1
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [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: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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2
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Clayton AHA. Spectroscopic and Microscopic Approaches for Investigating the Dynamic Interactions of Anti-microbial Peptides With Membranes and Cells. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 2:628552. [PMID: 35047900 PMCID: PMC8757865 DOI: 10.3389/fmedt.2020.628552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/30/2020] [Indexed: 11/13/2022] Open
Abstract
The emergence of microbes resistant to conventional antibiotics is a burgeoning threat to humanity with significant impacts on the health of people and on the health system itself. Antimicrobial peptides (AMPs) hold promise as potential future alternatives to conventional drugs because they form an integral part of the defense systems of other species in the animal, plant, and fungal kingdoms. To aid the design of the next generation of AMPs optimized for human use, we must first understand the mechanism of action of existing AMPs with their targets, ideally in the context of the complex landscape of the living (microbial) cell. Advances in lasers, optics, detectors, fluid dynamics and various probes has enabled the experimentalist to measure the kinetics of molecule–membrane, molecule–molecule, and molecule–cell interactions with increasing spatial and temporal resolution. The purpose of this review is to highlight studies into these dynamic interactions with a view to improving our understanding of AMP mechanisms.
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Affiliation(s)
- Andrew H A Clayton
- Cell Biophysics Laboratory, Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
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3
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Xu S, Wang W, Dong X, Sun Y. Molecular Insight into Cu 2+-Induced Conformational Transitions of Amyloid β-Protein from Fast Kinetic Analysis and Molecular Dynamics Simulations. ACS Chem Neurosci 2021; 12:300-310. [PMID: 33401892 DOI: 10.1021/acschemneuro.0c00502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cu2+-mediated amyloid β-protein (Aβ) aggregation is implicated in the pathogenesis of Alzheimer's disease, so it is of significance to understand Cu2+-mediated conformational transitions of Aβ. Herein, four Aβ mutants were created by using the environment-sensitive cyanophenylalanine to respectively substitute F4, Y10, F19, and F20 residues of Aβ40. By using stopped-flow fluorescence spectroscopy and molecular dynamics (MD) simulations, the early stage conformational transitions of the mutants mediated by Cu2+ binding were investigated. The fast kinetics unveils that Cu2+ has more significant influence on the conformational changes of N-terminal (F4 and Y10) than on the central hydrophobic core (CHC, F19, and F20) under different pH conditions (pH 6.6-8.0), especially Y10. Interestingly, lag periods of the conformational transitions are observed for the F19 and F20 mutants at pH 8.0, indicating the slow response of the two mutation sites on the conformational transitions. More importantly, significantly longer lag periods for F20 than for F19 indicate the conduction of the transition from F19 to F20. The conduction time (difference in lag period) decreases from 4.5 s at Cu2+ = 0 to undetectable (<1 ms) at Cu2+ = 10 μM. The significant difference in the response time of F19 and F20 and the fast local conformational changes of Y10 imply that the conformational transitions of Aβ start around Y10. MD simulations support the observation of hydrophobicity increase at N-terminal during the conformational transitions of Aβ-Cu2+. It also reveals that Y10 is immediately approached by Cu2+, supporting the speculation that the starting point of conformational transitions of Aβ is near Y10. The work has provided molecular insight into the early stage conformational transitions of Aβ40 mediated by Cu2+.
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Affiliation(s)
- Shaoying Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Wenjuan Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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4
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Roberson MG, Duncan JM, Flieth KJ, Geary LM, Tucker MJ. Photo-initiated rupture of azobenzene micelles to enable the spectroscopic analysis of antimicrobial peptide dynamics. RSC Adv 2020; 10:21464-21472. [PMID: 32879729 PMCID: PMC7449587 DOI: 10.1039/d0ra01920h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/27/2020] [Indexed: 01/03/2023] Open
Abstract
Antimicrobial peptides (AMPs) show promise for the treatment of bacterial infections, but many have undesired hemolytic activities. The AMP MP1 not only has broad spectrum bactericidal activity, but has been shown to have antitumor activity. The interaction between AMPs and cellular membranes gives rise to a peptide's cell-specificity and activity. However, direct analysis of the biophysical interactions between peptides and membrane is complex, in part due to the nature of membrane environments as well as structural changes in the peptide that occurs upon binding to the membrane. In order to investigate the interplay between cell selectivity, activity, and secondary structural changes involved in antimicrobial peptide activity, we sought to implement photolizable membrane mimics to assess the types of information available from infrared spectroscopic measurements that follow from photoinitiated peptide dynamics. Azo-surfactants (APEG) form micelles containing a photolizable azobenzene core, which upon irradiation can induce membrane deformation resulting in breakdown of micelles. Spectroscopic analysis of membrane deformation may provide insights into the physical behavior associated with unfolding and dissociation of antimicrobial peptides within a membrane environment. Herein, we synthesized and characterized two new azo-surfactants, APEGTMG and APEGNEt2MeI. Furthermore, we demonstrate the viability of azosurfactants as membrane mimics by examining both the membrane binding and dissociation induced secondary structural changes of the antimicrobial peptide, MP1.
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Affiliation(s)
- Matthew G Roberson
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Julia M Duncan
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Keveen J Flieth
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Laina M Geary
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
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5
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Shi J, Schneider JP. De novo Design of Selective Membrane-Active Peptides by Enzymatic Control of Their Conformational Bias on the Cell Surface. Angew Chem Int Ed Engl 2019; 58:13706-13710. [PMID: 31268617 PMCID: PMC6759387 DOI: 10.1002/anie.201902470] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Indexed: 01/07/2023]
Abstract
Selectively targeting the membrane-perturbing potential of peptides towards a distinct cellular phenotype allows one to target distinct populations of cells. We report the de novo design of a new class of peptide whose ability to perturb cellular membranes is coupled to an enzyme-mediated shift in the folding potential of the peptide into its bioactive conformation. Cells rich in negatively charged surface components that also highly express alkaline phosphatase, for example many cancers, are susceptible to the action of the peptide. The unfolded, inactive peptide is dephosphorylated, shifting its conformational bias towards cell-surface-induced folding to form a facially amphiphilic membrane-active conformer. The fate of the peptide can be further tuned by peptide concentration to affect either lytic or cell-penetrating properties, which are useful for selective drug delivery. This is a new design strategy to afford peptides that are selective in their membrane-perturbing activity.
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Affiliation(s)
- Junfeng Shi
- Chemical Biological Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD, 21702, USA
| | - Joel P Schneider
- Chemical Biological Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD, 21702, USA
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6
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Shi J, Schneider JP. De novo Design of Selective Membrane‐Active Peptides by Enzymatic Control of Their Conformational Bias on the Cell Surface. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Junfeng Shi
- Chemical Biological LaboratoryNational Cancer Institute, National Institutes of Health 376 Boyles Street Frederick MD 21702 USA
| | - Joel P. Schneider
- Chemical Biological LaboratoryNational Cancer Institute, National Institutes of Health 376 Boyles Street Frederick MD 21702 USA
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7
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Roberson MG, Smith DK, White SM, Wallace IS, Tucker MJ. Interspecies Bombolitins Exhibit Structural Diversity upon Membrane Binding, Leading to Cell Specificity. Biophys J 2019; 116:1064-1074. [PMID: 30824115 DOI: 10.1016/j.bpj.2019.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 02/05/2023] Open
Abstract
Bombolitins, a class of peptides produced by bees of the genus Bombus, target and disrupt cellular membranes, leading to lysis. Antimicrobial peptides exhibit various mechanisms of action resulting from the interplay between peptide structure, lipid composition, and cellular target membrane selectivity. Herein, two bombolitins displaying significant amino-acid-sequence similarity, BII and BL6, were assessed for antimicrobial activity as well as correlated dodecylphosphocholine (DPC) micelle binding and membrane-induced peptide conformational changes. Infrared and circular dichroism spectroscopies were used to assess the structure-function relationship of each bombolitin, and the results indicate that BII forms a rigid and helically ordered secondary structure upon binding to DPC micelles, whereas BL6 largely lacks secondary structural order. Moreover, the binding affinity of each peptide to DPC micelles was determined, revealing that BL6 displayed a difference in binding affinity by over two orders of magnitude. Further investigations into the growth-inhibitory activity of the two bombolitins were performed against Escherichia coli and Saccharomyces cerevisiae. Interestingly, BII specifically targeted S. cerevisiae, whereas BL6 more effectively inhibited E. coli growth. Overall, the antimicrobial selectivity and specificity of BII and BL6 are largely dependent on the primary as well as secondary structural content of the peptides and the membrane composition.
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Affiliation(s)
| | - Devin K Smith
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada
| | - Simon M White
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada
| | - Ian S Wallace
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada; Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada.
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada.
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8
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Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
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9
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Liu H, Morris C, Lantz R, Kent TW, Elbassal EA, Wojcikiewicz EP, Du D. Residue‐Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Haiyang Liu
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Clifford Morris
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Richard Lantz
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Thomas W. Kent
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Esmail A. Elbassal
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Ewa P. Wojcikiewicz
- Department of Biomedical ScienceFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Deguo Du
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
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10
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Liu H, Morris C, Lantz R, Kent TW, Elbassal EA, Wojcikiewicz EP, Du D. Residue-Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation. Angew Chem Int Ed Engl 2018; 57:8017-8021. [PMID: 29750857 DOI: 10.1002/anie.201802490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/12/2022]
Abstract
Elucidating local dynamics of protein aggregation is crucial for understanding the mechanistic details of protein amyloidogenesis. Herein, we studied the residue-specific dynamics and local environmental changes of Aβ40 along the course of aggregation by using para-cyanophenylalanine (PheCN ) as a fluorescent and vibrational probe. Our results show that the PheCN residues introduced at various positions all exhibited an immediate decay of fluorescence intensity, indicating a relatively synergistic process in early oligomer formation. The fast decreases in the fluorescence intensities of residues 19 and 20 in the central hydrophobic core region and residue 10 in the N-terminal region suggest that they play crucial roles in the formation of the oligomeric core. The PheCN 4 residue exhibits a remarkably slower decrease in fluorescence intensity, implicating its dynamic conformational characteristics in oligomer and fibril formation. Our results also suggest that the N-terminal residues in fibrils are surrounded by a relatively hydrophobic local environment, as opposed to being solvated.
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Affiliation(s)
- Haiyang Liu
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Clifford Morris
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Richard Lantz
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Thomas W Kent
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Esmail A Elbassal
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Ewa P Wojcikiewicz
- Department of Biomedical Science, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
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11
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Dong X, Qiao Q, Qian Z, Wei G. Recent computational studies of membrane interaction and disruption of human islet amyloid polypeptide: Monomers, oligomers and protofibrils. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018. [PMID: 29530482 DOI: 10.1016/j.bbamem.2018.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The amyloid deposits of human islet amyloid polypeptide (hIAPP) are found in type 2 diabetes patients. hIAPP monomer is intrinsically disordered in solution, whereas it can form amyloid fibrils both in vivo and in vitro. Extensive evidence suggests that hIAPP causes the disruption of cellular membrane, and further induces cytotoxicity and the death of islet β-cells in pancreas. The presence of membrane also accelerates the hIAPP fibril formation. hIAPP oligomers and protofibrils in the early stage of aggregation were reported to be the most cytotoxic, disrupting the membrane integrity and giving rise to the pathological process. The detailed molecular mechanisms of hIAPP-membrane interactions and membrane disruption are complex and remain mostly unknown. Here in this review, we focus on recent computational studies that investigated the interactions of full length and fragmentary hIAPP monomers, oligomers and protofibrils with anionic, zwitterionic and mixed anionic-zwitterionic lipid bilayers. We mainly discuss the binding orientation of monomers at membrane surface, the conformational ensemble and the oligomerization of hIAPP inside membranes, the effect of lipid composition on hIAPP oligomers/protofibrils-membrane interactions, and the hIAPP-induced membrane perturbation. This review provides mechanistic insights into the interactions between hIAPP and lipid bilayers with different lipid composition at an atomistic level, which is helpful to understand the hIAPP cytotoxicity mediated by membrane. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China
| | - Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai 200032, China.
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China.
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12
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Martin JP, Fetto NR, Tucker MJ. Comparison of biological chromophores: photophysical properties of cyanophenylalanine derivatives. Phys Chem Chem Phys 2018; 18:20750-7. [PMID: 27412819 DOI: 10.1039/c6cp04154j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Within this work, the family of cyanophenylalanine spectroscopic reporters is extended by showing the ortho and meta derivatives have intrinsic photophysical properties that are useful for studies of protein structure and dynamics. The molar absorptivities of 2-cyanophenylalanine and 3-cyanophenylalanine are shown to be comparable to that of 4-cyanophenylalanine with similar spectral features in their absorbance and emission profiles, demonstrating that these probes can be utilized interchangeably. The fluorescence quantum yields are also on the same scale as commonly used fluorophores in peptides and proteins, tyrosine and tryptophan. These new cyano-fluorophores can be paired with either 4-cyanophenylalanine or tryptophan to capture distances in peptide structure through Förster resonance energy transfer. Additionally, the spectroscopic properties of these chromophores can report the local solvent environment via changes in fluorescence emission intensity as a result of hydrogen bonding and/or hydration. A decrease in the quantum yield is also observed in basic environments due to photoinduced electron transfer from a deprotonated amine in the free PheCN species and at the N-terminus of a short peptide, providing an avenue to detect pH in biological systems. Our results show the potential of these probes, 2-cyanophenylalanine and 3-cyanophenylalanine, to be incorporated into a single peptide chain, either individually or in tandem with 4-cyanophenylalanine, tryptophan, or tyrosine, in order to obtain information about peptide structure and dynamics.
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Affiliation(s)
- Joshua P Martin
- Department of Chemistry, University of Nevada, Reno, 89557, USA.
| | - Natalie R Fetto
- Department of Chemistry, University of Nevada, Reno, 89557, USA.
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, 89557, USA.
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13
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Watson MD, Peran I, Zou J, Bilsel O, Raleigh DP. Selenomethionine Quenching of Tryptophan Fluorescence Provides a Simple Probe of Protein Structure. Biochemistry 2017; 56:1085-1094. [DOI: 10.1021/acs.biochem.6b01000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matthew D. Watson
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Ivan Peran
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer
Center for Physical and
Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Osman Bilsel
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer
Center for Physical and
Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York 11794, United States
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15
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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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16
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Oh KI, Smith-Dupont KB, Markiewicz BN, Gai F. Kinetics of peptide folding in lipid membranes. Biopolymers 2016; 104:281-90. [PMID: 25808575 DOI: 10.1002/bip.22640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/12/2015] [Accepted: 02/14/2015] [Indexed: 12/31/2022]
Abstract
Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Kathryn B Smith-Dupont
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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17
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Peran I, Watson MD, Bilsel O, Raleigh DP. Selenomethionine, p-cyanophenylalanine pairs provide a convenient, sensitive, non-perturbing fluorescent probe of local helical structure. Chem Commun (Camb) 2016; 52:2055-8. [PMID: 26686928 DOI: 10.1039/c5cc08232c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The use of selenomethionine (MSe)-p-cyanophenylalanine (FCN) pairs to probe protein structure is demonstrated. MSe quenches FCN fluorescence via electron transfer. Both residues can be incorporated recombinantly or by peptide synthesis. Time-resolved and steady-state fluorescence measurements demonstrate that MSe-FCN pairs provide specific local probes of helical structure.
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Affiliation(s)
- Ivan Peran
- Department of Chemistry, Stony Brook University, Stony Brook, New York, 11794-3400, USA.
| | - Matthew D Watson
- Department of Chemistry, Stony Brook University, Stony Brook, New York, 11794-3400, USA.
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York, 11794-3400, USA. and Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York, 11794-3400, USA
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18
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Bobone S, De Zotti M, Bortolotti A, Biondi B, Ballano G, Palleschi A, Toniolo C, Formaggio F, Stella L. The fluorescence and infrared absorption probepara-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides. Biopolymers 2015; 104:521-32. [DOI: 10.1002/bip.22674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Sara Bobone
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Annalisa Bortolotti
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Gema Ballano
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
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19
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Pazos IM, Ahmed IA, Berríos MIL, Gai F. Sensing pH via p-cyanophenylalanine fluorescence: Application to determine peptide pKa and membrane penetration kinetics. Anal Biochem 2015; 483:21-6. [PMID: 25935260 DOI: 10.1016/j.ab.2015.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/22/2022]
Abstract
We expand the spectroscopic utility of a well-known infrared and fluorescence probe, p-cyanophenylalanine, by showing that it can also serve as a pH sensor. This new application is based on the notion that the fluorescence quantum yield of this unnatural amino acid, when placed at or near the N-terminal end of a polypeptide, depends on the protonation status of the N-terminal amino group of the peptide. Using this pH sensor, we are able to determine the N-terminal pKa values of nine tripeptides and also the membrane penetration kinetics of a cell-penetrating peptide. Taken together, these examples demonstrate the applicability of using this unnatural amino acid fluorophore to study pH-dependent biological processes or events that accompany a pH change.
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Affiliation(s)
- Ileana M Pazos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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De Zotti M, Bobone S, Bortolotti A, Longo E, Biondi B, Peggion C, Formaggio F, Toniolo C, Dalla Bona A, Kaptein B, Stella L. 4-Cyano-α-methyl-l-phenylalanine as a Spectroscopic Marker for the Investigation of PeptaibioticMembrane Interactions. Chem Biodivers 2015; 12:513-27. [DOI: 10.1002/cbdv.201400404] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 11/10/2022]
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21
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New aspects of the structure and mode of action of the human cathelicidin LL-37 revealed by the intrinsic probe p-cyanophenylalanine. Biochem J 2015; 465:443-57. [PMID: 25378136 DOI: 10.1042/bj20141016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The human cathelicidin peptide LL-37 is an important effector of our innate immune system and contributes to host defence with direct antimicrobial activity and immunomodulatory properties, and by stimulating wound healing. Its sequence has evolved to confer specific structural characteristics that strongly affect these biological activities, and differentiate it from orthologues of other primate species. In the present paper we report a detailed study of the folding and self-assembly of this peptide in comparison with rhesus monkey peptide RL-37, taking into account the different stages of its trajectory from bulk solution to contact with, and insertion into, biological membranes. Phenylalanine residues in different positions throughout the native sequences of LL-37 and RL-37 were systematically replaced with the non-invasive fluorescent and IR probe p-cyanophenylalanine. Steady-state and time-resolved fluorescence studies showed that LL-37, in contrast to RL-37, forms oligomers with a loose hydrophobic core in physiological solutions, which persist in the presence of biological membranes. Fourier transform IR and surface plasmon resonance studies also indicated different modes of interaction for LL-37 and RL-37 with anionic and neutral membranes. This correlated with a distinctly different mode of bacterial membrane permeabilization, as determined using a flow cytometric method involving impermeant fluorescent dyes linked to polymers of defined sizes.
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22
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Liu H, Lantz R, Cosme P, Rivera N, Andino C, Gonzalez WG, Terentis AC, Wojcikiewicz EP, Oyola R, Miksovska J, Du D. Site-specific dynamics of amyloid formation and fibrillar configuration of Aβ1–23 using an unnatural amino acid. Chem Commun (Camb) 2015; 51:7000-3. [DOI: 10.1039/c5cc00149h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Distinct local dynamics of Aβ1–23 amyloid formation are characterized using an unnatural amino acid p-cyanophenylalanine as a spectroscopic probe.
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Affiliation(s)
- Haiyang Liu
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Richard Lantz
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Patrick Cosme
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Nelson Rivera
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Carlos Andino
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Walter G. Gonzalez
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Andrew C. Terentis
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | | | - Rolando Oyola
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Deguo Du
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
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23
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Reif MM, Oostenbrink C. Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies. J Comput Chem 2014; 35:2319-32. [PMID: 25338770 DOI: 10.1002/jcc.23756] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 09/02/2014] [Accepted: 09/21/2014] [Indexed: 01/19/2023]
Abstract
Förster resonance energy transfer (FRET) measurements are widely used to investigate (bio)molecular interactions or/and association. FRET efficiencies, the primary data obtained from this method, give, in combination with the common assumption of isotropic chromophore orientation, detailed insight into the lengthscale of molecular phenomena. This study illustrates the application of a FRET efficiency restraint during classical atomistic molecular dynamics simulations of a mutant mastoparan X peptide in either water or 7 M aqueous urea. The restraint forces acting on the donor and acceptor chromophores ensure that the sampled peptide configurational ensemble satisfies the experimental primary data by modifying interchromophore separation and chromophore transition dipole moment orientations. By means of a conformational cluster analysis, it is seen that indeed different configurational ensembles may be sampled without and with application of the restraint. In particular, while the FRET efficiency and interchromophore distances monitored in an unrestrained simulation may differ from the experimentally-determined values, they can be brought in agreement with experimental data through usage of the FRET efficiency restraining potential. Furthermore, the present results suggest that the assumption of isotropic chromophore orientation is not always justified. The FRET efficiency restraint allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom. Thus, it offers an additional tool to connect the realms of computer and wet-lab experimentation.
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Affiliation(s)
- Maria M Reif
- Department of Material Sciences and Process Engineering, Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna
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24
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Wu T, Zhang R, Li H, Yang L, Zhuang W. Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: a simulation study. J Chem Phys 2014; 140:055101. [PMID: 24511982 DOI: 10.1063/1.4863562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB(OBC) implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.
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Affiliation(s)
- Tianmin Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Huanhuan Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
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25
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Gonzalez JD, Levonyak NS, Schneider SC, Smith MJ, Cremeens ME. Using infrared spectroscopy of a nitrile labeled phenylalanine and tryptophan fluorescence to probe the α-MSH peptide’s side-chain interactions with a micelle model membrane. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.09.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Wu T, Yang L, Zhang R, Shao Q, Zhuang W. Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation. J Phys Chem A 2013; 117:6256-63. [PMID: 23496267 DOI: 10.1021/jp400625a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.
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Affiliation(s)
- Tianmin Wu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
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27
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Zhang S, Zhang Y, Ma X, Lu L, He Y, Deng Y. Benzonitrile as a Probe of Local Environment in Ionic Liquids. J Phys Chem B 2013; 117:2764-72. [DOI: 10.1021/jp312251q] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shiguo Zhang
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Yan Zhang
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Xiangyuan Ma
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Liujin Lu
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Yude He
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Youquan Deng
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
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28
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Du D, Liu H, Ojha B. Study protein folding and aggregation using nonnatural amino acid p-cyanophenylalanine as a sensitive optical probe. Methods Mol Biol 2013; 1081:77-89. [PMID: 24014435 DOI: 10.1007/978-1-62703-652-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Incorporation of nonnatural amino acids with a variety of special side groups into protein sequences has substantially expanded the experimental means of exploring protein structures and functions. Recently, p-cyanophenylalanine (PheCN), the nitrile analogue of phenylalanine, has been used as a novel optical probe for protein binding and folding studies. The fluorescence emission of PheCN is sensitive to solvent and local environment of the residue, making it a useful fluorescent probe of protein structural change at residue-specific resolution. Moreover, the utility of PheCN is increased by its ability to excite tryptophan fluorescence via the mechanism of fluorescence resonance energy transfer. PheCN could be applied to study a variety of biological problems, e.g., protein folding/unfolding and protein aggregation.
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Affiliation(s)
- Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL, USA
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29
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Xue L, Zou F, Zhao Y, Huang X, Qu Y. Nitrile group as infrared probe for the characterization of the conformation of bovine serum albumin solubilized in reverse micelles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 97:858-863. [PMID: 22902928 DOI: 10.1016/j.saa.2012.07.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/08/2012] [Accepted: 07/22/2012] [Indexed: 06/01/2023]
Abstract
Infrared spectroscopy is a powerful technique for structure characterization. For a protein hosted in a reversed micellar medium, the spectral features of the protein are always interfered by the IR absorption bands of the medium in addition to the congestion in their IR spectra. Fortunately, there is a transparent window in the 2500-2200 cm(-1) region. Incorporation of a vibrational probe with IR absorption frequencies in this region into proteins represents a promising strategy for the study of the conformation of a protein in a reverse micelle. In the present work, we incorporated 4-cyanobenzyl group (CN) into bovine serum albumin (BSA) via cysteine alkylation reactions under mild conditions. Circular dichroism spectroscopy showed that the CN modified BSA (CNBSA) could retain its conformation. When CNBSA was hosted in AOT reverse micelle, it was found that the nitrile group on BSA was sensitive to the conformational change of BSA induced by urea as an additive in the reverse micelle. The peak splitting of nitrile group was also observed when the size of AOT reverse micelle and the concentration of an electrolyte were varied. Obviously, the shift of the IR absorption peak and/or peak splitting of nitrile group on BSA are correlated with the change of BSA conformation in AOT reverse micelle. So we conclude that the nitrile infrared probe can be used to study protein conformation in a reverse micelle.
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Affiliation(s)
- Luyan Xue
- Key Laboratory of Colloid & Interface Chemistry of the Education Ministry of China, Shandong University, Jinan 250100, PR China
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30
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Hohlweg W, Kosol S, Zangger K. Determining the orientation and localization of membrane-bound peptides. Curr Protein Pept Sci 2012; 13:267-79. [PMID: 22044140 PMCID: PMC3394173 DOI: 10.2174/138920312800785049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 10/01/2011] [Accepted: 10/10/2011] [Indexed: 01/06/2023]
Abstract
Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance.
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Affiliation(s)
| | | | - Klaus Zangger
- Institute of Chemistry / Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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31
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Kreutzberger AJ, Pokorny A. On the origin of multiphasic kinetics in peptide binding to phospholipid vesicles. J Phys Chem B 2012; 116:951-7. [PMID: 22242648 DOI: 10.1021/jp209080m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We critically examined a series of exact kinetic models for their ability to describe binding of a typical α-helical amphipathic peptide to lipid bilayers. Binding of the model peptide lysette-26 was measured through fluorescence resonance energy transfer from a Trp residue on the peptide to a fluorescently labeled acceptor lipid included in vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. Experimental data was collected varying peptide and lipid concentrations over an order of magnitude. The kinetic models were fit to all the experimental data simultaneously. Of the four models examined, the simplest one that is sufficient to correctly describe the experimental data includes two coupled equilibria, one between peptide monomers in solution and bound to the lipid membrane, and a second one between lipid-bound peptides that oligomerize to form dimers. We found that individual kinetic binding curves are insufficient to distinguish among kinetic models of peptide binding to lipid bilayers but that a number of models can be excluded based on inspection of a simple set of experiments.
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Affiliation(s)
- Alex J Kreutzberger
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, USA
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32
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Taskent-Sezgin H, Marek P, Thomas R, Goldberg D, Chung J, Carrico I, Raleigh DP. Modulation of p-cyanophenylalanine fluorescence by amino acid side chains and rational design of fluorescence probes of alpha-helix formation. Biochemistry 2010; 49:6290-5. [PMID: 20565125 DOI: 10.1021/bi100932p] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p-Cyanophenylalanine is an extremely useful fluorescence probe of protein structure that can be recombinantly and chemically incorporated into proteins. The probe has been used to study protein folding, protein-membrane interactions, protein-peptide interactions, and amyloid formation; however, the factors that control its fluorescence are not fully understood. Hydrogen bonding to the cyano group is known to play a major role in modulating the fluorescence quantum yield, but the role of potential side-chain quenchers has not yet been elucidated. A systematic study of the effects of different side chains on p-cyanophenylalanine fluorescence is reported. Tyr is found to have the largest effect followed by deprotonated His, Met, Cys, protonated His, Asn, Arg, and protonated Lys. Deprotonated amino groups are much more effective fluorescence quenchers than protonated amino groups. Free neutral imidazole and hydroxide ion are also effective quenchers of p-cyanophenylalanine fluorescence with Stern-Volmer constants of 39.8 and 22.1 M(-1), respectively. The quenching of p-cyanophenylalanine fluorescence by specific side chains is exploited in developing specific, high-sensitivity, fluorescence probes of helix formation. The approach is demonstrated with Ala-based peptides that contain a p-cyanophenylalanine-His or a p-cyanophenylalanine-Tyr pair located at positions i and i + 4. The p-cyanophenylalanine-His pair is most useful when the His side chain is deprotonated and is, thus, complementary to the Trp-His pair which is most sensitive when the His side chain is protonated.
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Affiliation(s)
- Humeyra Taskent-Sezgin
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
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33
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Marek P, Mukherjee S, Zanni MT, Raleigh DP. Residue-specific, real-time characterization of lag-phase species and fibril growth during amyloid formation: a combined fluorescence and IR study of p-cyanophenylalanine analogs of islet amyloid polypeptide. J Mol Biol 2010; 400:878-88. [PMID: 20630475 DOI: 10.1016/j.jmb.2010.05.041] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 05/05/2010] [Accepted: 05/16/2010] [Indexed: 01/09/2023]
Abstract
Amyloid formation normally exhibits a lag phase followed by a growth phase, which leads to amyloid fibrils. Characterization of the species populated during the lag phase is experimentally challenging, but is critical since the most toxic entities may be pre-fibrillar species. p-Cyanophenylalanine (F(C[triple bond]N)) fluorescence is used to probe the nature of lag-phase species populated during the formation of amyloid by human islet amyloid polypeptide. The polypeptide contains two phenylalanines at positions 15 and 23 and a single tyrosine located at the C-terminus. Each aromatic residue was separately replaced by F(C[triple bond]N). The substitutions do not perturb amyloid formation relative to wild-type islet amyloid polypeptide as detected using thioflavin T fluorescence and electron microscopy. F(C[triple bond]N) fluorescence is high when the cyano group is hydrogen bonded and low when it is not. It can also be quenched via Förster resonance energy transfer to tyrosine. Fluorescence intensity was monitored in real time and revealed that all three positions remained exposed to solvent during the lag phase but less exposed than unstructured model peptides. The time course of amyloid formation as monitored by thioflavin T fluorescence and F(C[triple bond]N) fluorescence is virtually identical. Fluorescence quenching experiments confirmed that each residue remains exposed during the lag phase. These results place significant constraints on the nature of intermediates that are populated during the lag phase and indicate that significant sequestering of the aromatic side chains does not occur until beta-structure sufficient to bind thioflavin T has developed. Seeding studies and analysis of maximum rates confirm that sequestering of the cyano groups occurs concomitantly with the development of thioflavin T binding capability. Overall, the process of amyloid formation and growth appears to be remarkably homogenous in terms of side-chain ordering. F(C[triple bond]N) also provides information about fibril structure. Fluorescence emission measurements, infrared measurements, and quenching studies indicate that the aromatic residues are differentially exposed in the fibril state with Phe15 being the most exposed. F(C[triple bond]N) is readily accommodated into proteins; thus, the approach should be broadly applicable.
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Affiliation(s)
- Peter Marek
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
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34
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Denos S, Gotkowski E, Gruebele M. A Learning Algorithm to Discover Soluble Vesicle-Binding Helical Peptides. J Phys Chem B 2010; 114:4909-14. [DOI: 10.1021/jp912157g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sharlene Denos
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Eric Gotkowski
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Martin Gruebele
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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35
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Rogers JMG, Lippert LG, Gai F. Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications. Anal Biochem 2010; 399:182-9. [PMID: 20036210 PMCID: PMC2830288 DOI: 10.1016/j.ab.2009.12.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 12/15/2009] [Accepted: 12/21/2009] [Indexed: 11/29/2022]
Abstract
Fluorescence resonance energy transfer (FRET) provides a powerful means to study protein conformational changes. However, the incorporation of an exogenous FRET pair into a protein could lead to undesirable structural perturbations of the native fold. One of the viable strategies to minimizing such perturbations is to use non-natural amino acid-based FRET pairs. Previously, we showed that p-cyanophenylalanine (Phe(CN)) and tryptophan (Trp) constitute such a FRET pair, useful for monitoring protein folding-unfolding transitions. Here we further show that 7-azatryptophan (7AW) and 5-hydroxytryptophan (5HW) can also serve as a FRET acceptor to Phe(CN), and the resultant FRET pairs offer certain advantages over Phe(CN)-Trp. For example, the fluorescence spectrum of 7AW is sufficiently separated from that of Phe(CN), making it straightforward to decompose the FRET spectrum into donor and acceptor contributions. Moreover, we show that Phe(CN), Trp, and 7AW can be used together to form a multi-FRET system, allowing more structural information to be extracted from a single FRET experiment. The applicability of these FRET systems is demonstrated in a series of studies where they are employed to monitor the urea-induced unfolding transitions of the villin headpiece subdomain (HP35), a designed betabetaalpha motif (BBA5), and the human Pin1 WW domain.
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Affiliation(s)
- Julie M. G. Rogers
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - Lisa G. Lippert
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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36
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Magainin 2 revisited: a test of the quantitative model for the all-or-none permeabilization of phospholipid vesicles. Biophys J 2010; 96:116-31. [PMID: 19134472 DOI: 10.1016/j.bpj.2008.09.017] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 09/22/2008] [Indexed: 11/22/2022] Open
Abstract
The all-or-none kinetic model that we recently proposed for the antimicrobial peptide cecropin A is tested here for magainin 2. In mixtures of phosphatidylcholine (PC)/phosphatidylglycerol (PG) 50:50 and 70:30, release of contents from lipid vesicles occurs in an all-or-none fashion and the differences between PC/PG 50:50 and 70:30 can be ascribed mainly to differences in binding, which was determined independently and is approximately 20 times greater to PC/PG 50:50 than to 70:30. Only one variable parameter, beta, corresponding to the ratio of the rates of pore opening to pore closing, is used to fit dye release kinetics from these two mixtures, for several peptide/lipid ratios ranging from 1:25 to 1:200. However, unlike for cecropin A where it stays almost constant, beta increases five times as the PG content of the vesicles increases from 30 to 50%. Thus, magainin 2 is more sensitive to anionic lipid content than cecropin A. But overall, magainin follows the same all-or-none kinetic model as cecropin A in these lipid mixtures, with slightly different parameter values. When the PG content is reduced to 20 mol %, dye release becomes very low; the mechanism appears to change, and is consistent with a graded kinetic model. We suggest that the peptide may be inducing formation of PG domains. In either mechanism, no peptide oligomerization occurs and magainin catalyzes dye release in proportion to its concentration on the membrane in a peptide state that we call a pore. We envision this structure as a chaotic or stochastic type of pore, involving both lipids and peptides, not a well-defined, peptide-lined channel.
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37
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pH (low) insertion peptide (pHLIP) inserts across a lipid bilayer as a helix and exits by a different path. Proc Natl Acad Sci U S A 2010; 107:4081-6. [PMID: 20160113 DOI: 10.1073/pnas.0914330107] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
What are the molecular events that occur when a peptide inserts across a membrane or exits from it? Using the pH-triggered insertion of the pH low insertion peptide to enable kinetic analysis, we show that insertion occurs in several steps, with rapid (0.1 sec) interfacial helix formation, followed by a much slower (100 sec) insertion pathway to give a transmembrane helix. The reverse process of unfolding and peptide exit from the bilayer core, which can be induced by a rapid rise of the pH from acidic to basic, proceeds approximately 400 times faster than folding/insertion and through different intermediate states. In the exit pathway, the helix-coil transition is initiated while the polypeptide is still inside the membrane. The peptide starts to exit when about 30% of the helix is unfolded, and continues a rapid exit as it unfolds inside the membrane. These insights may guide understanding of membrane protein folding/unfolding and the design of medically useful peptides for imaging and drug delivery.
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38
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Role of membrane lipids for the activity of pore forming peptides and proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 677:31-55. [PMID: 20687479 DOI: 10.1007/978-1-4419-6327-7_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Bilayer lipids, far from being passive elements, have multiple roles in polypeptide-dependent pore formation. Lipids participate at all stages of the formation of pores by providing the binding site for proteins and peptides, conditioning their active structure and modulating the molecular reorganization of the membrane complex. Such general functions of lipids superimpose to other particular roles, from electrostatic and curvature effects to more specific actions in cases like cholesterol, sphingolipids or cardiolipin. Pores are natural phenomena in lipid membranes. Driven by membrane fluctuations and packing defects, transient water pores are related to spontaneous lipid flip-flop and non-assisted ion permeation. In the absence ofproteins or peptides, these are rare short living events, with properties dependent on the lipid composition of the membrane. Their frequency increases under conditions of internal membrane disturbance of the lipid packing, like in the presence of membrane-bound proteins or peptides. These latter molecules, in fact, form dynamic supramolecular assemblies together with the lipids and transmembrane pores are one of the possible structures of the complex. Active peptides and proteins can thus be considered inducers or enhancers of pores which increase their probability and lifetime by modifying the thermodynamic membrane balance. This includes destabilizing the membrane lamellar structure, lowering the activation energy for pore formation and stabilizing the open pore structure.
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39
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Taskent-Sezgin H, Chung J, Patsalo V, Miyake-Stoner SJ, Miller AM, Brewer SH, Mehl RA, Green DF, Raleigh DP, Carrico I. Interpretation of p-Cyanophenylalanine Fluorescence in Proteins in Terms of Solvent Exposure and Contribution of Side-Chain Quenchers: A Combined Fluorescence, IR and Molecular Dynamics Study. Biochemistry 2009; 48:9040-6. [DOI: 10.1021/bi900938z] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Humeyra Taskent-Sezgin
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Juah Chung
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Vadim Patsalo
- Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, Stony Brook, New York 11794
| | | | - Andrew M. Miller
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17603
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17603
| | - Ryan A. Mehl
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17603
| | - David F. Green
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794
- Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, Stony Brook, New York 11794
- Institute of Chemical Biology and Drug Discovery at State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Daniel P. Raleigh
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794
- Institute of Chemical Biology and Drug Discovery at State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Isaac Carrico
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794
- Institute of Chemical Biology and Drug Discovery at State University of New York at Stony Brook, Stony Brook, New York 11794
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40
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Tang J, Yin H, Qiu J, Tucker MJ, DeGrado WF, Gai F. Using two fluorescent probes to dissect the binding, insertion, and dimerization kinetics of a model membrane peptide. J Am Chem Soc 2009; 131:3816-7. [PMID: 19256494 DOI: 10.1021/ja809007f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Helix-helix association within a membrane environment represents one of the fundamental processes in membrane protein folding. However, studying the kinetics of such processes has been difficult because most membrane proteins are insoluble in aqueous solution. Here we present a stopped-flow fluorescence study of the membrane-interaction kinetics of a designed, water-soluble transmembrane (TM) peptide, anti-alpha(IIb), which is known to dimerize in phospholipid bilayers. We show that by using two fluorescent amino acids, tryptophan and p-cyanophenylalanine, we are able to kinetically dissect distinct phases in the peptide-membrane interaction, representing membrane binding, membrane insertion, and TM helix-helix association. Our results further show that the last process occurs on a time scale of seconds, indicating that the association of two TM helices is an intrinsically slow event.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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41
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Miyake-Stoner SJ, Miller AM, Hammill JT, Peeler JC, Hess KR, Mehl RA, Brewer SH. Probing Protein Folding Using Site-Specifically Encoded Unnatural Amino Acids as FRET Donors with Tryptophan. Biochemistry 2009; 48:5953-62. [DOI: 10.1021/bi900426d] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Andrew M. Miller
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Jared T. Hammill
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Jennifer C. Peeler
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Kenneth R. Hess
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Ryan A. Mehl
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
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42
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Tang J, Kang SG, Saven JG, Gai F. Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants. J Mol Biol 2009; 389:90-102. [PMID: 19361525 DOI: 10.1016/j.jmb.2009.03.074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/26/2009] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
Metals are the most commonly encountered protein cofactors, and they play important structural and functional roles in biology. In many cases, metal binding provides a major driving force for a polypeptide chain to fold. While there are many studies on the structure, stability, and function of metal-binding proteins, there are few studies focusing on understanding the kinetic mechanism of metal-induced folding. Herein, the Zn(2+)-induced folding kinetics of a small zinc-binding protein are studied; the CH1(1) peptide is derived from the first cysteine/histidine-rich region (CH1 domain) of the protein interaction domains of the transcriptional coregulator CREB-binding protein. Computational design is used to introduce tryptophan and histidine mutations that are structurally consistent with CH1(1); these mutants are studied using stopped-flow tryptophan fluorescence experiments. The Zn(2+)-induced CH1(1) folding kinetics are consistent with two parallel pathways, where the initial binding of Zn(2+) occurs at two sites. However, the initially formed Zn(2+)-bound complexes can proceed either directly to the folded state where zinc adopts a tetrahedral coordination or to an off-pathway misligated intermediate. While elimination of those ligands responsible for misligation simplifies the folding kinetics, it also leads to a decrease in the zinc binding constant. Therefore, these results suggest why these nonnative zinc ligands in the CH1(1) motif are conserved in several distantly related organisms and why the requirement for function can lead to kinetic frustration in folding. In addition, the loop closure rate of the CH1(1) peptide is determined based on the proposed model and temperature-dependent kinetic measurements.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, 19104, USA
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43
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Weeks CL, Polishchuk A, Getahun Z, DeGrado WF, Spiro TG. Investigation of an unnatural amino acid for use as a resonance Raman probe: Detection limits, solvent and temperature dependence of the νC≡N band of 4-cyanophenylalanine. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2008; 39:1606-1613. [PMID: 20648227 PMCID: PMC2905815 DOI: 10.1002/jrs.2067] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incorporation of unnatural amino acids into proteins that act as spectroscopic probes can be used to study protein structure and function. One such probe is 4-cyanophenylalanine (PheCN), the nitrile group of which has a stretching mode that occurs in a region of the vibrational spectrum that does not contain any modes from the usual components of proteins and the wavenumber is sensitive to the polarity of its environment. In this work we evaluate the potential of UV resonance Raman spectroscopy for monitoring the sensitivity of the νC≡N band of PheCN incorporated into proteins to the protein environment. Measurement of the Raman excitation profile of PheCN showed that considerable resonance enhancement of the Raman signal was obtained using UV excitation and the best signal-to-noise ratios were obtained with excitation wavelengths of 229 and 244 nm. The detection limit for PheCN in proteins was ~10 μM, approximately a hundred-fold lower than the concentrations used in IR studies, which increases the potential applications of PheCN as a vibrational probe. The wavenumber of the PheCN νC≡N band was strongly dependent on the polarity of its environment, when the solvent was changed from H(2)O to THF it decreased by 8 cm(-1). The presence of liposomes caused a similar though smaller decrease in νC≡N for a peptide, mastoparan X, modified to contain PheCN. The selectivity and sensitivity of resonance Raman spectroscopy of PheCN mean that it can be a useful probe of intra- and intermolecular interactions in proteins and opens the door to its application in the study of protein dynamics using time-resolved resonance Raman spectroscopy.
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Affiliation(s)
- Colin L. Weeks
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Alexei Polishchuk
- Department of Biochemistry and Biophysics, School of Medicine of the University of Pennsylvania, Philadelphia, PA, 19104-6059
| | - Zelleka Getahun
- Department of Biochemistry and Biophysics, School of Medicine of the University of Pennsylvania, Philadelphia, PA, 19104-6059
| | - William F. DeGrado
- Department of Chemistry, School of Medicine of the University of Pennsylvania, Philadelphia, PA, 19104-6059
- Department of Biochemistry and Biophysics, School of Medicine of the University of Pennsylvania, Philadelphia, PA, 19104-6059
| | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Seattle, WA, 98195
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44
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Ulmschneider MB, Ulmschneider JP. Folding Peptides into Lipid Bilayer Membranes. J Chem Theory Comput 2008; 4:1807-9. [DOI: 10.1021/ct800100m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Glasscock JM, Zhu Y, Chowdhury P, Tang J, Gai F. Using an amino acid fluorescence resonance energy transfer pair to probe protein unfolding: application to the villin headpiece subdomain and the LysM domain. Biochemistry 2008; 47:11070-6. [PMID: 18816063 DOI: 10.1021/bi8012406] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously, we have shown that p-cyanophenylalanine (Phe CN) and tryptophan (Trp) constitute an efficient fluorescence resonance energy transfer (FRET) pair that has several advantages over commonly used dye pairs. Here, we aim to examine the general applicability of this FRET pair in protein folding-unfolding studies by applying it to the urea-induced unfolding transitions of two small proteins, the villin headpiece subdomain (HP35) and the lysin motif (LysM) domain. Depending on whether Phe CN is exposed to solvent, we are able to extract either qualitative information about the folding pathway, as demonstrated by HP35, which has been suggested to unfold in a stepwise manner, or quantitative thermodynamic and structural information, as demonstrated by LysM, which has been shown to be an ideal two-state folder. Our results show that the unfolding transition of HP35 reported by FRET occurs at a denaturant concentration lower than that measured by circular dichroism (CD) and that the loop linking helix 2 and helix 3 remains compact in the denatured state, which are consistent with the notion that HP35 unfolds in discrete steps and that its unfolded state contains residual structures. On the other hand, our FRET results on the LysM domain allow us to develop a model for extracting structural and thermodynamic parameters about its unfolding, and we find that our results are in agreement with those obtained by other methods. Given the fact that Phe CN is a non-natural amino acid and, thus, amenable to incorporation into peptides and proteins via existing peptide synthesis and protein expression methods, we believe that the FRET method demonstrated here is widely applicable to protein conformational studies, especially to the study of relatively small proteins.
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Affiliation(s)
- Julie M Glasscock
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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46
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Tang J, Gai F. Dissecting the Membrane Binding and Insertion Kinetics of a pHLIP Peptide. Biochemistry 2008; 47:8250-2. [DOI: 10.1021/bi801103x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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47
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Krummel AT, Zanni MT. Evidence for Coupling between Nitrile Groups Using DNA Templates: A Promising New Method for Monitoring Structures with Infrared Spectroscopy. J Phys Chem B 2008; 112:1336-8. [DOI: 10.1021/jp711558a] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amber T. Krummel
- University of WisconsinMadison, Department of Chemistry, 1101 University Avenue, Madison, Wisconsin 53703
| | - Martin T. Zanni
- University of WisconsinMadison, Department of Chemistry, 1101 University Avenue, Madison, Wisconsin 53703
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48
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Tang J, Signarvic RS, DeGrado WF, Gai F. Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers. Biochemistry 2007; 46:13856-63. [PMID: 17994771 DOI: 10.1021/bi7018404] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many antimicrobial peptides undergo a coil-to-helix transition upon binding to membranes. While this conformational transition is critical for function, little is known about the underlying mechanistic details. Here, we explore the membrane-mediated folding mechanism of an antimicrobial peptide, mastoparan X. Using stopped-flow fluorescence techniques in conjunction with a fluorescence resonance energy transfer (FRET) pair, p-cyanophenylalanine (donor) and tryptophan (acceptor), we were able to probe, albeit in an indirect manner, the membrane-mediated folding kinetics of this peptide. Our results show that the association of mastoparan X with model lipid vesicles proceeds with biphasic kinetics. The first step shows a large change in the FRET signal, indicating that the helix forms early in the time course of the interaction, while the second step where a further increase in tryptophan fluorescence is observed presumably reflects deeper insertion of the peptide into the bilayer. Additional kinetic studies on a double mutant of mastoparan X, designed to form a nucleation site for alpha-helix formation through coordination with a metal ion (e.g., Zn2+ or Ni2+), indicate that while the coil-to-helix transition occurs in the first step, it follows the rate-determining docking of the peptide onto the membrane surface. Taken together, these results indicate that the initial association of the peptide with the membrane occurs in a nonhelical conformation, which rapidly converts to a helical state within the anisotropic environment of the bilayer surface.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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