marginally disordered protein sensitive to charge decoration. Proc Natl Acad Sci U S A 2024; 121:e2316408121. [PMID: 38657047 PMCID: PMC11067017 DOI: 10.1073/pnas.2316408121] [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: 09/20/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky's charge-hydropathy plot may behave as "marginal IDPs" and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK) near that boundary as a candidate; PKIα, also near that boundary, has lower secondary structure propensity; and Crk1, just across the boundary on the folded side, has higher secondary structure propensity. We used a qualitative Förster resonance energy transfer-based assay together with circular dichroism to simultaneously probe global and local conformation. HYPK shows several unique features indicating marginality: a cooperative transition in end-to-end distance with temperature, like Crk1 and folded proteins, but unlike PKIα; enhanced secondary structure upon crowding, in contrast to Crk1 and PKIα; and a cross-over from salt-induced expansion to compaction at high temperature, likely due to a structure-to-disorder transition not seen in Crk1 and PKIα. We then tested HYPK's sensitivity to charge patterning by designing charge-flipped variants including two specific sequences with identical amino acid composition that markedly differ in their predicted size and response to salt. The experimentally observed trends, also including mutants of PKIα, verify the predictions from sequence charge decoration metrics. Marginal proteins like HYPK show features of both folded and disordered proteins that make them sensitive to physicochemical perturbations and structural control by charge patterning.
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Affiliation(s)
- Arash Firouzbakht
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, Denver, CO80210
| | - Kari Gaalswyk
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Sepehr Alaeen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Department of Physics, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Carle-Illinois College of Medicine, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
- Center for Advanced Study, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
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4
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Cheng P, Zhao C, Pan Q, Xiong Z, Chen Q, Miao X, He Y. Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown. SENSORS (BASEL, SWITZERLAND) 2024; 24:2420. [PMID: 38676038 PMCID: PMC11053845 DOI: 10.3390/s24082420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.
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Affiliation(s)
| | | | | | | | - Qi Chen
- Hubei Yangtze Memory Laboratories, School of Integrated Circuit, Huazhong University of Science and Technology, Wuhan 430074, China
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5
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. J Chem Theory Comput 2024; 20:1398-1413. [PMID: 38241144 DOI: 10.1021/acs.jctc.3c00833] [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: 01/21/2024]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
- Department of Physics, The University of Texas at Austin, 2515 Speedway, Austin 78712, Texas, United States
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6
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Pennington H, Birtles D, Shi ZW, Lee J. A Salt Bridge and Disulfide Bond within the Lassa Virus Fusion Domain Are Required for the Initiation of Membrane Fusion. ACS OMEGA 2024; 9:4920-4930. [PMID: 38313535 PMCID: PMC10831964 DOI: 10.1021/acsomega.3c08632] [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: 10/31/2023] [Revised: 12/13/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
Infection with Lassa virus (LASV), an Old-World arenavirus that is endemic to West Africa, causes Lassa fever, a lethal hemorrhagic fever. Delivery of LASV's genetic material into the host cell is an integral component of its lifecycle. This is accomplished via membrane fusion, a process initiated by a hydrophobic sequence known as the fusion domain (FD). The LASV FD (G260-N295) consists of two structurally distinct regions: an N-terminal fusion peptide (FP: G260-T274) and an internal fusion loop (FL: C279-N295) that is connected by a short linker region (P275-Y278). However, the molecular mechanisms behind how the LASV FD initiates fusion remain unclear. Here, we demonstrate that the LASV FD adopts a fusogenic, helical conformation at a pH akin to that of the lysosomal compartment. Additionally, we identified a conserved disulfide bond (C279 and C292) and salt bridge (R282 and E289) within the FL that are pertinent to fusion. We found that the disulfide bond must be present so that the FD can bind to the lipid bilayer and subsequently initiate fusion. Moreover, the salt bridge is essential for the secondary structure of the FD such that it can associate with the lipid bilayer in the proper orientation for full functionality. In conclusion, our findings indicate that the LASV FD preferentially initiates fusion at a pH akin to that of the lysosome through a mechanism that requires a conserved salt bridge and, to a lesser extent, an intact disulfide bond within the internal FL.
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Affiliation(s)
- Hallie
N. Pennington
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
| | - Daniel Birtles
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
| | - Zoe W. Shi
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
| | - Jinwoo Lee
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
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7
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Nepal S, Holmstrom ED. Single-molecule-binding studies of antivirals targeting the hepatitis C virus core protein. J Virol 2023; 97:e0089223. [PMID: 37772835 PMCID: PMC10617558 DOI: 10.1128/jvi.00892-23] [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: 06/14/2023] [Accepted: 08/10/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE The hepatitis C virus is associated with nearly 300,000 deaths annually. At the core of the virus is an RNA-protein complex called the nucleocapsid, which consists of the viral genome and many copies of the core protein. Because the assembly of the nucleocapsid is a critical step in viral replication, a considerable amount of effort has been devoted to identifying antiviral therapeutics that can bind to the core protein and disrupt assembly. Although several candidates have been identified, little is known about how they interact with the core protein or how those interactions alter the structure and thus the function of this viral protein. Our work biochemically characterizes several of these binding interactions, highlighting both similarities and differences as well as strengths and weaknesses. These insights bolster the notion that this viral protein is a viable target for novel therapeutics and will help to guide future developments of these candidate antivirals.
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Affiliation(s)
- Sudip Nepal
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Erik D. Holmstrom
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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8
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544064. [PMID: 37333386 PMCID: PMC10274755 DOI: 10.1101/2023.06.07.544064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a dataset of high-resolution crystal structures. The only parameter in COFFEE is the strength (λ D N A P R O ) of the DNA-protein contact potential. For an optimal choice of λ D N A P R O , the crystallographic B-factors for DNA-protein complexes, with varying sizes and topologies, are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts the scattering profiles that are in quantitative agreement with SAXS experiments as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which does not alter the balance of electrostatic interactions, but affects chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway,Austin TX 78712, USA
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9
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Sun S, Zhang K, Wang Y, Zhou Z, Wang L, Zhao H, Zhang Y. Pharmacodynamic structure of deer antler base protein and its mammary gland hyperplasia inhibition mechanism by mediating Raf-1/MEK/ERK signaling pathway activation. Food Funct 2023; 14:3319-3331. [PMID: 36939833 DOI: 10.1039/d2fo03568e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Mammary gland hyperplasia (MGH) is a common mammary disease whose main pathogenesis is the disruption of estradiol (E2) and progesterone (P) secretion, thereby causing overproliferation of mammary epithelial cells and mammary gland tissue hyperplasia. Deer antler base is a traditional Chinese medicine that has been used for many years to treat MGH. However, its pharmacological mechanism and pharmacodynamic material basis are unclear. In this study, we for the first time used the graded salting method to classify deer antler base protein (CNCP) as CNCP-A, CNCP-B, and CNCP-C and explored the pharmacological mechanism of the anti-MGH properties of CNCP. We found that CNCP could regulate the hormonal levels of E2, P, and follicle stimulating hormone (FSH) and improve the histopathological condition. The potential mechanism might be related to the recombinant C-Raf proto oncogene serine/threonine protein kinase/mitogen-activated protein/extracellular regulated protein kinase (Raf-1/MEK/ERK) signaling pathway. By upregulating the protein expression of the follicle stimulating hormone receptor (FSHR), cyclic adenosine monophosphate (cAMP) and protein kinase A (PKA) inhibited the activation of the downstream Raf-1/MEK/ERK signaling pathway, which in turn inhibited the proliferation of mammary epithelial cells. We analyzed the physicochemical properties of CNCP-A, CNCP-B, and CNCP-C and obtained CNCP-C-I by column chromatographic purification of the best pharmacophore protein CNCP. Using high-performance liquid gel filtration chromatography (HPGFC), we determined the molecular weight of CNCP-C-I and identified it by high-performance liquid tandem mass spectrometry (LC-MS/MS) to obtain the first match for a high confidence protein KRT1. This study provides a theoretical basis for the development of effective traditional Chinese medicines with low toxicity levels for the prevention and treatment of mammary gland diseases.
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Affiliation(s)
- Shiqing Sun
- College of Pharmacy, Jiamusi University, Jiamusi, 154007 Heilongjiang, P. R. China.
| | - Kai Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, 154007 Heilongjiang, P. R. China.
| | - Yuliang Wang
- College of Pharmacy, Jiamusi University, Jiamusi, 154007 Heilongjiang, P. R. China.
| | - Zijun Zhou
- College of Pharmacy, Jiamusi University, Jiamusi, 154007 Heilongjiang, P. R. China.
| | - Lihong Wang
- College of Pharmacy, Jiamusi University, Jiamusi, 154007 Heilongjiang, P. R. China.
| | - Hong Zhao
- College of Pharmacy, Jiamusi University, Jiamusi, 154007 Heilongjiang, P. R. China.
| | - Yu Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, 154007 Heilongjiang, P. R. China.
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10
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Zeng J, Zhang Y, Huang C, Li L, Zhu B, Chen D. Detection of simple proteins by direct surface-enhanced Raman scattering based on the Hofmeister ion-specific effect. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 289:122235. [PMID: 36535223 DOI: 10.1016/j.saa.2022.122235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/13/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Surface-enhanced Raman scattering (SERS) spectroscopy has unique advantages in detecting biomolecules, but label-free determination of proteins with low scattering cross-sections remains challenging. In this study, such proteins' SERS signals have been optimized using the Hofmeister effect between protein molecules and CsI solution at physiological concentrations (A 100 mmol/L Cesium iodide, CsI). Cs+ as chaotro cation ion has a complex interaction mechanism with protein, can not only deprive hydrated water molecules on the surface of protein but also penetrate into the hydrophobic interior of protein. In addition to the above advantages, I- in excess CsI solution with appropriate concentration can removes the interference of citric acid-based impurities on the surface of silver nanoparticles, and Cs+ in excess CsI solution attracts the aggregation of negatively charged silver nanoparticles and cause local electromagnetic field enhancement to achieve high sensitivity in protein detection. This has been combined with principal component analysis to perform a comprehensive analysis of several proteins. Molecular dynamics simulations have been performed to study the mechanism of interaction between CsI and proteins. In addition, the vibrational peak of water has been used as an internal standard to quantify the protein content, and a good linear relationship between peak intensity and concentration was obtained.
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Affiliation(s)
- Jiayu Zeng
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University, Guiyang 550025, China
| | - Yufeng Zhang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University, Guiyang 550025, China
| | - Chao Huang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University, Guiyang 550025, China
| | - Longjiang Li
- Mining College of Guizhou University, Guiyang 550025, China
| | - Bixue Zhu
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University, Guiyang 550025, China
| | - Dongmei Chen
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University, Guiyang 550025, China.
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11
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Cheng S, Tan F, Wu X, Dong F, Liu J, Wang Y, Zhao H. Influences of protein-corona on stability and aggregation kinetics of Ti 3C 2T x nanosheets in aquatic environment. ENVIRONMENTAL RESEARCH 2023; 219:115131. [PMID: 36565845 DOI: 10.1016/j.envres.2022.115131] [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: 11/14/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Proteins existed in aquatic environments strongly influence the transport, fate of nanomaterials due to the formation of protein-corona surrounding nanomaterials. To date, how do proteins affect the aggregation behaviors of MXene, a new family of two-dimensional materials, in aquatic environment remains unknown. Here the aggregation kinetics of MXene Ti3C2Tx nanosheets in various electrolytes (NaCl, CaCl2 and Na2SO4) was investigated by time-resolved dynamic light scattering in absence or presence of bovine serum albumin (BSA). Results showed that BSA affected the aggregation of Ti3C2Tx in a concentration-dependent manner. Addition of 3 mg/L BSA decreased the critical coagulation concentrations (CCCs) of Ti3C2Tx about 1.6-2.1 times, showing obvious destabilization effect; while BSA greater than 30 mg/L created a high-protein environment covering Ti3C2Tx, producing high spatial repulsion and enhancing the dispersibility of Ti3C2Tx. Ca2+ ions have greater effect on the aggregation of Ti3C2Tx due to the larger surface charge and bridging effect. The interaction between Ti3C2Tx and BSA followed Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, and mainly attributed to hydrogen bonding and van der Waals forces, while positively charged lysine and arginine in BSA might attract onto Ti3C2Tx through electrostatic attraction. The interaction decreased the content of α-helix structure in BSA from 74.7% to 53.1%. Ti3C2Tx easily suffered from aggregation and their long-distance transport seemed impossible in synthetic or natural waters. The present findings provided new insights for understanding the transfer and fate of this nanomaterial in aquatic environments.
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Affiliation(s)
- Shizhu Cheng
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Feng Tan
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Xuri Wu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Fan Dong
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jinghua Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yan Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Hongxia Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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12
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Chau C, Marcuccio F, Soulias D, Edwards MA, Tuplin A, Radford SE, Hewitt E, Actis P. Probing RNA Conformations Using a Polymer-Electrolyte Solid-State Nanopore. ACS NANO 2022; 16:20075-20085. [PMID: 36279181 PMCID: PMC9798860 DOI: 10.1021/acsnano.2c08312] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single-molecule resolution. The conformation of biomolecules, such as RNA, is highly dependent on the electrolyte composition, but solid-state nanopore systems often require high salt concentration to operate, precluding analysis of macromolecular conformations under physiologically relevant conditions. Here, we report the implementation of a polymer-electrolyte solid-state nanopore system based on alkali metal halide salts dissolved in 50% w/v poly(ethylene) glycol (PEG) to augment the performance of our system. We show that polymer-electrolyte bath governs the translocation dynamics of the analyte which correlates with the physical properties of the salt used in the bath. This allowed us to identify CsBr as the optimal salt to complement PEG to generate the largest signal enhancement. Harnessing the effects of the polymer-electrolyte, we probed the conformations of the Chikungunya virus (CHIKV) RNA genome fragments under physiologically relevant conditions. Our system was able to fingerprint CHIKV RNA fragments ranging from ∼300 to ∼2000 nt length and subsequently distinguish conformations between the co-transcriptionally folded and the natively refolded ∼2000 nt CHIKV RNA. We envision that the polymer-electrolyte solid-state nanopore system will further enable structural and conformational analyses of individual biomolecules under physiologically relevant conditions.
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Affiliation(s)
- Chalmers Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Dimitrios Soulias
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Martin Andrew Edwards
- Department
of Chemistry & Biochemistry, University
of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Andrew Tuplin
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
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13
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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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14
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Prabhu GRD, Yang TH, Shiu RT, Witek HA, Urban PL. Scanning pH-metry for Observing Reversibility in Protein Folding. Biochemistry 2022; 61:2377-2389. [PMID: 36251331 DOI: 10.1021/acs.biochem.2c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the main factors affecting protein structure in solution is pH. Traditionally, to study pH-dependent conformational changes in proteins, the concentration of the H+ ions is adjusted manually, complicating real-time analyses, hampering dynamic pH regulation, and consequently leading to a limited number of tested pH levels. Here, we present a programmable device, a scanning pH-meter, that can automatically generate different types of pH ramps and waveforms in a solution. A feedback loop algorithm calculates the required flow rates of the acid/base titrants, allowing one, for example, to generate periodic pH sine waveforms to study the reversibility of protein folding by fluorescence spectroscopy. Interestingly, for some proteins, the fluorescence intensity profiles recorded in such a periodically oscillating pH environment display hysteretic behavior indicating an asymmetry in the sequence of the protein unfolding/refolding events, which can most likely be attributed to their distinct kinetics. Another useful application of the scanning pH-meter concerns coupling it with an electrospray ionization mass spectrometer to observe pH-induced structural changes in proteins as revealed by their varying charge-state distributions. We anticipate a broad range of applications of the scanning pH-meter developed here, including protein folding studies, determination of the optimum pH for achieving maximum fluorescence intensity, and characterization of fluorescent dyes and other synthetic materials.
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Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu300093, Taiwan
| | - Tzu-Hsin Yang
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
| | - Ruei-Tzung Shiu
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
| | - Henryk A Witek
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu300093, Taiwan
- Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu300093, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
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15
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Maity H, Baidya L, Reddy G. Salt-Induced Transitions in the Conformational Ensembles of Intrinsically Disordered Proteins. J Phys Chem B 2022; 126:5959-5971. [PMID: 35944496 DOI: 10.1021/acs.jpcb.2c03476] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Salts modulate the behavior of intrinsically disordered proteins (IDPs) and influence the formation of membraneless organelles through liquid-liquid phase separation (LLPS). In low ionic strength solutions, IDP conformations are perturbed by the screening of electrostatic interactions, independent of the salt identity. In this regime, insight into the IDP behavior can be obtained using the theory for salt-induced transitions in charged polymers. However, salt-specific interactions with the charged and uncharged residues, known as the Hofmeister effect, influence IDP behavior in high ionic strength solutions. There is a lack of reliable theoretical models in high salt concentration regimes to predict the salt effect on IDPs. We propose a simulation methodology using a coarse-grained IDP model and experimentally measured water to salt solution transfer free energies of various chemical groups that allowed us to study the salt-specific transitions induced in the IDPs conformational ensemble. We probed the effect of three different monovalent salts on five IDPs belonging to various polymer classes based on charged residue content. We demonstrate that all of the IDPs of different polymer classes behave as self-avoiding walks (SAWs) at physiological salt concentration. In high salt concentrations, the transitions observed in the IDP conformational ensembles are dependent on the salt used and the IDP sequence and composition. Changing the anion with the cation fixed can result in the IDP transition from a SAW-like behavior to a collapsed globule. An important implication of these results is that a suitable salt can be identified to induce condensation of an IDP through LLPS.
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Affiliation(s)
- Hiranmay Maity
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
| | - Lipika Baidya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
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16
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Rahman T, Petrus E, Segado M, Martin NP, Palys LN, Rambaran MA, Ohlin CA, Bo C, Nyman M. Predicting the Solubility of Inorganic Ion Pairs in Water. Angew Chem Int Ed Engl 2022; 61:e202117839. [DOI: 10.1002/anie.202117839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Tasnim Rahman
- Department of Chemistry Oregon State University Corvallis OR 97331 USA
| | - Enric Petrus
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science & Technology (BIST) Av. Països Catalans 16 43007 Tarragona Spain
| | - Mireia Segado
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science & Technology (BIST) Av. Països Catalans 16 43007 Tarragona Spain
| | - Nicolas P. Martin
- Department of Chemistry Oregon State University Corvallis OR 97331 USA
| | - Lauren N. Palys
- Department of Chemistry Oregon State University Corvallis OR 97331 USA
| | - Mark A. Rambaran
- Department of Chemistry Faculty of Science and Technology Umeå University 901 87 Umeå Sweden
| | - C. Andre Ohlin
- Department of Chemistry Faculty of Science and Technology Umeå University 901 87 Umeå Sweden
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science & Technology (BIST) Av. Països Catalans 16 43007 Tarragona Spain
- Departament de Química Física i Inorgànica Universitat Rovira i Virgili (URV) Marcel lí Domingo s/n 43007 Tarragona Spain
| | - May Nyman
- Department of Chemistry Oregon State University Corvallis OR 97331 USA
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17
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Lavagnini E, Cook JL, Warren PB, Hunter CA. Systematic Parameterization of Ion-Surfactant Interactions in Dissipative Particle Dynamics Using Setschenow Coefficients. J Phys Chem B 2022; 126:2308-2315. [PMID: 35290050 PMCID: PMC9098171 DOI: 10.1021/acs.jpcb.2c00101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Dissipative
particle dynamics (DPD) simulations of nonionic surfactants
with an added salt show that the Setschenow relationship is reproduced;
that is, the critical micelle concentration is log-linearly dependent
on the added salt concentration. The simulated Setschenow coefficients
depend on the DPD bead–bead repulsion amplitudes, and matching
to the experimentally determined values provides a systematic method
to parameterize the interactions between salt ion beads and surfactant
beads. The optimized ion-specific interaction parameters appear to
be transferrable and follow the same trends as the empirical Hofmeister
series.
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Affiliation(s)
- Ennio Lavagnini
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Joanne L Cook
- Unilever R&D Port Sunlight, Quarry Road East, Bebington CH63 3JW, U.K
| | - Patrick B Warren
- Unilever R&D Port Sunlight, Quarry Road East, Bebington CH63 3JW, U.K.,STFC Hartree Centre, Sci-Tech Daresbury, Warrington WA4 4AD, U.K
| | - Christopher A Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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18
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Han Q, Brown SJ, Drummond CJ, Greaves TL. Protein aggregation and crystallization with ionic liquids: Insights into the influence of solvent properties. J Colloid Interface Sci 2022; 608:1173-1190. [PMID: 34735853 DOI: 10.1016/j.jcis.2021.10.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
Ionic liquids (ILs) have been used in solvents for proteins in many applications, including biotechnology, pharmaceutics, and medicine due to their tunable physicochemical and biological properties. Protein aggregation is often undesirable, and predominantly occurs during bioprocesses, while the aggregation process can be reversible or irreversible and the aggregates formed can be native/non-native and soluble/insoluble. Recent studies have clearly identified key properties of ILs and IL-water mixtures related to protein performance, suggesting the use of the tailorable properties of ILs to inhibit protein aggregation, to promote protein crystallization, and to control protein aggregation pathways. This review discusses the critical properties of IL and IL-water mixtures and presents the latest understanding of the protein aggregation pathways and the development of IL systems that affect or control the protein aggregation process. Through this feature article, we hope to inspire further advances in understanding and new approaches to controlling protein behavior to optimize bioprocesses.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Stuart J Brown
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
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19
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Rahman T, Petrus E, Segado M, Martin N, Palys L, Rambaran MA, Ohlin CA, Bo C, Nyman M. Predicting solubility of ion pairs in aqueous inorganic chemistry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tasnim Rahman
- Oregon State University Department of Chemistry UNITED STATES
| | - Enric Petrus
- ICIQ: Institut Catala d'Investigacio Quimica Chemistry SPAIN
| | - Mireia Segado
- ICIQ: Institut Catala d'Investigacio Quimica Chemistry SPAIN
| | - Nicolas Martin
- Oregon State University Department of Chemistry chemistry UNITED STATES
| | - Lauren Palys
- Oregon State University Department of Chemistry Chemistry UNITED STATES
| | | | | | - Carles Bo
- ICIQ: Institut Catala d'Investigacio Quimica Chemistry SPAIN
| | - May Nyman
- Oregon State University Department of Chemistry 153 Gilbert Hall 97331-4003 Corvallis UNITED STATES
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20
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Laurent H, Baker DL, Soper AK, Ries ME, Dougan L. Bridging Structure, Dynamics, and Thermodynamics: An Example Study on Aqueous Potassium Halides. J Phys Chem B 2021; 125:12774-12786. [PMID: 34757756 DOI: 10.1021/acs.jpcb.1c06728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous salt systems are ubiquitous in all areas of life. The ions in these solutions impose important structural and dynamic perturbations to water. In this study, we employ a combined neutron scattering, nuclear magnetic resonance, and computational modeling approach to deconstruct ion-specific perturbations to water structure and dynamics and shed light on the molecular origins of bulk thermodynamic properties of the solutions. Our approach uses the atomistic scale resolution offered to us by neutron scattering and computational modeling to investigate how the properties of particular short-ranged microenvironments within aqueous systems can be related to bulk properties of the system. We find that by considering only the water molecules in the first hydration shell of the ions that the enthalpy of hydration can be determined. We also quantify the range over which ions perturb water structure by calculating the average enthalpic interaction between a central halide anion and the surrounding water molecules as a function of distance and find that the favorable anion-water enthalpic interactions only extend to ∼4 Å. We further validate this by showing that ions induce structure in their solvating water molecules by examining the distribution of dipole angles in the first hydration shell of the ions but that this perturbation does not extend into the bulk water. We then use these structural findings to justify mathematical models that allow us to examine perturbations to rotational and diffusive dynamics in the first hydration shell around the potassium halide ions from NMR measurements. This shows that as one moves down the halide series from fluorine to iodine, and ionic charge density is therefore reduced, that the enthalpy of hydration becomes less negative. The first hydration shell also becomes less well structured, and rotational and diffusive motions of the hydrating water molecules are increased. This reduction in structure and increase in dynamics are likely the origin of the previously observed increased entropy of hydration as one moves down the halide series. These results also suggest that simple monovalent potassium halide ions induce mostly local perturbations to water structure and dynamics.
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Affiliation(s)
- Harrison Laurent
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Daniel L Baker
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Alan K Soper
- ISIS Facility, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K
| | - Michael E Ries
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Lorna Dougan
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K.,Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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21
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Catalini S, Rossi B, Tortora M, Foggi P, Gessini A, Masciovecchio C, Bruni F. Hydrogen Bonding and Solvation of a Proline-Based Peptide Model in Salt Solutions. Life (Basel) 2021; 11:824. [PMID: 34440568 PMCID: PMC8400059 DOI: 10.3390/life11080824] [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: 07/26/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The hydrogen bonding of water and water/salt mixtures around the proline-based tripeptide model glycyl-l-prolyl-glycinamide·HCl (GPG-NH2) is investigated here by multi-wavelength UV resonance Raman spectroscopy (UVRR) to clarify the role of ion-peptide interactions in affecting the conformational stability of this peptide. The unique sensitivity and selectivity of the UVRR technique allow us to efficiently probe the hydrogen bond interaction between water molecules and proline residues in different solvation conditions, along with its influence on trans to cis isomerism in the hydrated tripeptide. The spectroscopic data suggest a relevant role played by the cations in altering the solvation shell at the carbonyl site of proline., while the fluoride and chloride anions were found to promote the establishment of the strongest interactions on the C=O site of proline. This latter effect is reflected in the greater stabilization of the trans conformers of the tripeptide in the presence of these specific ions. The molecular view provided by UVRR experiments was complemented by the results of circular dichroism (CD) measurements that show a strong structural stabilizing effect on the β-turn motif of GPG-NH2 observed in the presence of KF as a co-solute.
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Affiliation(s)
- Sara Catalini
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Mariagrazia Tortora
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
- Area Science Park, Padriciano, 99, 34149 Trieste, Italy
| | - Paolo Foggi
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Fabio Bruni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale, 84, 00146 Roma, Italy;
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22
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Borrelli MA, Turnquist HR, Little SR. Biologics and their delivery systems: Trends in myocardial infarction. Adv Drug Deliv Rev 2021; 173:181-215. [PMID: 33775706 PMCID: PMC8178247 DOI: 10.1016/j.addr.2021.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/14/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023]
Abstract
Cardiovascular disease is the leading cause of death around the world, in which myocardial infarction (MI) is a precipitating event. However, current therapies do not adequately address the multiple dysregulated systems following MI. Consequently, recent studies have developed novel biologic delivery systems to more effectively address these maladies. This review utilizes a scientometric summary of the recent literature to identify trends among biologic delivery systems designed to treat MI. Emphasis is placed on sustained or targeted release of biologics (e.g. growth factors, nucleic acids, stem cells, chemokines) from common delivery systems (e.g. microparticles, nanocarriers, injectable hydrogels, implantable patches). We also evaluate biologic delivery system trends in the entire regenerative medicine field to identify emerging approaches that may translate to the treatment of MI. Future developments include immune system targeting through soluble factor or chemokine delivery, and the development of advanced delivery systems that facilitate the synergistic delivery of biologics.
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Affiliation(s)
- Matthew A Borrelli
- Department of Chemical Engineering, University of Pittsburgh, 940 Benedum Hall, 3700 O'Hara Street, Pittsburgh, PA 15213, USA.
| | - Heth R Turnquist
- Starzl Transplantation Institute, 200 Darragh St, Pittsburgh, PA 15213, USA; Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Department of Immunology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15213, USA.
| | - Steven R Little
- Department of Chemical Engineering, University of Pittsburgh, 940 Benedum Hall, 3700 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Bioengineering, University of Pittsburgh, 302 Benedum Hall, 3700 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Clinical and Translational Science, University of Pittsburgh, Forbes Tower, Suite 7057, Pittsburgh, PA 15213, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219, USA; Department of Immunology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15213, USA; Department of Pharmaceutical Science, University of Pittsburgh, 3501 Terrace Street, Pittsburgh, PA 15213, USA; Department of Ophthalmology, University of Pittsburgh, 203 Lothrop Street, Pittsburgh, PA 15213, USA.
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23
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The high stability of the three-helix bundle UBA domain of p62 protein as revealed by molecular dynamics simulations. J Mol Model 2021; 27:102. [PMID: 33665744 DOI: 10.1007/s00894-021-04698-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
The ubiquitin-associated (UBA) domain is an important motif in the modulation of many molecular functionalities. It has been mainly associated with ubiquitin-mediated proteolysis, a multistep mechanism in which undesirable proteins are tagged with polyubiquitin chains for degradation in the proteasome complex. Comparison among UBA domains reveals a quite small structural variability, displaying an overall fold with a tightly packed three-helix bundle, and a common conserved hydrophobic patch on their surface that is important for ubiquitin binding. Mutations in the UBA domain, mainly in the highly conserved hydrophobic patch, induce conformational instabilities, which can be related to weak affinity for ubiquitin. This raises the question whether such hydrophobic patch presents conserved structural arrangement for selective recognition and protein binding. A concern that led us to investigate the stability of the p62-UBA domain as a case study regarding its structural arrangement as a function of temperature and two NaCl concentrations. Our results reveal that the temperature range and ionic strengths considered in this work produced a negligible effect on the three-helix bundle fold of p62-UBA domain.
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24
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Mohajeri S, Burke-Kleinman J, Maurice DH, Amsden BG. Formulation parameters governing sustained protein delivery from degradable viscous liquid aliphatic polycarbonates. Int J Pharm 2020; 590:119965. [PMID: 33045320 DOI: 10.1016/j.ijpharm.2020.119965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022]
Abstract
Viscous liquid degradable polymers have advantages as drug depots for sustained protein delivery. We have created a new aliphatic polycarbonate for this purpose, poly(trimethylene carbonate-co-5-hydroxy trimethylene carbonate), which upon degradation retains a near neutral micro-environmental pH. As such, this copolymer is highly suited to the delivery of acid sensitive proteins. We show that the mechanism of protein release from this liquid copolymer is consistent with the formation of super-hydrated regions as a result of the osmotic activity of the solution formed upon distributed protein particle dissolution. Protein release can be manipulated by controlling polymer hydrophobicity which can be adjusted by molecular weight and choice of initiator. Moreover, protein release is highly dependent on protein solubility which impacts the osmotic activity of the solution formed upon dissolution of the protein particles while protein molecular size and isoelectric point are not as influential. As demonstrated by the release of highly bioactive vascular endothelial growth factor, formulations of this copolymer are suitable for prolonged delivery of protein therapeutics.
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Affiliation(s)
- Sara Mohajeri
- Department of Chemical Engineering, Queen's University, Kingston, Ontario K7L 3N6, Canada; Human Mobility Research Centre, Kingston General Hospital, Kingston, Ontario K7L 2V7, Canada
| | - Jonah Burke-Kleinman
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Donald H Maurice
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Brian G Amsden
- Department of Chemical Engineering, Queen's University, Kingston, Ontario K7L 3N6, Canada; Human Mobility Research Centre, Kingston General Hospital, Kingston, Ontario K7L 2V7, Canada.
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A chemometric investigation on the influence of the nature and concentration of supporting electrolyte on charging currents in electrochemistry. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Cosolvent effects on the growth of amyloid fibrils. Curr Opin Struct Biol 2020; 60:101-109. [DOI: 10.1016/j.sbi.2019.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/08/2019] [Accepted: 12/16/2019] [Indexed: 02/05/2023]
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Ji S, Ahn DU, Zhao Y, Li K, Li S, Huang X. An easy and rapid separation method for five major proteins from egg white: Successive extraction and MALDI-TOF-MS identification. Food Chem 2020; 315:126207. [PMID: 31991252 DOI: 10.1016/j.foodchem.2020.126207] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 01/02/2020] [Accepted: 01/11/2020] [Indexed: 12/23/2022]
Abstract
Five major proteins from egg white were separated using a successive extraction/precipitation protocol. The yield and purity of the separated proteins were measured. The separated proteins were confirmed by MALDI-TOF-MS, and their structures were characterized by CD spectrum. Lysozyme was first separated using FPC 3500 resin and then ovomucin from the lysozyme-free egg white. Ammonium sulfate and citric acid were added to the resulting lysozyme- and ovomucin-free egg white solution to precipitate ovotransferrin. Ovomucoid and ovalbumin were separated from the resulting supernatant using ethanol. The separated proteins were further purified and the optimal conditions for the further purifications were suggested. The purity and yield of lysozyme, ovotransferrin, ovalbumin, and ovomucoid were higher than 90% and 77%, while those of ovomucin were about 72% and 75%, respectively. This study separated five major proteins in egg white successively using resin adsorption, pH adjustment, salt/ethanol precipitation, and ultrafiltration.
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Affiliation(s)
- Shengnan Ji
- National Research and Development Centre for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Dong Uk Ahn
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Yunlong Zhao
- National Research and Development Centre for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Kai Li
- National Research and Development Centre for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Shugang Li
- Hubei University of Technology, Wuhan, Hubei 430070, PR China
| | - Xi Huang
- National Research and Development Centre for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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Mazal H, Haran G. Single-molecule FRET methods to study the dynamics of proteins at work. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019; 12:8-17. [PMID: 31989063 PMCID: PMC6984960 DOI: 10.1016/j.cobme.2019.08.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Feynman commented that "Everything that living things do can be understood in terms of the jiggling and wiggling of atoms". Proteins can jiggle and wiggle large structural elements such as domains and subunits as part of their functional cycles. Single-molecule fluorescence resonance energy transfer (smFRET) is an excellent tool to study conformational dynamics and decipher coordinated large-scale motions within proteins. smFRET methods introduced in recent years are geared toward understanding the time scales and amplitudes of function-related motions. This review discusses the methodology for obtaining and analyzing smFRET temporal trajectories that provide direct dynamic information on transitions between conformational states. It also introduces correlation methods that are useful for characterizing intramolecular motions. This arsenal of techniques has been used to study multiple molecular systems, from membrane proteins through molecular chaperones, and we examine some of these studies here. Recent exciting methodological novelties permit revealing very fast, submillisecond dynamics, whose relevance to protein function is yet to be fully grasped.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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Muttathukattil AN, Srinivasan S, Halder A, Reddy G. Role of Guanidinium-Carboxylate Ion Interaction in Enzyme Inhibition with Implications for Drug Design. J Phys Chem B 2019; 123:9302-9311. [DOI: 10.1021/acs.jpcb.9b06130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Aswathy N. Muttathukattil
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sriraksha Srinivasan
- Department of Chemistry, St. Joseph’s College, Bangalore, Karnataka 560027, India
| | - Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Konar M, Sahoo H. Phosphate and sulphate-mediated structure and stability of bone morphogenetic protein - 2 (BMP - 2): A spectroscopy enabled investigation. Int J Biol Macromol 2019; 135:1123-1133. [DOI: 10.1016/j.ijbiomac.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 01/20/2023]
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