1
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Has C, Das SL. The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation. J Membr Biol 2023; 256:343-372. [PMID: 37650909 DOI: 10.1007/s00232-023-00289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.
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Affiliation(s)
- Chandra Has
- Department of Chemical Engineering, GSFC University, Vadodara, 391750, Gujarat, India.
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology, Palakkad, 678623, Kerala, India
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2
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Brahma R, Raghuraman H. Measuring Membrane Penetration Depths and Conformational Changes in Membrane Peptides and Proteins. J Membr Biol 2022; 255:469-483. [PMID: 35274157 DOI: 10.1007/s00232-022-00224-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
The structural organization and dynamic nature of the biomembrane components are important determinants for numerous cellular functions. Particularly, membrane proteins are critically important for various physiological functions and are important drug targets. The mechanistic insights on the complex functionality of membrane lipids and proteins can be elucidated by understanding the interplay between structure and dynamics. In this regard, membrane penetration depth represents an important parameter to obtain the precise depth of membrane-embedded molecules that often define the conformation and topology of membrane probes and proteins. In this review, we discuss about the widely used fluorescence quenching-based methods (parallax method, distribution analysis, and dual-quencher analysis) to accurately determine the membrane penetration depths of fluorescent probes that are either membrane-embedded or attached to lipids and proteins. Further, we also discuss a relatively novel fluorescence quenching method that utilizes tryptophan residue as the quencher, namely the tryptophan-induced quenching, which is sensitive to monitor small-scale conformational changes (short distances of < 15 Å) and useful in mapping distances in proteins. We have provided numerous examples for the benefit of readers to appreciate the importance and applicability of these simple yet powerful methods to study membrane proteins.
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Affiliation(s)
- Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF, Bidhannagar, Kolkata, 700 064, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF, Bidhannagar, Kolkata, 700 064, India.
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3
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Zeth K, Sancho-Vaello E. Structural Plasticity of LL-37 Indicates Elaborate Functional Adaptation Mechanisms to Bacterial Target Structures. Int J Mol Sci 2021; 22:ijms22105200. [PMID: 34068993 PMCID: PMC8156758 DOI: 10.3390/ijms22105200] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
The human cathelicidin LL-37 is a multifunctional peptide of the human innate immune system. Among the various functions of LL-37, its antimicrobial activity is important in controlling the microorganisms of the human body. The target molecules of LL-37 in bacteria include membrane lipids, lipopolysaccharides (LPS), lipoteichoic acid (LTA), proteins, DNA and RNA. In this mini-review, we summarize the entity of LL-37 structural data determined over the last 15 years and specifically discuss features implicated in the interactions with lipid-like molecules. For this purpose, we discuss partial and full-length structures of LL-37 determined in the presence of membrane-mimicking detergents. This constantly growing structural database is now composed of monomers, dimers, tetramers, and fiber-like structures. The diversity of these structures underlines an unexpected plasticity and highlights the conformational and oligomeric adaptability of LL-37 necessary to target different molecular scaffolds. The recent co-crystal structures of LL-37 in complex with detergents are particularly useful to understand how these molecules mimic lipids and LPS to induce oligomerization and fibrillation. Defined detergent binding sites provide deep insights into a new class of peptide scaffolds, widening our view on the fascinating world of the LL-37 structural factotum. Together, the new structures in their evolutionary context allow for the assignment of functionally conserved residues in oligomerization and target interactions. Conserved phenylalanine and arginine residues primarily mediate those interactions with lipids and LPS. The interactions with macromolecules such as proteins or DNA remain largely unexplored and open a field for future studies aimed at structures of LL-37 complexes. These complexes will then allow for the structure-based rational design of LL-37-derived peptides with improved antibiotic properties.
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Affiliation(s)
- Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
- Correspondence: (K.Z.); (E.S.-V.); Tel.: +45-604-666-29 (K.Z.)
| | - Enea Sancho-Vaello
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Correspondence: (K.Z.); (E.S.-V.); Tel.: +45-604-666-29 (K.Z.)
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4
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Anti-bacterial activity of inorganic nanomaterials and their antimicrobial peptide conjugates against resistant and non-resistant pathogens. Int J Pharm 2020; 586:119531. [PMID: 32540348 DOI: 10.1016/j.ijpharm.2020.119531] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 12/20/2022]
Abstract
This review details the antimicrobial applications of inorganic nanomaterials of mostly metallic form, and the augmentation of activity by surface conjugation of peptide ligands. The review is subdivided into three main sections, of which the first describes the antimicrobial activity of inorganic nanomaterials against gram-positive, gram-negative and multidrug-resistant bacterial strains. The second section highlights the range of antimicrobial peptides and the drug resistance strategies employed by bacterial species to counter lethality. The final part discusses the role of antimicrobial peptide-decorated inorganic nanomaterials in the fight against bacterial strains that show resistance. General strategies for the preparation of antimicrobial peptides and their conjugation to nanomaterials are discussed, emphasizing the use of elemental and metallic oxide nanomaterials. Importantly, the permeation of antimicrobial peptides through the bacterial membrane is shown to aid the delivery of nanomaterials into bacterial cells. By judicious use of targeting ligands, the nanomaterial becomes able to differentiate between bacterial and mammalian cells and, thus, reduce side effects. Moreover, peptide conjugation to the surface of a nanomaterial will alter surface chemistry in ways that lead to reduction in toxicity and improvements in biocompatibility.
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5
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The effect of chitosan and PEG polymers on stabilization of GF-17 structure: A molecular dynamics study. Carbohydr Polym 2020; 237:116124. [PMID: 32241401 DOI: 10.1016/j.carbpol.2020.116124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 01/18/2023]
Abstract
We examine the interactions of chitosan and polyethylene glycol (PEG) with antimicrobial peptide GF-17 to identify a suitable carrier to improve the peptide drug delivery systems. To this end, the molecular dynamics simulations are used to determine the interactions of a typical antimicrobial peptide GF-17 with the chitosan and PEG polymers. The findings indicate the great potential of the peptide to maintain its secondary structure in the adjacent to chitosan polymers. During the interaction with chitosan polymers, the structure of the peptide has smaller fluctuations compared to the PEG polymers. Also, in the presence of both the polymers, the PEG polymers are situated closer to the peptide than chitosan polymers. Moreover, the analysis indicates that the acidic residues and phenylalanine play a crucial role in peptide-polymer interactions. This research provides a valuable insight into the design of polymer surfaces for drug delivery applications such as controlled-release peptide delivery systems.
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6
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de Miguel Catalina A, Forbrig E, Kozuch J, Nehls C, Paulowski L, Gutsmann T, Hildebrandt P, Mroginski MA. The C-Terminal VPRTES Tail of LL-37 Influences the Mode of Attachment to a Lipid Bilayer and Antimicrobial Activity. Biochemistry 2019; 58:2447-2462. [DOI: 10.1021/acs.biochem.8b01297] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Enrico Forbrig
- Department of Physical Chemistry, Institut für Chemie, Technische Universität Berlin, Berlin 10623, Germany
| | - Jacek Kozuch
- Division of Chemistry, Stanford University, Stanford, Californa 94305, United States
| | - Christian Nehls
- Biophysics Department, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel 23845, Germany
| | - Laura Paulowski
- Biophysics Department, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel 23845, Germany
| | - Thomas Gutsmann
- Biophysics Department, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel 23845, Germany
| | - Peter Hildebrandt
- Department of Physical Chemistry, Institut für Chemie, Technische Universität Berlin, Berlin 10623, Germany
| | - Maria Andrea Mroginski
- Department of Physical Chemistry, Institut für Chemie, Technische Universität Berlin, Berlin 10623, Germany
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7
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Anderson CM, Cardenas A, Elber R, Webb LJ. Preferential Equilibrium Partitioning of Positively Charged Tryptophan into Phosphatidylcholine Bilayer Membranes. J Phys Chem B 2019; 123:170-179. [PMID: 30481465 PMCID: PMC6331081 DOI: 10.1021/acs.jpcb.8b09872] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/19/2018] [Indexed: 11/29/2022]
Abstract
The interactions between small molecules and lipid bilayers play a critical role in the function of cellular membranes. Understanding how a small molecule interacts with the lipid bilayer differently based on its charge reveals primordial mechanisms of transport across membranes and assists in the design of drug molecules that can penetrate cells. We have previously reported that tryptophan permeated through a phosphatidylcholine lipid bilayer membrane at a faster rate when it was positively charged (Trp+) than when negatively charged (Trp-), which corresponded to a lower potential of mean force (PMF) barrier determined through simulations. In this report, we demonstrate that Trp+ partitions into the lipid bilayer membrane to a greater degree than Trp- by interacting with the ester linkage of a phosphatidylcholine lipid, where it is stabilized by the electron withdrawing glycerol functional group. These results are in agreement with tryptophan's known role as an anchor for transmembrane proteins, though the tendency for binding of a positively charged tryptophan is surprising. We discuss the implications of our results on the mechanisms of unassisted permeation and penetration of small molecules within and across lipid bilayer membranes based on molecular charge, shape, and molecular interactions within the bilayer structure.
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Affiliation(s)
- Cari M. Anderson
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
| | - Alfredo Cardenas
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
| | - Ron Elber
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
| | - Lauren J. Webb
- Department
of Chemistry, Institute for Computational Engineering and Sciences, Institute for Cellular
and Molecular Biology, Texas Materials Institute, The University of Texas at Austin, 2506 Speedway STOP A5300, Austin, Texas 78712, United States
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8
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Jahangiri S, Jafari M, Arjomand M, Mehrnejad F. Molecular insights into the interactions of GF‐17 with the gram‐negative and gram‐positive bacterial lipid bilayers. J Cell Biochem 2018; 119:9205-9216. [DOI: 10.1002/jcb.27187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/24/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Samira Jahangiri
- Department of Chemical Engineering South Tehran Branch, Islamic Azad University Tehran Iran
| | - Majid Jafari
- Computational Nanobiotechnology Laboratory, Department of Life Sciences Engineering Faculty of New Sciences and Technologies, University of Tehran Tehran Iran
| | - Mehdi Arjomand
- Department of Chemical Engineering South Tehran Branch, Islamic Azad University Tehran Iran
| | - Faramarz Mehrnejad
- Computational Nanobiotechnology Laboratory, Department of Life Sciences Engineering Faculty of New Sciences and Technologies, University of Tehran Tehran Iran
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9
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Zhao L, Cao Z, Bian Y, Hu G, Wang J, Zhou Y. Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers. Int J Mol Sci 2018; 19:ijms19041186. [PMID: 29652823 PMCID: PMC5979298 DOI: 10.3390/ijms19041186] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 12/29/2022] Open
Abstract
Cathelicidins are a large family of cationic antimicrobial peptides (AMPs) found in mammals with broad spectrum antimicrobial activity. LL-37 is the sole amphipathic α-helical AMP from human Cathelicidins family. In addition to its bactericidal capability, LL-37 has antiviral, anti-tumor, and immunoregulatory activity. Despite many experimental studies, its molecular mechanism of action is not yet fully understood. Here, we performed three independent molecular dynamics simulations (600 ns or more) of a LL-37 peptide in the presence of 256 lipid bilayers with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) mimicking bacterial and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) mimicking mammalian membranes. We found that LL-37 can be quickly absorbed onto the POPG bilayer without loss of its helical conformation in the core region and with the helix lying in parallel to the bilayer. The POPG bilayer was deformed. In contrast, LL-37 is slower in reaching the POPC surface and loss much of its helical conformation during the interaction with the bilayer. LL-37 only partially entered the POPC bilayer without significant deformation of the membrane. The observed difference for different bilayers is largely due to the fact that LL-37 is positively charged, POPG is negatively charged, and POPC is neutral. Our simulation results demonstrated the initial stage of disruption of the bacterial membrane by LL-37 in atomic details. Comparison to experimental results on LL-37 and simulation studies in other systems was made.
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Affiliation(s)
- Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, Queensland 4222, Australia.
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10
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Kim EY, Rajasekaran G, Shin SY. LL-37-derived short antimicrobial peptide KR-12-a5 and its d -amino acid substituted analogs with cell selectivity, anti-biofilm activity, synergistic effect with conventional antibiotics, and anti-inflammatory activity. Eur J Med Chem 2017; 136:428-441. [DOI: 10.1016/j.ejmech.2017.05.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/21/2017] [Accepted: 05/09/2017] [Indexed: 12/25/2022]
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11
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Mohapatra S, Saha A, Mondal P, Jana B, Ghosh S, Biswas A, Ghosh S. Synergistic Anticancer Effect of Peptide-Docetaxel Nanoassembly Targeted to Tubulin: Toward Development of Dual Warhead Containing Nanomedicine. Adv Healthc Mater 2017; 6. [PMID: 27782376 DOI: 10.1002/adhm.201600718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/12/2016] [Indexed: 01/09/2023]
Abstract
Microtubule dynamics play a crucial role in cancer cell division. Various drugs are developed to target microtubule. Although a few of them show potential in treatment of cancer, but success rate is limited due to their poor bioavailability and lack of specificity. Thus, development of highly bioavailable and target specific anticancer drug is extremely necessary. To address these key issues, here, a combination of approaches such as development of a dodecapeptide-docetaxel nanoassembly targeted to tubulin and MUC1 (mucin 1, cell surface associated glycoprotein) targeting oligonucleotide aptamer conjugated liposome for delivering peptide-docetaxel nanoassembly into the breast cancer cell have been demonstrated. These studies reveal that the peptide forms nanoassembly and entraps docetaxel drug. Further, the liposomal formulation of peptide-docetaxel exerts synergistic anticancer effect, activates key mitotic check point proteins, and inhibits bipolar spindle formation, metastatic cancer cell migration, and growth of tumor mimicking 3D multicellular spheroid.
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Affiliation(s)
- Saswat Mohapatra
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Indian Institute of Chemical Biology Campus; 4, Raja S. C. Mullick Road Kolkata 700 032 West Bengal India
| | - Abhijit Saha
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Prasenjit Mondal
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Indian Institute of Chemical Biology Campus; 4, Raja S. C. Mullick Road Kolkata 700 032 West Bengal India
| | - Batakrishna Jana
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Subhajit Ghosh
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Atanu Biswas
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Indian Institute of Chemical Biology Campus; 4, Raja S. C. Mullick Road Kolkata 700 032 West Bengal India
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12
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López-Peña I, Leigh BS, Schlamadinger DE, Kim JE. Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy. Biochemistry 2015. [PMID: 26219819 DOI: 10.1021/acs.biochem.5b00514] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Raman spectroscopy is a form of vibrational spectroscopy based on inelastic scattering of light. In resonance Raman spectroscopy, the wavelength of the incident light falls within an absorption band of a chromophore, and this overlap of excitation and absorption energy greatly enhances the Raman scattering efficiency of the absorbing species. The ability to probe vibrational spectra of select chromophores within a complex mixture of molecules makes resonance Raman spectroscopy an excellent tool for studies of biomolecules. In this Current Topic, we discuss the type of molecular insights obtained from steady-state and time-resolved resonance Raman studies of a prototypical photoactive protein, rhodopsin. We also review recent efforts in ultraviolet resonance Raman investigations of soluble and membrane-associated biomolecules, including integral membrane proteins and antimicrobial peptides. These examples illustrate that resonance Raman is a sensitive, selective, and practical method for studying the structures of biological molecules, and the molecular bonding, geometry, and environments of protein cofactors, the backbone, and side chains.
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Affiliation(s)
- Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Diana E Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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13
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Armijo G, Okerblom J, Cauvi DM, Lopez V, Schlamadinger DE, Kim J, Arispe N, De Maio A. Interaction of heat shock protein 70 with membranes depends on the lipid environment. Cell Stress Chaperones 2014; 19:877-86. [PMID: 24789271 PMCID: PMC4389847 DOI: 10.1007/s12192-014-0511-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/03/2014] [Accepted: 04/04/2014] [Indexed: 12/24/2022] Open
Abstract
Heat shock proteins (hsp) are well recognized for their protein folding activity. Additionally, hsp expression is enhanced during stress conditions to preserve cellular homeostasis. Hsp are also detected outside cells, released by an active mechanism independent of cell death. Extracellular hsp appear to act as signaling molecules as part of a systemic response to stress. Extracellular hsp do not contain a consensus signal for their secretion via the classical ER-Golgi compartment. Therefore, they are likely exported by an alternative mechanism requiring translocation across the plasma membrane. Since Hsp70, the major inducible hsp, has been detected on surface of stressed cells, we propose that membrane interaction is the first step in the export process. The question that emerges is how does this charged cytosolic protein interact with lipid membranes? Prior studies have shown that Hsp70 formed ion conductance pathways within artificial lipid bilayers. These early observations have been extended herewith using a liposome insertion assay. We showed that Hsp70 selectively interacted with negatively charged phospholipids, particularly phosphatidyl serine (PS), within liposomes, which was followed by insertion into the lipid bilayer, forming high-molecular weight oligomers. Hsp70 displayed a preference for less fluid lipid environments and the region embedded into the lipid membrane was mapped toward the C-terminus end of the molecule. The results from our studies provide evidence of an unexpected ability of a large, charged protein to become inserted into a lipid membrane. This observation provides a new paradigm for the interaction of proteins with lipid environments. In addition, it may explain the export mechanism of an increasing number of proteins that lack the consensus secretory signals.
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Affiliation(s)
- Gabrielle Armijo
- />Initiative for Maximizing Student Development (IMSD) Program, University of California San Diego, La Jolla, CA USA
| | - Jonathan Okerblom
- />Initiative for Maximizing Student Development (IMSD) Program, University of California San Diego, La Jolla, CA USA
| | - David M. Cauvi
- />Department of Surgery, School of Medicine, La Jolla, CA USA
| | - Victor Lopez
- />Initiative for Maximizing Student Development (IMSD) Program, University of California San Diego, La Jolla, CA USA
| | - Diana E. Schlamadinger
- />Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Judy Kim
- />Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | | | - Antonio De Maio
- />Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA USA
- />Departments of Surgery and Neuroscience, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739 CA USA
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14
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High-quality 3D structures shine light on antibacterial, anti-biofilm and antiviral activities of human cathelicidin LL-37 and its fragments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2160-72. [PMID: 24463069 DOI: 10.1016/j.bbamem.2014.01.016] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/26/2013] [Accepted: 01/10/2014] [Indexed: 01/07/2023]
Abstract
Host defense antimicrobial peptides are key components of human innate immunity that plays an indispensible role in human health. While there are multiple copies of cathelicidin genes in horses, cattle, pigs, and sheep, only one cathelicidin gene is found in humans. Interestingly, this single cathelicidin gene can be processed into different forms of antimicrobial peptides. LL-37, the most commonly studied form, is not only antimicrobial but also possesses other functional roles such as chemotaxis, apoptosis, wound healing, immune modulation, and cancer metastasis. This article reviews recent advances made in structural and biophysical studies of human LL-37 and its fragments, which serve as a basis to understand their antibacterial, anti-biofilm and antiviral activities. High-quality structures were made possible by using improved 2D NMR methods for peptide fragments and 3D NMR spectroscopy for intact LL-37. The two hydrophobic domains in the long amphipathic helix (residues 2-31) of LL-37 separated by a hydrophilic residue serine 9 explain its cooperative binding to bacterial lipopolysaccharides (LPS). Both aromatic rings (F5, F6, F17, and F27) and interfacial basic amino acids of LL-37 directly interact with anionic phosphatidylglycerols (PG). Although the peptide sequences reported in the literature vary slightly, there is a consensus that the central helix of LL-37 is essential for disrupting superbugs (e.g., MRSA), bacterial biofilms, and viruses such as human immunodeficiency virus 1 (HIV-1) and respiratory syncytial virus (RSV). In the central helix, the central arginine R23 is of particular importance in binding to bacterial membranes or DNA. Mapping the functional roles of the cationic amino acids of the major antimicrobial region of LL-37 provides a basis for designing antimicrobial peptides with desired properties. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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He Y, Lazaridis T. Activity determinants of helical antimicrobial peptides: a large-scale computational study. PLoS One 2013; 8:e66440. [PMID: 23776672 PMCID: PMC3680375 DOI: 10.1371/journal.pone.0066440] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/09/2013] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial peptides (AMPs), produced by a wide range of organisms, have attracted attention due to their potential use as novel antibiotics. The majority of these peptides are cationic and are thought to function by permeabilizing the bacterial membrane, either by making pores or by dissolving it ('carpet' model). A key hypothesis in the literature is that antimicrobial and hemolytic activity correlate with binding affinity to anionic and zwitterionic membranes, respectively. Here we test this hypothesis by using binding free energy data collected from the literature and theoretical binding energies calculated from implicit membrane models for 53 helical AMPs. We indeed find a correlation between binding energy and biological activity, depending on membrane anionic content: antibacterial activity correlates best with transfer energy to membranes with anionic lipid fraction higher than 30% and hemolytic activity correlates best with transfer energy to a 10% anionic membrane. However, the correlations are weak, with correlation coefficient up to 0.4. Weak correlations of the biological activities have also been found with other physical descriptors of the peptides, such as surface area occupation, which correlates significantly with antibacterial activity; insertion depth, which correlates significantly with hemolytic activity; and structural fluctuation, which correlates significantly with both activities. The membrane surface coverage by many peptides at the MIC is estimated to be much lower than would be required for the 'carpet' mechanism. Those peptides that are active at low surface coverage tend to be those identified in the literature as pore-forming. The transfer energy from planar membrane to cylindrical and toroidal pores was also calculated for these peptides. The transfer energy to toroidal pores is negative in almost all cases while that to cylindrical pores is more favorable in neutral than in anionic membranes. The transfer energy to pores correlates with the deviation from predictions of the 'carpet' model.
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Affiliation(s)
- Yi He
- Department of Chemistry, City College of New York, New York, New York, United States of America
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Saar-Dover R, Ashkenazi A, Shai Y. Peptide interaction with and insertion into membranes. Methods Mol Biol 2013; 1033:173-83. [PMID: 23996178 DOI: 10.1007/978-1-62703-487-6_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Natural and synthetic membrane active peptides as well as fragments from membrane proteins interact with membranes. In several cases, such interactions cause the insertion of the peptides to the membrane and their assembly within the lipid bilayer. Here we present spectroscopic approaches utilizing NBD and rhodamine fluorescently labeled peptides to measure peptide-membrane interaction and peptide-peptide interaction within the membrane. The usage of the physical properties of NBD and rhodamine in solution and in membranes provides useful information on the interplay between peptides and lipids.
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Affiliation(s)
- Ron Saar-Dover
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Patois E, Larmour I, Bell S, Palais C, Capelle M, Gurny R, Arvinte T. Ultraviolet Resonance Raman spectroscopy used to study formulations of salmon calcitonin, a starch–peptide conjugate and TGF-β3. Eur J Pharm Biopharm 2012; 81:392-8. [DOI: 10.1016/j.ejpb.2012.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 01/27/2012] [Accepted: 02/27/2012] [Indexed: 10/28/2022]
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Real-time attack on single Escherichia coli cells by the human antimicrobial peptide LL-37. Proc Natl Acad Sci U S A 2011; 108:E77-81. [PMID: 21464330 DOI: 10.1073/pnas.1101130108] [Citation(s) in RCA: 197] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural antimicrobial peptides (AMPs) provide prototypes for the design of unconventional antimicrobial agents. Existing bulk assays measure AMP activity but do not provide details of the growth-halting mechanism. We use fluorescence microscopy to directly observe the attack of the human antimicrobial peptide LL-37 on single Escherichia coli cells in real time. Our findings strongly suggest that disruption of the cytoplasmic membrane is not the growth-halting mechanism. At 8 μM, LL-37 binding saturates the outer membrane (OM) within 1 min. Translocation across the OM and access to the periplasmic space (5-25 min later) correlates in time with the halting of growth. Septating cells are attacked more readily than nonseptating cells. The halting of growth may occur because of LL-37 interference with cell wall biogenesis. Only well after growth halts does the peptide permeabilize the cytoplasmic membrane to GFP and the small dye Sytox Green. The assay enables dissection of antimicrobial design criteria into two parts: translocation across the OM and the subsequent halting of growth.
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Schlamadinger DE, Daschbach MM, Gokel GW, Kim JE. UV resonance Raman study of cation-π interactions in an indole crown ether. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2011; 42:633-638. [PMID: 25635155 PMCID: PMC4307609 DOI: 10.1002/jrs.2781] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
UV resonance Raman (UVRR) spectroscopy is used to probe changes in vibrational structure associated with cation-π interactions for the most prevalent amino acid π -donor, tryptophan. The model compound studied here is a diaza crown ether with two indole substituents. In the presence of sodium or potassium sequestered in the crown ether, or a protonated diaza group on the compound, the indole moieties participate in a cation-π interaction in which the pyrrolo group acts as the primary π-donor. Systematic shifts in relative intensity in the 760-780 cm-1 region are observed upon formation of this cation-π interaction; we propose that these modifications reflect shifts of the delocalized, ring-breathing W18 and hydrogen-out-of-plane (HOOP) vibrational modes in this spectral region. The observed changes are attributed to perturbations of the π-electron density as well as of normal modes that involve large displacement of the hydrogen atom on the C2 position of the pyrrole ring. Modest variations in the UVRR spectra for the three complexes studied here are correlated to differences in cation-π strength. Specifically, the UVRR spectrum of the sodium-bound complex differs from those of the potassium-bound or protonated-diaza complexes, and may reflect the observation that the C2 hydrogen atom in the sodium-bound complex exhibits the greatest perturbation relative to the other species. Normal modes sensitive to hydrogen-bonding, such as the tryptophan W10, W9, and W8 modes, also undergo shifts in the presence of the salts. These shifts reflect the strength of interaction of the indole N-H group with the iodide or hexafluorophosphate counteranion. The current observation that the W18 and HOOP normal mode regions of the indole crown ether compound are sensitive to cation-pyrrolo π interactions suggests that this region may provide reliable spectroscopic evidence of these important interactions in proteins.
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Affiliation(s)
- Diana E. Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 USA
| | | | - George W. Gokel
- Department of Chemistry, Washington University, St. Louis, MO 63110 USA
- Departments of Chemistry and Biochemistry, and Biology, Center for Nanoscience, University of Missouri – St. Louis, St. Louis, MO 63121 USA
- Department of Developmental Biology, Washington University, St. Louis, MO 63110 USA
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 USA
- Correspondence to: Judy E. Kim, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA.
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