1
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Zhao J, Yu P, Dong T, Wu Y, Yang F, Wang J. Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy. Commun Chem 2024; 7:82. [PMID: 38605209 PMCID: PMC11009226 DOI: 10.1038/s42004-024-01170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.
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Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tiantian Dong
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanzhou Wu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Yang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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High Throughput Proteomic Exploration of Hypothermic Preservation Reveals Active Processes within the Cell Associated with Cold Ischemia Kinetic. Int J Mol Sci 2021; 22:ijms22052384. [PMID: 33673561 PMCID: PMC7956856 DOI: 10.3390/ijms22052384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/28/2022] Open
Abstract
The demand for organs to be transplanted increases pressure on procurement centers, to the detriment of organ quality, increasing complications. New preservation protocols are urgently needed, requiring an in-depth understanding of ischemia-reperfusion mechanisms. We performed a proteomic analysis using LC-MS/MS-TOF data analyzed through R software and Cytoscape's ClueGO application, comparing the proteome of kidney endothelial cells, key cell type, subjected to 3, 6, 12, 19, and 24 h of cold ischemia and 6 h reperfusion. Critical pathways such as energy metabolism, cytoskeleton structure/transport system, and gene transcription/translation were modulated. Important time windows were revealed: a-during the first 3 h, central proteins were upregulated within these pathways; b-the majority of these upregulations were maintained until 12 h cold ischemia time (CIT); c-after that time, the overall decrease in protein expression was observed; d-at reperfusion, proteins expressed in response to cold ischemia were all downregulated. This shows that cold ischemia is not a simple slowing down of metabolism, as deep changes take place within the proteome on major pathways. Time-sensitive expression of key protein reveals possible quality biomarkers as well as potential targets for new strategies to maintain or optimize organ quality.
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3
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Destabilisation of the structure of transthyretin is driven by Ca 2. Int J Biol Macromol 2020; 166:409-423. [PMID: 33129902 DOI: 10.1016/j.ijbiomac.2020.10.199] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/08/2020] [Accepted: 10/24/2020] [Indexed: 12/19/2022]
Abstract
Tetrameric transthyretin (TTR) transports thyroid hormones and retinol in plasma and cerebrospinal fluid and performs protective functions under stress conditions. Ageing and mutations result in TTR destabilisation and the formation of the amyloid deposits that dysregulate Ca2+ homeostasis. Our aim was to determine whether Ca2+ affects the structural stability of TTR. We show, using multiple techniques, that Ca2+ does not induce prevalent TTR dissociation and/or oligomerisation. However, in the presence of Ca2+, TTR exhibits altered conformational flexibility and different interactions with the solvent molecules. These structural changes lead to the formation of the sub-populations of non-native TTR conformers and to the destabilisation of the structure of TTR. Moreover, the sub-population of TTR molecules undergoes fragmentation that is augmented by Ca2+. We postulate that Ca2+ constitutes the structural and functional switch between the native and non-native forms of TTR, and therefore tip the balance towards age-dependent pathological calcification.
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4
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Pang WC, Ramli ANM, Hamid AAA. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 2020; 26:142. [PMID: 32417971 DOI: 10.1007/s00894-020-04398-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/28/2020] [Indexed: 12/25/2022]
Abstract
Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
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Affiliation(s)
- Wei Cheng Pang
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia. .,Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
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5
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Nephomnyshy I, Rosen-Kligvasser J, Davidovich-Pinhas M. The development of a direct approach to formulate high oil content zein-based emulsion gels using moderate temperatures. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2019.105528] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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6
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Daudey G, Schwieger C, Rabe M, Kros A. Influence of Membrane-Fusogen Distance on the Secondary Structure of Fusogenic Coiled Coil Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5501-5508. [PMID: 30908063 PMCID: PMC6484379 DOI: 10.1021/acs.langmuir.8b04195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Liposomal membrane fusion is an important tool to study complex biological fusion mechanisms. We use lipidated derivatives of the specific heterodimeric coiled coil pair E: (EIAALEK)3 and K: (KIAALKE)3 to study and control the fusion of liposomes. In this model system, peptides are tethered to their liposomes via a poly(ethylene glycol) (PEG) spacer and a lipid anchor. The efficiency of the fusion mechanism and function of the peptides is highly affected by the PEG-spacer length and the lipid anchor type. Here, the influence of membrane-fusogen distance on the peptide-membrane interactions and the peptide secondary structures is studied with Langmuir film balance and infrared reflection absorption spectroscopy. We found that the introduction of a spacer to monolayer-tethered peptide E changes its conformation from solvated random coils to homo-oligomers. In contrast, the described peptide-monolayer interaction of peptide K is not affected by the PEG-spacer length. Furthermore, the coexistence of different conformations when both lipopeptides E and K are present at the membrane surface is demonstrated empirically, which has many implications for the design of effective fusogenic recognition units and the field of artificial membrane fusion.
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Affiliation(s)
| | | | - Martin Rabe
- Department
of Interface Chemistry and Surface Engineering, Max-Planck-Institut für Eisenforschung GmbH, 40237 Düsseldorf, Germany
| | - Alexander Kros
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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7
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Zhao J, Su H, Vansuch GE, Liu Z, Salaita K, Dyer RB. Localized Nanoscale Heating Leads to Ultrafast Hydrogel Volume-Phase Transition. ACS NANO 2019; 13:515-525. [PMID: 30574782 PMCID: PMC6467806 DOI: 10.1021/acsnano.8b07150] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rate of the volume-phase transition for stimuli-responsive hydrogel particles ranging in size from millimeters to nanometers is limited by the rate of water transport, which is proportional to the surface area of the particle. Here, we hypothesized that the rate of volume-phase transition could be accelerated if the stimulus is geometrically controlled from the inside out, thus facilitating outward water ejection. To test this concept, we applied transient absorption spectroscopy, laser temperature-jump spectroscopy, and finite-element analysis modeling to characterize the dynamics of the volume-phase transition of hydrogel particles with a gold nanorod core. Our results demonstrate that the nanoscale heating of the hydrogel particle core led to an ultrafast, 60 ns particle collapse, which is 2-3 orders of magnitude faster than the response generated from conventional heating. This is the fastest recorded response time of a hydrogel material, thus opening potential applications for such stimuli-responsive materials.
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Affiliation(s)
- Jing Zhao
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hanquan Su
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Gregory E. Vansuch
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Zheng Liu
- Institute for Advanced Studies, Wuhan University, Wuhan, PR China
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Corresponding Authors
| | - R. Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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8
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Nagarajan S, Xiao S, Raleigh DP, Dyer RB. Heterogeneity in the Folding of Villin Headpiece Subdomain HP36. J Phys Chem B 2018; 122:11640-11648. [PMID: 30118232 DOI: 10.1021/acs.jpcb.8b07683] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small single domain proteins that fold on the microsecond time scale have been the subject of intense interest as models for probing the complexity of folding energy landscapes. The villin headpiece subdomain (HP36) has been extensively studied because of its simple three helix structure, ultrafast folding lifetime of a few microseconds, and stable native fold. We have previously shown that folding as measured by a single 13C═18O isotopic label on residue A57 in helix 2 occurs at a different rate than that measured by global probes of folding, indicating noncooperative complexity in the folding of HP36. In order to determine whether this complexity reflects intermediates or parallel pathways over a small activation barrier, 13C═18O labels were individually incorporated at six different positions in HP36, including into all 3 helices. The equilibrium thermal unfolding transitions and the folding/unfolding dynamics were monitored using the unique IR signature of the 13C═18O label by temperature dependent FTIR and temperature jump IR spectroscopy, respectively. Equilibrium experiments reveal that the 13C═18O labels at different positions in HP36 show drastic differences in the midpoint of their transitions ( Tm), ranging from 45 to 67 °C. Heterogeneity is also observed in the relaxation kinetics; there are differences in the microsecond phase when different labeled positions are probed. At a final temperature of 45 °C, the relaxation rate for 13C═18O A57 is 2.4e + 05 s-1 whereas for 13C═18O L69 HP36 the relaxation rate is 5.1e + 05 s-1, two times faster. The observation of site-dependent midpoints for the equilibrium unfolding transitions and differences in the relaxation rates of the labeled positions enables us to probe the progressive accumulation of the folded structure, providing insight into the microscopic details of the folding mechanism.
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Affiliation(s)
- Sureshbabu Nagarajan
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Shifeng Xiao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen 518060 , China
| | - Daniel P Raleigh
- Department of Chemistry , State University of New York at Stony Brook , Stony Brook , New York 11794 , United States.,Institute of Structural and Molecular Biology , University College London , Gower Street , London WC1E 6BT , United Kingdom
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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9
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Schuler EE, Nagarajan S, Dyer RB. Submillisecond Dynamics of Mastoparan X Insertion into Lipid Membranes. J Phys Chem Lett 2016; 7:3365-3370. [PMID: 27513014 PMCID: PMC5019822 DOI: 10.1021/acs.jpclett.6b01512] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The mechanism of protein insertion into a lipid bilayer is poorly understood because the kinetics of this process is difficult to measure. We developed a new approach to study insertion of the antimicrobial peptide Mastoparan X into zwitterionic lipid vesicles, using a laser-induced temperature-jump to initiate insertion on the microsecond time scale and infrared and fluorescence spectroscopies to follow the kinetics. Infrared probes the desolvation of the peptide backbone and yields biphasic kinetics with relaxation lifetimes of 12 and 117 μs, whereas fluorescence probes the intrinsic tryptophan residue located near the N-terminus and yields a single exponential phase with a lifetime of 440 μs. Arrhenius analysis of the temperature-dependent rates yields an activation energy for insertion of 96 kJ/mol. These results demonstrate the complexity of the insertion process and provide mechanistic insight into the interplay between peptides and the lipid bilayer required for peptide transport across cellular membranes.
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Affiliation(s)
| | | | - R. Brian Dyer
- Corresponding Author: Address: Emory University, Department of Chemistry, 1515 Dickey Drive, Atlanta, GA 30322. Phone: 404-727-6637;
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10
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Light TP, Corbett KM, Metrick MA, MacDonald G. Hofmeister Ion-Induced Changes in Water Structure Correlate with Changes in Solvation of an Aggregated Protein Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1360-1369. [PMID: 26760222 DOI: 10.1021/acs.langmuir.5b04489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RecA is a naturally aggregating Escherichia coli protein that catalyzes the strand exchange reaction utilized in DNA repair. Previous studies have shown that the presence of salts influence RecA activity, aggregation, and stability and that salts stabilize RecA in an inverse-anionic Hofmeister series. Here we utilized attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and circular dichroism (CD) to investigate how various Hofmeister salts alter the water structure and RecA solvation and aggregation. Spectroscopic studies performed in water and deuterium oxide suggest that salts alter water O-(1)H and O-(2)H stretch and bend vibrations as well as protein amide I (or I') and amide II (or II') vibrations. Anions have a much larger influence on water vibrations than cations. Water studies also show increased water-water and/or water-ion interactions in the presence of strongly hydrated SO4(2-) salts and evidence for decreased interactions with weakly hydrated Cl(-) and ClO4(-) salts. Salt-water difference infrared spectra show that kosmotropic salts are more hydrated than chaotropic salts. Interestingly, this is the opposite trend to the changes in protein solvation. Infrared spectra of RecA show that vibrations associated with protein desolvation were observed in the presence of SO4(2-) salts. Conversely, vibrations associated with protein solvation were observed in the presence of Cl(-) and ClO4(-) salts. Difference infrared studies on the dehydration of model proteins aided in identifying changes in RecA-solvent interactions. This study provides evidence that salt-induced changes in water vibrations correlate to changes in protein solvent interactions and thermal stability.
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Affiliation(s)
- Taylor P Light
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Karen M Corbett
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Michael A Metrick
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Gina MacDonald
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
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11
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Murshid N, Wang X. Iron-Carbonyl Aqueous Vesicles (MCsomes) by Hydration of [Fe(CO){CO(CH2)5CH3}(Cp)(PPh3)] (FpC6): Highly Integrated Colloids with Aggregation-Induced Self-Enhanced IR Absorption (AI-SEIRA). Chemistry 2015; 21:19223-30. [PMID: 26563745 DOI: 10.1002/chem.201502121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Indexed: 11/11/2022]
Abstract
Self-assembly of hydrophobic molecules into aqueous colloids contradicts common chemical intuition, but has been achieved through hydration of [Fe(CO){CO(CH2)5CH3}(Cp)(PPh3)] (FpC6). FpC6 has no surface activity, no NMR signals in D2O and no critical aggregation concentration (CAC) in H2O. The molecule, however, contains both acyl and terminal CO groups that are prone to being hydrated. By adding water to a solution in THF, self-assembly of FpC6 can be initiated through water-carbonyl interactions (WCIs) with the highly polarized acyl CO groups. This aggregation subsequently enhances the hydration of the acyl CO groups and also induces the WCI of otherwise unhydrated terminal CO groups. The resultant metal-carbonyl aggregates have been proved to be bilayer vesicles with iron complexes exposed towards water and alkyl chains forming inner walls (MCsomes). These MCsomes show high structure integration upon dilution due to the hydrophobic nature of the building blocks. The highly polarized CO groups on the surface of the MCsomes result in a negative zeta potential (-65 mV) and create a local electric field, which significantly enhances the IR absorption of CO groups by more than 100-fold. This is the first discovery of aggregation-induced self-enhanced IR absorption (AI-SRIRA) without the assistant of external dielectric substrates. Highly integrated MCsomes are, therefore, promising as a novel group of materials, for example, for IR-based sensing and imaging.
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Affiliation(s)
- Nimer Murshid
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue west, Waterloo, Ontario, N2L 3G1 (Canada)
| | - Xiaosong Wang
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue west, Waterloo, Ontario, N2L 3G1 (Canada).
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12
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Anisotropic energy flow and allosteric ligand binding in albumin. Nat Commun 2015; 5:3100. [PMID: 24445265 DOI: 10.1038/ncomms4100] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/12/2013] [Indexed: 11/08/2022] Open
Abstract
Allosteric interactions in proteins generally involve propagation of local structural changes through the protein to a remote site. Anisotropic energy transport is thought to couple the remote sites, but the nature of this process is poorly understood. Here, we report the relationship between energy flow through the structure of bovine serum albumin and allosteric interactions between remote ligand binding sites of the protein. Ultrafast infrared spectroscopy is used to probe the flow of energy through the protein backbone following excitation of a heater dye, a metalloporphyrin or malachite green, bound to different binding sites in the protein. We observe ballistic and anisotropic energy flow through the protein structure following input of thermal energy into the flexible ligand binding sites, without local heating of the rigid helix bundles that connect these sites. This efficient energy transport mechanism enables the allosteric propagation of binding energy through the connecting helix structures.
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13
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Cao K, Murshid N, Li L, Lopez A, Tam KC, Wang X. Hydration of Hydrophobic Iron–Carbonyl Homopolymers via Water–Carbonyl Interaction (WCI): Creation of Uniform Organometallic Aqueous Vesicles with Exceptionally High Encapsulation Capacity. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01531] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Kai Cao
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Waterloo Institute
for Nanotechnology (WIN), University of Waterloo, 200 University
Ave West, Waterloo, Canada N2L 3G1
| | - Nimer Murshid
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Waterloo Institute
for Nanotechnology (WIN), University of Waterloo, 200 University
Ave West, Waterloo, Canada N2L 3G1
| | - Lu Li
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Waterloo Institute
for Nanotechnology (WIN), University of Waterloo, 200 University
Ave West, Waterloo, Canada N2L 3G1
| | - Anand Lopez
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Waterloo Institute
for Nanotechnology (WIN), University of Waterloo, 200 University
Ave West, Waterloo, Canada N2L 3G1
| | - Kam C. Tam
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Waterloo Institute
for Nanotechnology (WIN), University of Waterloo, 200 University
Ave West, Waterloo, Canada N2L 3G1
| | - Xiaosong Wang
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Waterloo Institute
for Nanotechnology (WIN), University of Waterloo, 200 University
Ave West, Waterloo, Canada N2L 3G1
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14
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Rabe M, Zope HR, Kros A. Interplay between Lipid Interaction and Homo-coiling of Membrane-Tethered Coiled-Coil Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9953-9964. [PMID: 26302087 DOI: 10.1021/acs.langmuir.5b02094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The designed coiled-coil-forming peptides E [(EIAALEK)3] and K [(KIAALKE)3] are known to trigger efficient membrane fusion when they are tethered to lipid vesicles in the form of lipopeptides. Knowledge of their secondary structure is a key element in understanding their role in membrane fusion. Special conditions can be found at the interface of the membrane, where the peptides are confined in close proximity to other peptide molecules as well as to the lipid interface. Consequently, different structural states were proposed for the peptides when tethered to this interface. Due to the multitude of possible states, determining the structure solely on the basis of circular dichroism (CD) spectra at a single temperature can be misleading. In addition, it has not yet been possible to unambiguously distinguish between the membrane-bound and the coiled-coil states of these peptides by means of infrared (IR) spectroscopy due to their very similar amide I' bands. Here, the molecular basis of this similarity is investigated by means of site-specific (13)C-labeled FTIR spectroscopy. Structural similarities between the membrane-interacting helix of K and the homo-coiled-coil-forming helix of E are shown to cause the similar spectroscopic properties. Furthermore, the peptide structure is investigated using temperature-dependent CD and IR spectroscopy, and it is shown that the different states can be distinguished on the basis of their thermal behavior. It is shown that the two peptides behave fundamentaly differently when tethered to the lipid membrane, which implies that their role during membrane fusion is different and the mechanism of this process is asymmetric.
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Affiliation(s)
- Martin Rabe
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Harshal R Zope
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
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15
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Rabe M, Schwieger C, Zope HR, Versluis F, Kros A. Membrane interactions of fusogenic coiled-coil peptides: implications for lipopeptide mediated vesicle fusion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7724-7735. [PMID: 24914996 DOI: 10.1021/la500987c] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fusion of lipid membranes is an important natural process for the intra- and intercellular exchange of molecules. However, little is known about the actual fusion mechanism at the molecular level. In this study we examine a system that models the key features of this process. For the molecular recognition between opposing membranes two membrane anchored heterodimer coiled-coil forming peptides called 'E' (EIAALEK)3 and 'K' (KIAALKE)3 were used. Lipid monolayers and IR reflection absorption spectroscopy (IRRAS) revealed the interactions of the peptides 'E', 'K', and their parallel coiled-coil complex 'E/K' with the phospholipid membranes and thereby mimicked the pre- and postfusion states, respectively. The peptides adopted α-helical structures and were incorporated into the monolayers with parallel orientation. The strength of binding to the monolayer differed for the peptides and tethering them to the membrane increased the interactions even further. Remarkably, these interactions played a role even in the postfusion state. These findings shed light on important mechanistic details of the membrane fusion process in this model system. Furthermore, their implications will help to improve the rational design of new artificial membrane fusion systems, which have a wide range of potential applications in supramolecular chemistry and biomedicine.
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Affiliation(s)
- Martin Rabe
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
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16
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Yamamoto S, Furukawa T, Bouř P, Ozaki Y. Solvated States of Poly-l-alanine α-Helix Explored by Raman Optical Activity. J Phys Chem A 2014; 118:3655-62. [DOI: 10.1021/jp500794s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shigeki Yamamoto
- Department
of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tatsuya Furukawa
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic
| | - Yukihiro Ozaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan
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17
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Kubelka J. Multivariate Analysis of Spectral Data with Frequency Shifts: Application to Temperature Dependent Infrared Spectra of Peptides and Proteins. Anal Chem 2013; 85:9588-95. [DOI: 10.1021/ac402083p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Kubelka
- Department
of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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18
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Sethi A, Anunciado D, Tian J, Vu DM, Gnanakaran S. Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics. Chem Phys 2013; 422:10.1016/j.chemphys.2013.05.005. [PMID: 24187427 PMCID: PMC3810979 DOI: 10.1016/j.chemphys.2013.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
As it remains practically impossible to generate ergodic ensembles for large intrinsically disordered proteins (IDP) with molecular dynamics (MD) simulations, it becomes critical to compare spectroscopic characteristics of the theoretically generated ensembles to corresponding measurements. We develop a Bayesian framework to infer the ensemble properties of an IDP using a combination of conformations generated by MD simulations and its measured infrared spectrum. We performed 100 different MD simulations totaling more than 10 µs to characterize the conformational ensemble of αsynuclein, a prototypical IDP, in water. These conformations are clustered based on solvent accessibility and helical content. We compute the amide-I band for these clusters and predict the thermodynamic weights of each cluster given the measured amide-I band. Bayesian analysis produces a reproducible and non-redundant set of thermodynamic weights for each cluster, which can then be used to calculate the ensemble properties. In a rigorous validation, these weights reproduce measured chemical shifts.
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Affiliation(s)
- Anurag Sethi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Divina Anunciado
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jianhui Tian
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Dung M. Vu
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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19
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20
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Vita N, Brubach JB, Hienerwadel R, Bremond N, Berthomieu D, Roy P, Berthomieu C. Electrochemically Induced Far-Infrared Difference Spectroscopy on Metalloproteins Using Advanced Synchrotron Technology. Anal Chem 2013; 85:2891-8. [DOI: 10.1021/ac303511g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nicolas Vita
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Jean-Blaise Brubach
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Rainer Hienerwadel
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Lab Genet Biophys Plantes, Aix-Marseille Université, Marseille, F-13009,
France
- Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Marseille,
F-13009, France
| | - Nicolas Bremond
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
| | - Dorothée Berthomieu
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue
de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Pascale Roy
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Catherine Berthomieu
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
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21
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Vu DM, Brewer SH, Dyer RB. Early turn formation and chain collapse drive fast folding of the major cold shock protein CspA of Escherichia coli. Biochemistry 2012; 51:9104-11. [PMID: 23098216 DOI: 10.1021/bi301296y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The folding mechanism of the β-sheet protein CspA, the major cold shock protein of Escherichia coli, was previously reported to be a concerted, two-state process. We have reexamined the folding of CspA using multiple spectroscopic probes of the equilibrium transition and laser-induced temperature jump (T-jump) to achieve better time resolution of the kinetics. Equilibrium temperature-dependent Fourier transform infrared (1634 cm(-1)) and tryptophan fluorescence measurements reveal probe-dependent thermal transitions with midpoints (T(m)) of 66 ± 1 and 61 ± 1 °C, respectively. Singular-value decomposition analysis with global fitting of the temperature-dependent infrared (IR) difference spectra reveals two spectral components with distinct melting transitions with different midpoints. T-jump relaxation measurements of CspA probed by IR and fluorescence spectroscopy show probe-dependent multiexponential kinetics characteristic of non-two-state folding. The frequency-dependent IR transients all show biphasic relaxation with average time constants of 50 ± 7 and 225 ± 25 μs at a T(f) of 77 °C and almost equal amplitudes. Similar biphasic kinetics are observed using Trp fluorescence of the wild-type protein and the Y42W and T68W mutants, with comparable lifetimes. All of these observations support a model for the folding of CspA through a compact intermediate state. The transient IR and fluorescence spectra are consistent with a diffuse intermediate having β-turns and substantial β-sheet structure. The loop β3-β4 structure is likely not folded in the intermediate state, allowing substantial solvent penetration into the barrel structure.
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Affiliation(s)
- Dung M Vu
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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