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Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins. CRYSTALS 2021. [DOI: 10.3390/cryst11091032] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.
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The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins. Int J Mol Sci 2020; 21:ijms21228776. [PMID: 33233627 PMCID: PMC7699789 DOI: 10.3390/ijms21228776] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Tryptophan (Trp) holds a unique place in biology for a multitude of reasons. It is the largest of all twenty amino acids in the translational toolbox. Its side chain is indole, which is aromatic with a binuclear ring structure, whereas those of Phe, Tyr, and His are single-ring aromatics. In part due to these elaborate structural features, the biosynthetic pathway of Trp is the most complex and the most energy-consuming among all amino acids. Essential in the animal diet, Trp is also the least abundant amino acid in the cell, and one of the rarest in the proteome. In most eukaryotes, Trp is the only amino acid besides Met, which is coded for by a single codon, namely UGG. Due to the large and hydrophobic π-electron surface area, its aromatic side chain interacts with multiple other side chains in the protein, befitting its strategic locations in the protein structure. Finally, several Trp derivatives, namely tryptophylquinone, oxitriptan, serotonin, melatonin, and tryptophol, have specialized functions. Overall, Trp is a scarce and precious amino acid in the cell, such that nature uses it parsimoniously, for multiple but selective functions. Here, the various aspects of the uniqueness of Trp are presented in molecular terms.
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McKay MJ, Afrose F, Koeppe RE, Greathouse DV. Helix formation and stability in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2108-2117. [PMID: 29447916 DOI: 10.1016/j.bbamem.2018.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023]
Abstract
In this article we review current understanding of basic principles for the folding of membrane proteins, focusing on the more abundant alpha-helical class. Membrane proteins, vital to many biological functions and implicated in numerous diseases, fold into their active conformations in the complex environment of the cell bilayer membrane. While many membrane proteins rely on the translocon and chaperone proteins to fold correctly, others can achieve their functional form in the absence of any translation apparatus or other aides. Nevertheless, the spontaneous folding process is not well understood at the molecular level. Recent findings suggest that helix fraying and loop formation may be important for overall structure, dynamics and regulation of function. Several types of membrane helices with ionizable amino acids change their topology with pH. Additionally we note that some peptides, including many that are rich in arginine, and a particular analogue of gramicidin, are able passively to translocate across cell membranes. The findings indicate that a final protein structure in a lipid-bilayer membrane is sequence-based, with lipids contributing to stability and regulation. While much progress has been made toward understanding the folding process for alpha-helical membrane proteins, it remains a work in progress. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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Beaven AH, Sodt AJ, Pastor RW, Koeppe RE, Andersen OS, Im W. Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. J Chem Theory Comput 2017; 13:5054-5064. [PMID: 28870079 DOI: 10.1021/acs.jctc.7b00400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Previous experiments have shown that the lifetime of a gramicidin A dimer channel (which forms from two nonconducting monomers) in a lipid bilayer is modulated by mutations of the tryptophan (Trp) residues at the bilayer-water interface. We explore this further using extensive molecular dynamics simulations of various gA dimer and monomer mutants at the Trp positions in phosphatidylcholine bilayers with different tail lengths. gA interactions with the surrounding bilayer are strongly modulated by mutating these Trp residues. There are three principal effects: eliminating residue hydrogen bonding ability (i.e., reducing the channel-monolayer coupling strength) reduces the extent of the bilayer deformation caused by the assembled dimeric channel; a residue's size and geometry affects its orientation, leading to different hydrogen bonding partners; and increasing a residue's hydrophobicity increases the depth of gA monomer insertion relative to the bilayer center, thereby increasing the lipid bending frustration.
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Affiliation(s)
- Andrew H Beaven
- Department of Chemistry, The University of Kansas , Lawrence, Kansas 66045, United States
| | | | | | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College , New York, New York 10065, United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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Chaudhuri A, Haldar S, Sun H, Koeppe RE, Chattopadhyay A. Importance of indole N-H hydrogen bonding in the organization and dynamics of gramicidin channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:419-28. [PMID: 24148157 DOI: 10.1016/j.bbamem.2013.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 01/25/2023]
Abstract
The linear ion channel peptide gramicidin represents an excellent model for exploring the principles underlying membrane protein structure and function, especially with respect to tryptophan residues. The tryptophan residues in gramicidin channels are crucial for the structure and function of the channel. In order to test the importance of indole hydrogen bonding for the biophysical properties of gramicidin channels, we monitored the effect of N-methylation of gramicidin tryptophans, using a combination of steady state and time-resolved fluorescence approaches along with circular dichroism spectroscopy. We show here that in the absence of the hydrogen bonding ability of tryptophans, tetramethyltryptophan gramicidin (TM-gramicidin) is unable to maintain the single stranded, head-to-head dimeric channel conformation in membranes. Our results show that TM-gramicidin displays a red-shifted fluorescence emission maximum, lower red edge excitation shift (REES), and higher fluorescence intensity and lifetime, consistent with its nonchannel conformation. This is in agreement with the measured location (average depth) of the 1-methyltryptophans in TM-gramicidin using the parallax method. These results bring out the usefulness of 1-methyltryptophan as a fluorescent tool to examine the hydrogen bonding ability of tryptophans in proteins and peptides. We conclude that changes in the hydrogen bonding ability of tryptophans, along with coupled changes in peptide backbone structure induce the loss of single stranded β(6.3) helical dimer conformation. These results agree with earlier results from size-exclusion chromatography and single-channel measurements for TM-gramicidin, and confirm the importance of indole hydrogen bonding for the conformation and function of ion channels and membrane proteins.
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Affiliation(s)
- Arunima Chaudhuri
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Sychev SV, Barsukov LI, Ivanov VT. Conformation of gramicidin A in Triton X-100 micelles from CD and FTIR data: a clean example of antiparallel double β5.6 helix formation. J Pept Sci 2013; 19:452-8. [DOI: 10.1002/psc.2519] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/09/2013] [Accepted: 04/19/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Sergei V. Sychev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
| | - Leonid I. Barsukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
| | - Vadim T. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; 16/10 Miklukho-Maklaya str. Moscow 117997 Russia
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de Jesus AJ, Allen TW. The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:864-76. [PMID: 22989724 DOI: 10.1016/j.bbamem.2012.09.009] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/27/2022]
Abstract
Tryptophan (Trp) is abundant in membrane proteins, preferentially residing near the lipid-water interface where it is thought to play a significant anchoring role. Using a total of 3 μs of molecular dynamics simulations for a library of hydrophobic WALP-like peptides, a long poly-Leu α-helix, and the methyl-indole analog, we explore the thermodynamics of the Trp movement in membranes that governs the stability and orientation of transmembrane protein segments. We examine the dominant hydrogen-bonding interactions between the Trp and lipid carbonyl and phosphate moieties, cation-π interactions to lipid choline moieties, and elucidate the contributions to the thermodynamics that serve to localize the Trp, by ~4 kcal/mol, near the membrane glycerol backbone region. We show a striking similarity between the free energy to move an isolated Trp side chain to that found from a wide range of WALP peptides, suggesting that the location of this side chain is nearly independent of the host transmembrane segment. Our calculations provide quantitative measures that explain Trp's role as a modulator of responses to hydrophobic mismatch, providing a deeper understanding of how lipid composition may control a range of membrane active peptides and proteins.
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Haldar S, Chaudhuri A, Gu H, Koeppe RE, Kombrabail M, Krishnamoorthy G, Chattopadhyay A. Membrane organization and dynamics of "inner pair" and "outer pair" tryptophan residues in gramicidin channels. J Phys Chem B 2012; 116:11056-64. [PMID: 22892073 PMCID: PMC3442126 DOI: 10.1021/jp304846f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The linear ion channel peptide gramicidin serves as an excellent prototype for monitoring the organization, dynamics, and function of membrane-spanning channels. The tryptophan residues in gramicidin channels are crucial for establishing and maintaining the structure and function of the channel in the membrane bilayer. In order to address the basis of differential importance of tryptophan residues in the gramicidin channel, we monitored the effects of pairwise substitution of two of the four gramicidin tryptophans, the inner pair (Trp-9 and -11) and the outer pair (Trp-13 and -15), using a combination of steady state and time-resolved fluorescence approaches and circular dichroism spectroscopy. We show here that these double tryptophan gramicidin analogues adopt different conformations in membranes, suggesting that the conformational preference of double tryptophan gramicidin analogues is dictated by the positions of the tryptophans in the sequence. These results assume significance in the context of recent observations that the inner pair of tryptophans (Trp-9 and -11) is more important for gramicidin channel formation and channel conductance. These results could be potentially useful in analyzing the effect of tryptophan substitution on the functioning of ion channels and membrane proteins.
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Affiliation(s)
- Sourav Haldar
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India
| | - Arunima Chaudhuri
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India
| | - Hong Gu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, U.S.A
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, U.S.A
| | - Mamata Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - G. Krishnamoorthy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Amitabha Chattopadhyay
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India
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Vostrikov VV, Gu H, Ingólfsson HI, Hinton JF, Andersen OS, Roux B, Koeppe RE. Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments. J Phys Chem B 2011; 115:7427-32. [PMID: 21574558 PMCID: PMC3114435 DOI: 10.1021/jp200906y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motional properties are important for understanding protein function and are accessible to NMR relaxation measurements. The goal of this study is to investigate the internal dynamics occurring in gramicidin A (gA) channels in order to provide benchmark experimental data for comparison with the results of molecular dynamics simulations. We therefore synthesized several (15)N isotope-enriched gA samples, covering all backbone residues as well as the Trp indole side chains for NMR relaxation experiments. On the basis of the (15)N NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we determined T(1), T(2), and heteronuclear NOE values for backbone and indole (15)NH groups. The results indicate that the SDS-incorporated gA channel is a constrained structure without an especially "floppy" region. The NMR observables, particularly those for backbone groups, are predicted well by the molecular dynamics simulations in the accompanying article (DOI 10.1021/jp200904d ).
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Affiliation(s)
- Vitaly V Vostrikov
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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Gu H, Lum K, Kim JH, Greathouse DV, Andersen OS, Koeppe RE. The membrane interface dictates different anchor roles for "inner pair" and "outer pair" tryptophan indole rings in gramicidin A channels. Biochemistry 2011; 50:4855-66. [PMID: 21539360 DOI: 10.1021/bi200136e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the effects of substituting two of the four tryptophans (the "inner pair" Trp(9) and Trp(11) or the "outer pair" Trp(13) and Trp(15)) in gramicidin A (gA) channels. The conformational preferences of the doubly substituted gA analogues were assessed using circular dichroism spectroscopy and size-exclusion chromatography, which show that the inner tryptophans 9 and 11 are critical for the gA's conformational preference in lipid bilayer membranes. [Phe(13,15)]gA largely retains the single-stranded helical channel structure, whereas [Phe(9,11)]gA exists primarily as double-stranded conformers. Within this context, the (2)H NMR spectra from labeled tryptophans were used to examine the changes in average indole ring orientations, induced by the Phe substitutions and by the shift in conformational preference. Using a method for deuterium labeling of already synthesized gAs, we introduced deuterium selectively onto positions C2 and C5 of the remaining tryptophan indole rings in the substituted gA analogues for solid-state (2)H NMR spectroscopy. The (least possible) changes in orientation and overall motion of each indole ring were estimated from the experimental spectra. Regardless of the mixture of backbone folds, the indole ring orientations observed in the analogues are similar to those found previously for gA channels. Both Phe-substituted analogues form single-stranded channels, as judged from the formation of heterodimeric channels with the native gA. [Phe(13,15)]gA channels have Na(+) currents that are ~50% and lifetimes that are ~80% of those of native gA channels. The double-stranded conformer(s) of [Phe(9,11)]gA do not form detectable channels. The minor single-stranded population of [Phe(9,11)]gA forms channels with Na(+) currents that are ~25% and single-channel lifetimes that are ~300% of those of native gA channels. Our results suggest that Trp(9) and Trp(11), when "reaching" for the interface, tend to drive both monomer folding (to "open" a channel) and dimer dissociation (to "close" a channel). Furthermore, the dipoles of Trp(9) and Trp(11) are relatively more important for the single-channel conductance than are the dipoles of Trp(13) and Trp(15).
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Affiliation(s)
- Hong Gu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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11
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Svensson FR, Lincoln P, Nordén B, Esbjörner EK. Tryptophan orientations in membrane-bound gramicidin and melittin—a comparative linear dichroism study on transmembrane and surface-bound peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:219-28. [DOI: 10.1016/j.bbamem.2010.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 09/20/2010] [Accepted: 10/08/2010] [Indexed: 10/18/2022]
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Schlamadinger DE, Gable JE, Kim JE. Hydrogen bonding and solvent polarity markers in the uv resonance raman spectrum of tryptophan: application to membrane proteins. J Phys Chem B 2010; 113:14769-78. [PMID: 19817473 DOI: 10.1021/jp905473y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ultraviolet resonance Raman (UVRR) spectra of tryptophan compounds in various solvents and a model peptide are presented and reveal systematic changes that reflect solvent polarity, hydrogen bond strength, and cation-pi interaction. The commonly utilized UVRR spectral marker for environment polarity that has been based on off-resonance Raman data, the tryptophan Fermi doublet ratio I1360/I1340, exhibits different values in on- and off-resonance Raman spectra as well as for different tryptophan derivatives. Specifically, the UVRR Fermi doublet ratio for indole ranges from 0.3 in polar solvents to 0.8 in nonpolar solvents, whereas the respective values reported here and previously for off-resonance Raman spectra are 0.5-1.3. UVRR Fermi doublet ratios for the more biologically relevant molecule, N-acetyl tryptophan ethyl ester (NATEE), are in a smaller range of 1.1 (polar solvent) to 1.7 (nonpolar solvent) and correlate to the solvent polarity/polarization parameters pi* and ETN. As has been reported previously, several UVRR modes are also sensitive to the hydrogen bond strength of the indole N-H moiety. Here, we report a new unambiguous marker for H-bonding: the ratio of the W10 (approximately 1237 cm-1) intensity to that of the W9 (approximately 1254 cm-1) mode (RW10). This ratio is 0.7 for NATEE in the absence of hydrogen bond acceptors and increases to 3.1 in the presence of strong hydrogen bond acceptors, with a value of 2.3 in water. The W8 and W17 modes shift more than +10 and approximately -5 cm-1 upon increase in hydrogen bond strength; this range for W17 is smaller than that reported previously and reflects a more realistic range for proteins and peptides in solution. Finally, our data provide evidence for change in the W18 and W16 relative intensity in the presence of cation-pi interactions. These UVRR markers are utilized to interpret spectra of model membrane-bound systems tryptophan octyl ester and the peptide toxin melittin. These spectra reveal the importance of intra- and intermolecular hydrogen bonding and cation-pi interactions that likely influence the partitioning of membrane-associated biomolecules to lipid bilayers or self-associated soluble oligomers. The UVRR analysis presented here modifies and augments prior reports and provides an unambiguous set of spectral makers that can be applied to elucidate the molecular microenvironment and structure of a wide range of complex systems, including anchoring tryptophan residues in membrane proteins and peptides.
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Affiliation(s)
- Diana E Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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Mori T, Okamoto Y. Folding simulations of gramicidin A into the β-helix conformations: Simulated annealing molecular dynamics study. J Chem Phys 2009; 131:165103. [DOI: 10.1063/1.3247578] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Abad C, Martínez-Gil L, Tamborero S, Mingarro I. Membrane topology of gp41 and amyloid precursor protein: interfering transmembrane interactions as potential targets for HIV and Alzheimer treatment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2132-41. [PMID: 19619504 PMCID: PMC7094694 DOI: 10.1016/j.bbamem.2009.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 06/29/2009] [Accepted: 07/13/2009] [Indexed: 01/08/2023]
Abstract
The amyloid precursor protein (APP), that plays a critical role in the development of senile plaques in Alzheimer disease (AD), and the gp41 envelope protein of the human immunodeficiency virus (HIV), the causative agent of the acquired immunodeficiency syndrome (AIDS), are single-spanning type-1 transmembrane (TM) glycoproteins with the ability to form homo-oligomers. In this review we describe similarities, both in structural terms and sequence determinants of their TM and juxtamembrane regions. The TM domains are essential not only for anchoring the proteins in membranes but also have functional roles. Both TM segments contain GxxxG motifs that drive TM associations within the lipid bilayer. They also each possess similar sequence motifs, positioned at the membrane interface preceding their TM domains. These domains are known as cholesterol recognition/interaction amino acid consensus (CRAC) motif in gp41 and CRAC-like motif in APP. Moreover, in the cytoplasmic domain of both proteins other α-helical membranotropic regions with functional implications have been identified. Recent drug developments targeting both diseases are reviewed and the potential use of TM interaction modulators as therapeutic targets is discussed.
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Affiliation(s)
- Concepción Abad
- Departament de Bioquímica i Biologia Molecular, Universitat de València. Dr. Moliner, 50, E-46100 Burjassot, Spain
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Sun H, Greathouse DV, Andersen OS, Koeppe RE. The preference of tryptophan for membrane interfaces: insights from N-methylation of tryptophans in gramicidin channels. J Biol Chem 2008; 283:22233-43. [PMID: 18550546 PMCID: PMC2494914 DOI: 10.1074/jbc.m802074200] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 06/03/2008] [Indexed: 11/06/2022] Open
Abstract
To better understand the structural and functional roles of tryptophan at the membrane/water interface in membrane proteins, we examined the structural and functional consequences of Trp --> 1-methyl-tryptophan substitutions in membrane-spanning gramicidin A channels. Gramicidin A channels are miniproteins that are anchored to the interface by four Trps near the C terminus of each subunit in a membrane-spanning dimer. We masked the hydrogen bonding ability of individual or multiple Trps by 1-methylation of the indole ring and examined the structural and functional changes using circular dichroism spectroscopy, size exclusion chromatography, solid state (2)H NMR spectroscopy, and single channel analysis. N-Methylation causes distinct changes in the subunit conformational preference, channel-forming propensity, single channel conductance and lifetime, and average indole ring orientations within the membrane-spanning channels. The extent of the local ring dynamic wobble does not increase, and may decrease slightly, when the indole NH is replaced by the non-hydrogen-bonding and more bulky and hydrophobic N-CH(3) group. The changes in conformational preference, which are associated with a shift in the distribution of the aromatic residues across the bilayer, are similar to those observed previously with Trp --> Phe substitutions. We conclude that indole N-H hydrogen bonding is of major importance for the folding of gramicidin channels. The changes in ion permeability, however, are quite different for Trp --> Phe and Trp --> 1-methyl-tryptophan substitutions, indicating that the indole dipole moment and perhaps also ring size and are important for ion permeation through these channels.
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Affiliation(s)
- Haiyan Sun
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
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Yoshida N, Mita T, Onda M. Susceptibilities of Phospholipid Membranes Containing Cholesterol or Ergosterol to Gramicidin and its Derivative Incorporated in Lysophospholipid Micelles. J Biochem 2008; 144:167-76. [DOI: 10.1093/jb/mvn056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Abstract
The linear peptide gramicidin forms prototypical ion channels specific for monovalent cations and has been used extensively to study the organization, dynamics, and function of membrane-spanning channels. The tryptophan residues in gramicidin channels are crucial for maintaining the structure and function of the channel. We explored the structural basis for the reduction in channel conductance in the case of single-tryptophan analogs of gramicidin with three Trp --> hydrophobic substitutions using a combination of fluorescence approaches, which include red edge excitation shift and membrane penetration depth analysis, size-exclusion chromatography, and circular dichroism spectroscopy. We show here that the gramicidin analogs containing single-tryptophan residues adopt a mixture of nonchannel and channel conformations, as evident from analysis of membrane penetration depth, size-exclusion chromatography, and backbone circular dichroism data. These results are potentially useful in analyzing the effect of tryptophan substitution on the functioning of other ion channels and membrane proteins.
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Kelkar DA, Chattopadhyay A. The gramicidin ion channel: A model membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2011-25. [PMID: 17572379 DOI: 10.1016/j.bbamem.2007.05.011] [Citation(s) in RCA: 264] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 05/09/2007] [Accepted: 05/10/2007] [Indexed: 02/07/2023]
Abstract
The linear peptide gramicidin forms prototypical ion channels specific for monovalent cations and has been extensively used to study the organization, dynamics and function of membrane-spanning channels. In recent times, the availability of crystal structures of complex ion channels has challenged the role of gramicidin as a model membrane protein and ion channel. This review focuses on the suitability of gramicidin as a model membrane protein in general, and the information gained from gramicidin to understand lipid-protein interactions in particular. Special emphasis is given to the role and orientation of tryptophan residues in channel structure and function and recent spectroscopic approaches that have highlighted the organization and dynamics of the channel in membrane and membrane-mimetic media.
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Affiliation(s)
- Devaki A Kelkar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Abstract
The lipid bilayer component of biological membranes is important for the distribution, organization, and function of bilayer-spanning proteins. This regulation is due to both specific lipid-protein interactions and general bilayer-protein interactions, which modulate the energetics and kinetics of protein conformational transitions, as well as the protein distribution between different membrane compartments. The bilayer regulation of membrane protein function arises from the hydrophobic coupling between the protein's hydrophobic domains and the bilayer hydrophobic core, which causes protein conformational changes that involve the protein/bilayer boundary to perturb the adjacent bilayer. Such bilayer perturbations, or deformations, incur an energetic cost, which for a given conformational change varies as a function of the bilayer material properties (bilayer thickness, intrinsic lipid curvature, and the elastic compression and bending moduli). Protein function therefore is regulated by changes in bilayer material properties, which determine the free-energy changes caused by the protein-induced bilayer deformation. The lipid bilayer thus becomes an allosteric regulator of membrane function.
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Affiliation(s)
- Olaf S Andersen
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA.
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Becucci L, Santucci A, Guidelli R. Gramicidin Conducting Dimers in Lipid Bilayers Are Stabilized by Single-File Ionic Flux along Them. J Phys Chem B 2007; 111:9814-20. [PMID: 17672492 DOI: 10.1021/jp072051p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gramicidin D was incorporated in a biomimetic membrane consisting of a lipid bilayer tethered to a mercury electrode via a hydrophilic spacer, and its behavior was investigated in aqueous 0.1 M KCl by potential-step chronocoulometry and electrochemical impedance spectroscopy. The impedance spectra, recorded from 0.1 to 1 x 10(5) Hz over a potential range of 0.7 V, were fitted to a series of RC meshes, which were related to the different substructural elements of the biomimetic membrane. These impedance spectra were compared with those obtained by incorporating valinomycin, under otherwise identical conditions. The potential dependence of the stationary currents reported on bilayer lipid membranes by Bamberg and Läuger (Bamberg, E.; Läuger, P. J. Membrane Biol. 1973, 11, 177-194) as well as those extracted from potential-step chronocoulometric measurements was interpreted by relating the increase in gramicidin dimerization to a progressive increase in single-file K+ flux along the dimeric channels. An analogous approach was adopted in explaining the difference between the impedance spectra obtained with gramicidin D and those obtained with valinomycin. It is concluded that gramicidin has a low tendency to form dimers in the absence of ionic flux.
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Affiliation(s)
- Lucia Becucci
- Department of Chemistry, Florence University, via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy
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22
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Chattopadhyay A, Rawat SS. Wavelength-selective fluorescence in ion channels formed by gramicidin A in membranes. J CHEM SCI 2007. [DOI: 10.1007/s12039-007-0020-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Kelkar DA, Chattopadhyay A. Modulation of gramicidin channel conformation and organization by hydrophobic mismatch in saturated phosphatidylcholine bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1103-13. [PMID: 17321493 DOI: 10.1016/j.bbamem.2007.01.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 01/18/2007] [Accepted: 01/22/2007] [Indexed: 11/25/2022]
Abstract
The matching of hydrophobic lengths of integral membrane proteins and the surrounding lipid bilayer is an important factor that influences both structure and function of integral membrane proteins. The ion channel gramicidin is known to be uniquely sensitive to membrane properties such as bilayer thickness and membrane mechanical properties. The functionally important carboxy terminal tryptophan residues of gramicidin display conformation-dependent fluorescence which can be used to monitor gramicidin conformations in membranes [S.S. Rawat, D.A. Kelkar, A. Chattopadhyay, Monitoring gramicidin conformations in membranes: a fluorescence approach, Biophys. J. 87 (2004) 831-843]. We have examined the effect of hydrophobic mismatch on the conformation and organization of gramicidin in saturated phosphatidylcholine bilayers of varying thickness utilizing the intrinsic conformation-dependent tryptophan fluorescence. Our results utilizing steady state and time-resolved fluorescence spectroscopic approaches, in combination with circular dichroism spectroscopy, show that gramicidin remains predominantly in the channel conformation and gramicidin tryptophans are at the membrane interfacial region over a range of mismatch conditions. Interestingly, gramicidin conformation shifts toward non-channel conformations in extremely thick gel phase membranes although it is not excluded from the membrane. In addition, experiments utilizing self quenching of tryptophan fluorescence indicate peptide aggregation in thicker gel phase membranes.
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Affiliation(s)
- Devaki A Kelkar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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24
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Andersen OS, Bruno MJ, Sun H, Koeppe RE. Single-molecule methods for monitoring changes in bilayer elastic properties. Methods Mol Biol 2007; 400:543-570. [PMID: 17951759 DOI: 10.1007/978-1-59745-519-0_37] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Membrane-spanning proteins perturb the organization and dynamics of the adjacent bilayer lipids. For example, when the hydrophobic length (l) of a bilayer-spanning protein differs from the average thickness (d0) of the host bilayer, the bilayer thickness will vary locally in the vicinity of the protein in order to "match" the length of the protein's hydrophobic exterior to the thickness of the bilayer hydrophobic core. Such bilayer deformations incur an energetic cost, the bilayer deformation energy (DeltaG0def), which will vary as a function of the protein shape, the protein-bilayer hydrophobic mismatch (d0 - l), the lipid bilayer elastic properties, and the lipid intrinsic curvature (c0). Thus, if the membrane protein conformational changes underlying protein function involve the protein/bilayer interface, the ensuing changes in DeltaG0def (DeltaDeltaG0def) will contribute to the overall free-energy change of the conformational changes (DeltaG0tot)-meaning that the host lipid bilayer will modulate protein function. For a given protein, (DeltaDeltaG0def) varies as a function of the bilayer geometric properties (thickness and intrinsic curvature) and the elastic (bending and compression) moduli, which vary as a function of changes in lipid composition or with the adsorption of amphiphiles at the bilayer/solution interface. To understand how changes in bilayer properties modulate the function of bilayer-spanning proteins, single-molecule methods have been developed to probe changes in bilayer elastic properties using gramicidins as molecular force transducers. Different approaches to measuring the deformation energy are described: (1) measurements of changes in channel lifetimes and appearance rates as the lipid bilayer thickness or channel length are varied, (2) measurements of the equilibrium distribution among channels of different lengths, formed by homo- and heterodimers between gramicidin subunits of different lengths, and (3) measurements of the ratio of the appearance rates of heterodimer channels relative to parent homodimer channels formed by gramicidin subunits of different lengths.
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Affiliation(s)
- Olaf S Andersen
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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25
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Pulay P, Scherer EM, van der Wel PCA, Koeppe RE. Importance of tensor asymmetry for the analysis of 2H NMR spectra from deuterated aromatic rings. J Am Chem Soc 2006; 127:17488-93. [PMID: 16332101 PMCID: PMC2532822 DOI: 10.1021/ja054935x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used ab initio calculations to compute all of the tensor elements of the electric field gradient for each carbon-deuterium bond in the ring of deuterated 3-methyl-indole. Previous analyses have ignored the smaller tensor elements perpendicular to principal component Vzz which is aligned with the C-2H bond (local bond z-axis). At each ring position, the smallest element Vxx is in the molecular plane and Vyy is normal to the plane of the ring. The asymmetry parameter = (Vyy - Vxx)/Vzz ranges from 0.07 at C4 to 0.11 at C2. We used the perpendicular (off-bond) tensor elements, in concert with an improved understanding of the indole ring geometry, to analyze prototype 2H NMR spectra from well-oriented, hydrated peptide/lipid samples. For each of the four tryptophans of membrane-spanning gramicidin A (gA) channels, the inclusion of the perpendicular elements changes the deduced ring tilt by nearly 10 and increases the ring principal order parameter Szz for overall "wobble" with respect to the membrane normal (molecular z-axis). With the improved analysis, the magnitude of Szz for the outermost indole rings of Trp13 and Trp15 is indistinguishable from that observed previously for backbone atoms (0.93 +/- 0.03). For the Trp9 and Trp11 rings, which are slightly more buried within the membrane, Szz is slightly lower (0.86 +/- 0.03). The results show that the perpendicular elements are important for the detailed analysis of 2H NMR spectra from aromatic ring systems.
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Affiliation(s)
- Peter Pulay
- To whom correspondence should be addressed: Phone: 479−575−4601. Fax: 479−575−4049. E-mail: or
| | | | | | - Roger E. Koeppe
- To whom correspondence should be addressed: Phone: 479−575−4601. Fax: 479−575−4049. E-mail: or
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Vila-Romeu N, Nieto-Suárez M, Castro-Silva M. Behavior of gramicidin A–ethyl nonadecanoate mixed Langmuir monolayers spread at the air–water interface. Colloids Surf A Physicochem Eng Asp 2005. [DOI: 10.1016/j.colsurfa.2005.05.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Vila-Romeu N, Nieto-Suarez M, Dynarowicz-Łatka P. Miscibility of Gramicidin A−Ethyl Nonadecanoate in Langmuir Monolayers in the Presence of Salts Dissolved in the Subphase. J Phys Chem B 2005; 109:14965-70. [PMID: 16852895 DOI: 10.1021/jp050920+] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The behavior of binary mixed Langmuir monolayers from gramicidin A (GA) and ethyl nonadecanoate (EN), spread on aqueous subphases containing NaCl and CaCl2, was investigated on the basis of the analysis of surface pressure-average area per molecule (pi-A) isotherms complemented with Brewster angle microscopy (BAM) images. Compression modulus versus surface pressure (C(S-1)-pi) curves indicate the existence of interactions in the GA-EN mixed monolayers at low surface pressures (below 5 mN m(-1)). However, for mixtures in which the ester is the predominant component, both GA and EN are miscible within regions from fully expanded to collapse. To examine the interactions between both components in the studied system, values of the mean molecular area per molecule (A12) were plotted as a function of molar fraction of gramicidin A (X(GA)). A12-X(GA) plots exhibit negative deviations from ideality at high surface pressures, wherein beta-helices of GA are vertically oriented in respect to the interface. However, at surface pressures below the plateau transition, which is due to reorientation of GA, the binary system obeys the additive rule. Brewster angle microscopy (BAM) was applied for a direct visualization of the monolayers morphologies. The obtained images prove that for molar ratios of GA > or = 0.3 and at surface pressures above 5 mN m(-1), both components are immiscible at the interface. The observed negative deviations from the additively rule were attributed to the formation of a three-dimensional phase in the mixed film, which provokes its contraction at the interface.
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Affiliation(s)
- N Vila-Romeu
- Department of Physical Chemistry-Faculty of Sciences, University of Vigo, Campus As Lagoas s/n 32004 Ourense, Spain.
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28
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Abstract
Gramicidin channels are mini-proteins composed of two tryptophan-rich subunits. The conducting channels are formed by the transbilayer dimerization of nonconducting subunits, which are tied to the bilayer/solution interface through hydrogen bonds between the indole NH groups and the phospholipid backbone and water. The channel structure is known at atomic resolution and the channel's permeability characteristics are particularly well defined: gramicidin channels are selective for monovalent cations, with no measurable permeability to anions or polyvalent cations; ions and water move through a pore whose wall is formed by the peptide backbone; and the single-channel conductance and cation selectivity vary when the amino acid sequence is varied, even though the permeating ions make no contact with the amino acid side chains. Given the amount of experimental information that is available--for both the wild-type channels and for channels formed by amino acid-substituted gramicidin analogues--gramicidin channels provide important insights into the microphysics of ion permeation through bilayer-spanning channels. For the same reason, gramicidin channels constitute the system of choice for evaluating computational strategies for obtaining mechanistic insights into ion permeation through the complex channels formed by integral membrane proteins.
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Affiliation(s)
- Olaf S Andersen
- Weill Medical College of Cornell University, New York, NY 10021, USA.
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29
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Lin TH, Huang HB, Wei HA, Shiao SH, Chen YC. The effect of temperature and lipid on the conformational transition of gramicidin A in lipid vesicles. Biopolymers 2005; 78:179-86. [PMID: 15765548 DOI: 10.1002/bip.20269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The present study investigated the effect of temperature and lipid/peptide molar ratio on the conformational changes of the membrane peptide gramicidin A from a double-stranded helix to a single-stranded helical dimmer in 1,2-dimyristoyl-glycerol-3-phosphochloine (DMPC) vesicles. Tryptophan fluorescence spectroscopy results suggested that the conformational transition fitted a three-state (two-step) "folding" model. Rate constants, k(1) and k(2), were determined for each of the two steps. Since k(1) and k(2) increased with an increase in temperature, we hypothesized that the process corresponded to the breakage and formation of the backbone hydrogen bonds. The k(1) was from 10 to 45 folds faster than k(2), except for lipid/peptide molar ratios above 89.21, where k(2) increased rapidly. At molar ratios below 89.21, k(2) was insensitive to changes in lipid concentration. To account for this phenomenon, we proposed that while the driving interaction at high molar ratios is between the indole rings of the tryptophan residues and the lipid head groups, at low molar ratios there may be an intermolecular interaction between the tryptophan residues that causes gramicidin A to form an organized aggregated network. This aggregated network, caused by the tryptophan-tryptophan interaction, may be the main effect responsible for the slow down of the conformation change.
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Affiliation(s)
- Ta-Hsien Lin
- Department of Medical Research & Education, Veterans General Hospital-Taipei, and Institute of Biochemistry, National Yang-Ming University, Shih-Pai, Taipei 11217, Taiwan, ROC
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30
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Rawat SS, Kelkar DA, Chattopadhyay A. Monitoring gramicidin conformations in membranes: a fluorescence approach. Biophys J 2004; 87:831-43. [PMID: 15298892 PMCID: PMC1304493 DOI: 10.1529/biophysj.104.041715] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Accepted: 04/12/2004] [Indexed: 12/16/2022] Open
Abstract
We have monitored the membrane-bound channel and nonchannel conformations of gramicidin utilizing red-edge excitation shift (REES), and related fluorescence parameters. In particular, we have used fluorescence lifetime, polarization, quenching, chemical modification, and membrane penetration depth analysis in addition to REES measurements to distinguish these two conformations. Our results show that REES of gramicidin tryptophans can be effectively used to distinguish conformations of membrane-bound gramicidin. The interfacially localized tryptophans in the channel conformation display REES of 7 nm whereas the tryptophans in the nonchannel conformation exhibit REES of 2 nm which highlights the difference in their average environments in terms of localization in the membrane. This is supported by tryptophan penetration depth measurements using the parallax method and fluorescence lifetime and polarization measurements. Further differences in the average tryptophan microenvironments in the two conformations are brought out by fluorescence quenching experiments using acrylamide and chemical modification of the tryptophans by N-bromosuccinimide. In summary, we report novel fluorescence-based approaches to monitor conformations of this important ion channel peptide. Our results offer vital information on the organization and dynamics of the functionally important tryptophan residues in gramicidin.
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31
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López-García B, Marcos JF, Abad C, Pérez-Payá E. Stabilisation of mixed peptide/lipid complexes in selective antifungal hexapeptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1660:131-7. [PMID: 14757228 DOI: 10.1016/j.bbamem.2003.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The design of antimicrobial peptides could have benefited from structural studies of known peptides having specific activity against target microbes, but not toward other microorganisms. We have previously reported the identification of a series of peptides (PAF-series) active against certain postharvest fungal phytopathogens, and devoid of toxicity towards E. coli and S. cerevisiae [López-García et al. Appl. Environ. Microbiol. 68 (2002) 2453]. The peptides inhibited the conidia germination and hyphal growth. Here, we present a comparative structural characterisation of selected PAF peptides obtained by single-amino-acid replacement, which differ in biological activity. The peptides were characterised in solution using fluorescence and circular dichroism (CD) spectroscopies. Membrane and membrane mimetic-peptide interactions and the lipid-bound structures were studied using fluorescence with the aid of extrinsic fluorescent probes that allowed the identification of mixed peptide/lipid complexes. A direct correlation was found between the capability of complex formation and antifungal activity. These studies provide a putative structural basis for the mechanism of action of selective antifungal peptides.
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Affiliation(s)
- Belén López-García
- Departamento de Ciencia de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos-CSIC, Apartado de Correos 73, Burjassot, E-46100 Valencia, Spain
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32
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Koeppe RE, Sun H, van der Wel PCA, Scherer EM, Pulay P, Greathouse DV. Combined experimental/theoretical refinement of indole ring geometry using deuterium magnetic resonance and ab initio calculations. J Am Chem Soc 2004; 125:12268-76. [PMID: 14519012 DOI: 10.1021/ja035052d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used experimental deuterium NMR spectra from labeled tryptophans in membrane-spanning gramicidin A (gA)(1) channels to refine the geometry of the indole ring and, specifically, the C2-(2)H bond direction. By using partial exchange in a cold organic acid, we were able to selectively deuterate ring positions C2 and C5 and, thereby, define unambiguous spectral assignments. In a backbone-independent analysis, the assigned spectra from four distinct labeled tryptophans were used to assess the geometry of the planar indole ring. We found that the C2-(2)H bond makes an angle of about 6 degrees with respect to the normal to the indole ring bridge, and the experimental geometry was confirmed by density functional calculations using a 6-311G** basis set. The precisely determined ring geometry and the experimental spectra in turn are the foundation for calculations of the orientation of each tryptophan indole ring, with respect to the bilayer membrane normal, and of a principal order parameter S(zz) for each ring. The results have general significance for revising the tryptophan ring geometry that is used in protein molecular modeling, as well as for the analysis of tryptophan ring orientations in membrane-spanning proteins. The experimental precision in the definition of the indole ring geometry demonstrates yet another practical application emanating from fundamental research on the robust gramicidin channel.
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Affiliation(s)
- Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
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Bañó MC, Salom D, Abad C. Size-exclusion high-performance liquid chromatography in the study of the autoassociating antibiotic gramicidin A in micellar milieu. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2003; 56:297-309. [PMID: 12834985 DOI: 10.1016/s0165-022x(03)00067-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Gramicidin A (gA) is a polypeptide antibiotic which forms dimeric channels specific for monovalent cations in biological membranes. It is a polymorphic molecule that adopts several different conformations, double-stranded (ds) helical dimers (pore conformation) and single-stranded beta-helical dimers (channel conformation). This study investigated the conformational adaptability of gramicidin A when incorporated into micelles as membrane-mimetic model system. Taking advantage of our reported, versatile, size-exclusion high-performance liquid chromatography (SE-HPLC) strategy that allows the separation of double-stranded dimers and monomers, we have quantitatively characterized the conformational transition undergone by the peptide in the micellar milieu. The importance of both hydrophobic/hydrophilic moieties of the amphipaths in the stabilization of concrete conformational species is demonstrated using detergents with different hydrocarbon chain length and/or polar head. SE-HPLC is a valuable, rapid, accurate technique for the structural characterization of hydrophobic autoassociating peptides that work in lipid environments such as biological membranes.
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Affiliation(s)
- Maria Carmen Bañó
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/ Doctor Moliner 50, E-46100 Burjassot, Valencia, Spain
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34
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Gómez CM, Codoñer A, Campos A, Abad C. Thermodynamic Study of Small Hydrophobic Ions at the Water–Lipid Interface. J Colloid Interface Sci 2002; 251:172-81. [PMID: 16290716 DOI: 10.1006/jcis.2002.8381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2001] [Accepted: 03/23/2002] [Indexed: 11/22/2022]
Abstract
The thermodynamics of binding of two small hydrophobic ions such as norharman and tryptophan to neutral and negatively charged small unilamellar vesicles was investigated at pH 7.4 using fluorescence spectroscopy. Vesicles were formed at room temperature from dimyristoyl phosphatidylcholine (DMPC) or DMPC/dimyristoylphosphatidic acid and DMPC/dimyristoylphosphatidylglycerol. The changes in fluorescence properties were used to obtain association isotherms at variable membrane surface negative charge and at different ionic strengths. The binding of both ions was found to be quantitatively enhanced as the percentage of negative phospholipid increases in the membrane. Also, a decrease in ion binding was found to occur as the concentration of monovalent salt was increased (0.045-0.345 M). If electrostatic effects were ignored, the experimental data showed biphasic behavior in Scatchard plots. When electrostatic effects were taken into account by means of the Gouy-Chapman theory, the same data yielded linear Scatchard plots that were described by a simple partition equilibrium of the hydrophobic ion into the lipid-water interface. We demonstrate that the effective interfacial charge, nu, of the ion is a determinant factor to obtain a unique value of the intrinsic (hydrophobic) binding constant independently of the surface charge density of the lipid membrane.
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Affiliation(s)
- Clara M Gómez
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, València, E-46100, Spain
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35
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de Groot BL, Tieleman DP, Pohl P, Grubmüller H. Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys J 2002; 82:2934-42. [PMID: 12023216 PMCID: PMC1302081 DOI: 10.1016/s0006-3495(02)75634-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Multinanosecond molecular dynamics simulations of gramicidin A embedded in a dimyristoylphosphatidylcholine bilayer show a remarkable structural stability for both experimentally determined conformations: the head-to-head helical dimer and the double helix. Water permeability was found to be much higher in the double helical conformation, which is explained by lower hydrogen bond-mediated enthalpic barriers at the channel entrance and its larger pore size. Free-energy perturbation calculations show that the double helical structure is stabilized by the positive charges at the N termini introduced by the desformylation, whereas the helical dimer is destabilized. Together with the recent experimental observation that desformyl gramicidin conducts water hundredfold better than gramicidin, this suggests that desformyl gramicidin A predominantly occurs in the double helical conformation.
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Affiliation(s)
- Bert L de Groot
- Theoretical Molecular Biophysics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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36
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Koeppe RE, Greathouse DV, Providence LL, Shobana S, Andersen OS. Design and characterization of gramicidin channels with side chain or backbone mutations. NOVARTIS FOUNDATION SYMPOSIUM 2001; 225:44-55; discussion 55-61. [PMID: 10472047 DOI: 10.1002/9780470515716.ch4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Mutations and chemical substitutions of amino acid side chains and backbone atoms have proved vital for understanding the folding, structure and function of gramicidin channels in phospholipid membranes. The channel's pore is lined by peptide backbone groups; their importance for channel structure and function is shown by a single amide-to-ester replacement within the backbone, which greatly reduces the resulting channel conductance and lifetime. The four tryptophans and the intervening leucines together govern the formation and dissociation of conducting channels from single-stranded subunits. Conducting double-stranded gramicidin conformations (channels) occur rarely in membranes--except when the sequence has been altered to permit special arrangements of tryptophans or (infrequently) in unusually thick membranes. The tryptophans anchor the single-stranded channels to the membrane/solution interface, and the indole dipoles promote cation transport through the channels. Removal of any indole dipole reduces ion conductance; whereas 5-fluorination of an indole, which increases its dipole moment, enhances ion conductance. Some sequence changes at the formyl-NH-terminus (in the membrane interior, away from the tryptophans), including fluorination of the formyl-NH-terminal valine, introduce voltage-dependent channel gating. Gramicidin channels are not just static conductors, but also dynamic entities whose structure and function can be manipulated by backbone and side chain modifications.
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Affiliation(s)
- R E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville 72701, USA
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37
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Jude AR, Greathouse DV, Leister MC, Koeppe RE. Steric interactions of valines 1, 5, and 7 in [valine 5, D-alanine 8] gramicidin A channels. Biophys J 1999; 77:1927-35. [PMID: 10512813 PMCID: PMC1300474 DOI: 10.1016/s0006-3495(99)77034-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When the central valine residues 6, 7, and 8 of gramicidin A (gA) are shifted by one position, the resulting [Val(5), D-Ala(8)]gA forms right-handed channels with a single-channel conductance and average duration somewhat less than gA channels. The reduction in channel duration has been attributed to steric conflict between the side chains of Val(1) and Val(5) in opposing monomers (Koeppe, R. E. II, D. V. Greathouse, A. Jude, G. Saberwal, L. L. Providence, and O. S. Andersen. 1994. J. Biol. Chem. 269:12567-12576). To investigate the orientations and motions of valines in [Val(5), D-Ala(8)]gA, we have incorporated (2)H labels at Val 1, 5, or 7 and recorded (2)H-NMR spectra of oriented and nonoriented samples in hydrated dimyristoylphosphatidylcholine. Spectra of nonoriented samples at 4 degrees C reveal powder patterns that indicate rapid side chain "hopping" for Val(5), and an intermediate rate of hopping for Val(1) and Val(7) that is somewhat slower than in gA. Oriented samples of deuterated Val(1) and Val(7) show large changes in the methyl and C(beta)-(2)H quadrupolar splittings (Deltanu(q)) when Ala(5) in native gA is changed to Val(5). Three or more peaks for the Val(1) methyls with Deltanu(q) values that vary with the echo delay, together with an intermediate spectrum for nonoriented samples at 4 degrees C, suggest unusual side chain dynamics for Val(1) in [Val(5), D-Ala(8)]gA. These results are consistent with a steric conflict that has been introduced between the two opposing monomers. In contrast, the acylation of gA has little influence on the side chain dynamics of Val(1), regardless of the identity of residue 5.
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Affiliation(s)
- A R Jude
- Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701 USA
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Pastor MT, Diez A, Pérez-Payá E, Abad C. Addressing substrate glutamine requirements for tissue transglutaminase using substance P analogues. FEBS Lett 1999; 451:231-4. [PMID: 10371195 DOI: 10.1016/s0014-5793(99)00572-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have investigated the effect on the substrate requirements for guinea pig liver (tissue) transglutaminase of a set of 11 synthetic glutamine substitution analogues making up the full sequence of the naturally occurring tissue transglutaminase substrate substance P. While a number of peptide sequences derived from proteins that are well-recognized as tissue transglutaminase substrates have been studied, the enzyme activity using substitution analogues of full-length natural substrates has not been investigated as thoroughly. Thus, our set of substance P analogues only differs from one to other by one amino acid mutation while the length (of the peptide) is maintained as in the natural parent peptide. Our results indicate that a glutamine residue is not recognized as substrate by the enzyme whether it is placed at the N- or C-terminal or between two positively charged residues or between two proline residues. To further address the effect on enzyme activity of charged amino acids in the vicinity of the reactive glutamine residue, a new set of synthetic charge replacement analogues of substance P has been also studied. Together, the results have identified new minimal requirements for modification of a particular glutamine residue in a polypeptide chain. It would be of interest to set up a full set of such requirements in order to highlight potential glutamine residues as enzyme targets in the growing list of proteins that are being described as transglutaminase substrates.
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Affiliation(s)
- M T Pastor
- Department de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
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Fairbanks TG, Andrus CL, Busath DD. Lorentzian noise in single gramicidin A channel formamidinium currents. NOVARTIS FOUNDATION SYMPOSIUM 1999; 225:74-87; discussion 87-92. [PMID: 10472049 DOI: 10.1002/9780470515716.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Seoh & Busath (1995) showed that in the presence of formamidinium, single gramicidin A channels were lengthened, had uniformly noisy currents at low voltages and had superlinear current-voltage relationships, all three properties being absent in gramicidin M- channels in which the interfacial tryptophan residues in gramicidin A are all replaced by phenylalanine. We measured the single channel noise power spectra (PSDs) in small monoolein (GMO) bilayers with formamidinium chloride solutions to help identify the mechanism of noise process. PSDs were Lorentzian with characteristic frequencies of 0.1-1.0 kHz in 0.1 and 0.3 M formamidinium chloride solutions, and from. 1-6 kHz in 1 M solution. Si(0), where measurable, ranged from approximately 50-200 fA2/Hz. The time course of the noise process could not be detected in these experiments. The low fc suggests slow motions or rare states of the blocking 'gates' which, judging from the result with gramicidin M-, must be equal to or related to the Trp residues.
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Affiliation(s)
- T G Fairbanks
- Zoology Department, Brigham Young University, Provo, UT 84602, USA
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