51
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Hydrophobic mismatch demonstrated for membranolytic peptides, and their use as molecular rulers to measure bilayer thickness in native cells. Sci Rep 2015; 5:9388. [PMID: 25807192 PMCID: PMC5224518 DOI: 10.1038/srep09388] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/20/2015] [Indexed: 11/16/2022] Open
Abstract
Hydrophobic mismatch is a well-recognized principle in the interaction of transmembrane proteins with lipid bilayers. This concept was extended here to amphipathic membranolytic α-helices. Nine peptides with lengths between 14 and 28 amino acids were designed from repeated KIAGKIA motifs, and their helical nature was confirmed by circular dichroism spectroscopy. Biological assays for antimicrobial activity and hemolysis, as well as fluorescence vesicle leakage and solid-state NMR spectroscopy, were used to correlate peptide length with membranolytic activity. These data show that the formation of transmembrane pores is only possible under the condition of hydrophobic matching: the peptides have to be long enough to span the hydrophobic bilayer core to be able to induce vesicle leakage, kill bacteria, and cause hemolysis. By correlating the threshold lengths for biological activity with the biophysical results on model vesicles, the peptides could be utilized as molecular rulers to measure the membrane thickness in different cells.
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52
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Hinks J, Poh WH, Chu JJH, Loo JSC, Bazan GC, Hancock LE, Wuertz S. Oligopolyphenylenevinylene-conjugated oligoelectrolyte membrane insertion molecules selectively disrupt cell envelopes of Gram-positive bacteria. Appl Environ Microbiol 2015; 81:1949-58. [PMID: 25576607 PMCID: PMC4345381 DOI: 10.1128/aem.03355-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/26/2014] [Indexed: 12/11/2022] Open
Abstract
The modification of microbial membranes to achieve biotechnological strain improvement with exogenous small molecules, such as oligopolyphenylenevinylene-conjugated oligoelectrolyte (OPV-COE) membrane insertion molecules (MIMs), is an emerging biotechnological field. Little is known about the interactions of OPV-COEs with their target, the bacterial envelope. We studied the toxicity of three previously reported OPV-COEs with a selection of Gram-negative and Gram-positive organisms and demonstrated that Gram-positive bacteria are more sensitive to OPV-COEs than Gram-negative bacteria. Transmission electron microscopy demonstrated that these MIMs disrupt microbial membranes and that this occurred to a much greater degree in Gram-positive organisms. We used a number of mutants to probe the nature of MIM interactions with the microbial envelope but were unable to align the membrane perturbation effects of these compounds to previously reported membrane disruption mechanisms of, for example, cationic antimicrobial peptides. Instead, the data support the notion that OPV-COEs disrupt microbial membranes through a suspected interaction with diphosphatidylglycerol (DPG), a major component of Gram-positive membranes. The integrity of model membranes containing elevated amounts of DPG was disrupted to a greater extent by MIMs than those prepared from Escherichia coli total lipid extracts alone.
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Affiliation(s)
- Jamie Hinks
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Wee Han Poh
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Joachim Say Chye Loo
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guillermo C Bazan
- Department of Chemistry & Biochemistry and Materials, Center for Polymers and Organic Solids, University of California, Santa Barbara, California, USA
| | - Lynn E Hancock
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Stefan Wuertz
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore Department of Civil and Environmental Engineering, University of California, Davis, California, USA
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53
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Dynamic regulation of lipid-protein interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1849-59. [PMID: 25666872 DOI: 10.1016/j.bbamem.2015.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 02/07/2023]
Abstract
We review the importance of helix motions for the function of several important categories of membrane proteins and for the properties of several model molecular systems. For voltage-gated potassium or sodium channels, sliding, tilting and/or rotational movements of the S4 helix accompanied by a swapping of cognate side-chain ion-pair interactions regulate the channel gating. In the seven-helix G protein-coupled receptors, exemplified by the rhodopsins, collective helix motions serve to activate the functional signaling. Peptides which initially associate with lipid-bilayer membrane surfaces may undergo dynamic transitions from surface-bound to tilted-transmembrane orientations, sometimes accompanied by changes in the molecularity, formation of a pore or, more generally, the activation of biological function. For single-span membrane proteins, such as the tyrosine kinases, an interplay between juxtamembrane and transmembrane domains is likely to be crucial for the regulation of dimer assembly that in turn is associated with the functional responses to external signals. Additionally, we note that experiments with designed single-span transmembrane helices offer fundamental insights into the molecular features that govern protein-lipid interactions. This article is part of a Special Issue entitled: Lipid-protein interactions.
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54
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3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides. Biophys J 2015; 106:2385-94. [PMID: 24896117 DOI: 10.1016/j.bpj.2014.04.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 11/22/2022] Open
Abstract
The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/.
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55
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Vanegas JM, Arroyo M. Force transduction and lipid binding in MscL: a continuum-molecular approach. PLoS One 2014; 9:e113947. [PMID: 25437007 PMCID: PMC4250078 DOI: 10.1371/journal.pone.0113947] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/30/2014] [Indexed: 01/22/2023] Open
Abstract
The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this detailed chemical information and current mechanical models of MscL gating. Here, we investigate the MscL bilayer-protein interface through molecular dynamics simulations, and take a combined continuum-molecular approach to connect chemistry and mechanics. We quantify the effect of membrane tension on the forces acting on the surface of the channel, and identify interactions that may be critical in the force transduction between the membrane and MscL. We find that the local stress distribution on the protein surface is largely asymmetric, particularly under tension, with the cytoplasmic side showing significantly larger and more localized forces, which pull the protein radially outward. The molecular interactions that mediate this behavior arise from hydrogen bonds between the electronegative oxygens in the lipid headgroup and a cluster of positively charged lysine residues on the amphipathic S1 domain and the C-terminal end of the second trans-membrane helix. We take advantage of this strong interaction (estimated to be 10–13 kT per lipid) to actuate the channel (by applying forces on protein-bound lipids) and explore its sensitivity to the pulling magnitude and direction. We conclude by highlighting the simple motif that confers MscL with strong anchoring to the bilayer, and its presence in various integral membrane proteins including the human mechanosensitive channel K2P1 and bovine rhodopsin.
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Affiliation(s)
- Juan M. Vanegas
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Barcelona, Spain
- * E-mail:
| | - Marino Arroyo
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Barcelona, Spain
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56
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Liang Q, Wu QY, Wang ZY. Effect of hydrophobic mismatch on domain formation and peptide sorting in the multicomponent lipid bilayers in the presence of immobilized peptides. J Chem Phys 2014; 141:074702. [DOI: 10.1063/1.4891931] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, People's Republic of China
- Department of Physics, Ningbo University, Ningbo 315211, People's Republic of China
| | - Qing-Yan Wu
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Zhi-Yong Wang
- School of Optoelectronic Information, Chongqing University of Technology, Chongqing 400054, People's Republic of China
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57
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Flinner N, Mirus O, Schleiff E. The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation. Int J Mol Sci 2014; 15:14247-68. [PMID: 25196522 PMCID: PMC4159849 DOI: 10.3390/ijms150814247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/14/2014] [Accepted: 08/06/2014] [Indexed: 11/17/2022] Open
Abstract
The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA.
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Affiliation(s)
- Nadine Flinner
- Cluster of Excellence Macromolecular Complexes, Center of Membrane Proteomics, Department of Biosciences, Molecular Cell Biology of Plants, GU Frankfurt am Main, 60439 Frankfurt, Germany.
| | - Oliver Mirus
- Cluster of Excellence Macromolecular Complexes, Center of Membrane Proteomics, Department of Biosciences, Molecular Cell Biology of Plants, GU Frankfurt am Main, 60439 Frankfurt, Germany.
| | - Enrico Schleiff
- Cluster of Excellence Macromolecular Complexes, Center of Membrane Proteomics, Department of Biosciences, Molecular Cell Biology of Plants, GU Frankfurt am Main, 60439 Frankfurt, Germany.
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58
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Walther TH, Ulrich AS. Transmembrane helix assembly and the role of salt bridges. Curr Opin Struct Biol 2014; 27:63-8. [DOI: 10.1016/j.sbi.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 10/25/2022]
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59
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Sparks KA, Gleason NJ, Gist R, Langston R, Greathouse DV, Koeppe RE. Comparisons of interfacial Phe, Tyr, and Trp residues as determinants of orientation and dynamics for GWALP transmembrane peptides. Biochemistry 2014; 53:3637-45. [PMID: 24829070 PMCID: PMC4053069 DOI: 10.1021/bi500439x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Aromatic
amino acids often flank the transmembrane alpha helices
of integral membrane proteins. By favoring locations within the membrane–water
interface of the lipid bilayer, aromatic residues Trp, Tyr, and sometimes
Phe may serve as anchors to help stabilize a transmembrane orientation.
In this work, we compare the influence of interfacial Trp, Tyr, or
Phe residues upon the properties of tilted helical transmembrane peptides.
For such comparisons, it has been critical to start with no more than
one interfacial aromatic residue near each end of a transmembrane
helix, for example, that of GWALP23 (acetyl-GGALW5(LA)6LW19LAGA-[ethanol]amide). To this end, we have
employed 2H-labeled alanines and solid-state NMR spectroscopy
to investigate the consequences of moving or replacing W5 or W19 in
GWALP23 with selected Tyr, Phe, or Trp residues at the same or proximate
locations. We find that GWALP23 peptides having F5, Y5, or W5 exhibit
essentially the same average tilt and similar dynamics in bilayer
membranes of 1,2-dilauroylphosphatidylcholine (DLPC) or 1,2-dioleoylphosphatidylcholine
(DOPC). When double Tyr anchors are present, in Y4,5GWALP23
the NMR observables are markedly more subject to dynamic averaging
and at the same time are less responsive to the bilayer thickness.
Decreased dynamics are nevertheless observed when ring hydrogen bonding
is removed, such that F4,5GWALP23 exhibits a similar extent
of low dynamic averaging as GWALP23 itself. When F5 is the sole aromatic
group in the N-interfacial region, the dynamic averaging is (only)
slightly more extensive than with W5, Y5, or Y4 alone or with F4,5,
yet it is much less than that observed for Y4,5GWALP23.
Interestingly, moving Y5 to Y4 or W19 to W18, while retaining only
one hydrogen-bond-capable aromatic ring at each interface, maintains
the low level of dynamic averaging but alters the helix azimuthal
rotation. The rotation change is about 40° for Y4 regardless
of whether the host lipid bilayer is DLPC or DOPC. The rotational
change (Δρ) is more dramatic and more complex when W19
is moved to W18, as Δρ is about +90° in DLPC but
about −60° in DOPC. Possible reasons for this curious
lipid-dependent helix rotation could include not only the separation
distances between flanking aromatic or hydrophobic residues but also
the absolute location of the W19 indole ring. For the more usual cases,
when the helix azimuthal rotation shows little dependence on the host
bilayer identity, excepting W18GWALP23, the transmembrane
helices adapt to different lipids primarily by changing the magnitude
of their tilt. We conclude that, in the absence of other functional
groups, interfacial aromatic residues determine the preferred orientations
and dynamics of membrane-spanning peptides. The results furthermore
suggest possibilities for rotational and dynamic control of membrane
protein function.
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Affiliation(s)
- Kelsey A Sparks
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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60
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Wadhwani P, Strandberg E, van den Berg J, Mink C, Bürck J, Ciriello RA, Ulrich AS. Dynamical structure of the short multifunctional peptide BP100 in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:940-9. [DOI: 10.1016/j.bbamem.2013.11.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/25/2013] [Accepted: 11/01/2013] [Indexed: 11/26/2022]
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61
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Ion channel stability of Gramicidin A in lipid bilayers: Effect of hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:328-38. [DOI: 10.1016/j.bbamem.2013.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/20/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022]
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62
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Yeagle PL. Non-covalent binding of membrane lipids to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1548-59. [PMID: 24269542 DOI: 10.1016/j.bbamem.2013.11.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/01/2013] [Accepted: 11/09/2013] [Indexed: 01/30/2023]
Abstract
Polar lipids and membrane proteins are major components of biological membranes, both cell membranes and membranes of enveloped viruses. How these two classes of membrane components interact with each other to influence the function of biological membranes is a fundamental question that has attracted intense interest since the origins of the field of membrane studies. One of the most powerful ideas that driven the field is the likelihood that lipids bind to membrane proteins at specific sites, modulating protein structure and function. However only relatively recently has high resolution structure determination of membrane proteins progressed to the point of providing atomic level structure of lipid binding sites on membrane proteins. Analysis of X-ray diffraction, electron crystallography and NMR data over 100 specific lipid binding sites on membrane proteins. These data demonstrate tight lipid binding of both phospholipids and cholesterol to membrane proteins. Membrane lipids bind to membrane proteins by their headgroups, or by their acyl chains, or binding is mediated by the entire lipid molecule. When headgroups bind, binding is stabilized by polar interactions between lipid headgroups and the protein. When acyl chains bind, van der Waals effects dominate as the acyl chains adopt conformations that complement particular sites on the rough protein surface. No generally applicable motifs for binding have yet emerged. Previously published biochemical and biophysical data link this binding with function. This Article is Part of a Special Issue Entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.
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Affiliation(s)
- Philip L Yeagle
- Rutgers University Newark, 325 Hill Hall, 360 MLK Blvd, Newark, NJ 07102-1801, USA.
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63
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Gleason NJ, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Single tryptophan and tyrosine comparisons in the N-terminal and C-terminal interface regions of transmembrane GWALP peptides. J Phys Chem B 2013; 117:13786-94. [PMID: 24111589 DOI: 10.1021/jp407542e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrophobic membrane-spanning helices often are flanked by interfacial aromatic or charged residues. In this paper, we compare the consequences of single Trp → Tyr substitutions at each interface for the properties of a defined transmembrane helix in the absence of charged residues. The choice of molecular framework is critical for these single-residue experiments because the presence of "too many" aromatic residues (more than one at either membrane-water interface) introduces excess dynamic averaging of solid state NMR observables. To this end, we compare the outcomes when changing W(5) or W(19), or both of them, to tyrosine in the well-characterized transmembrane peptide acetyl-GGALW(5)(LA)6LW(19)LAGA-amide ("GWALP23"). By means of solid-state (2)H and (15)N NMR experiments, we find that Y(19)GW(5)ALP23 displays similar magnitudes of peptide helix tilt as Y(5)GW(19)ALP23 and responds similarly to changes in bilayer thickness, from DLPC to DMPC to DOPC. The presence of Y(19) changes the azimuthal rotation angle ρ (about the helix axis) to a similar extent as Y(5), but in the opposite direction. When tyrosines are substituted for both tryptophans to yield GY(5,19)ALP23, the helix tilt angle is again of comparable magnitude, and furthermore, the preferred azimuthal rotation angle ρ is relatively unchanged from that of GW(5,19)ALP23. The extent of dynamic averaging increases marginally when Tyr replaces Trp. Yet, importantly, all members of the peptide family having single Tyr or Trp residues near each interface exhibit only moderate and not highly extensive dynamic averaging. The results provide important benchmarks for evaluating conformational and dynamic control of membrane protein function.
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Affiliation(s)
- Nicholas J Gleason
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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64
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Rangamani P, Benjamini A, Agrawal A, Smit B, Steigmann DJ, Oster G. Small scale membrane mechanics. Biomech Model Mechanobiol 2013; 13:697-711. [PMID: 24081650 DOI: 10.1007/s10237-013-0528-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/05/2013] [Indexed: 11/28/2022]
Abstract
Large scale changes to lipid bilayer shapes are well represented by the Helfrich model. However, there are membrane processes that take place at smaller length scales that this model cannot address. In this work, we present a one-dimensional continuum model that captures the mechanics of the lipid bilayer membrane at the length scale of the lipids themselves. The model is developed using the Cosserat theory of surfaces with lipid orientation, or 'tilt', as the fundamental degree of freedom. The Helfrich model can be recovered as a special case when the curvatures are small and the lipid tilt is everywhere zero. We use the tilt model to study local membrane deformations in response to a protein inclusion. Parameter estimates and boundary conditions are obtained from a coarse-grained molecular model using dissipative particle dynamics (DPD) to capture the same phenomenon. The continuum model is able to reproduce the membrane bending, stretch and lipid tilt as seen in the DPD model. The lipid tilt angle relaxes to the bulk tilt angle within 5-6 nm from the protein inclusion. Importantly, for large tilt gradients induced by the proteins, the tilt energy contribution is larger than the bending energy contribution. Thus, the continuum model of tilt accurately captures behaviors at length scales shorter than the membrane thickness.
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Affiliation(s)
- Padmini Rangamani
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, 94720, USA
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65
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Sánchez-Muñoz OL, Strandberg E, Esteban-Martín E, Grage SL, Ulrich AS, Salgado J. Canonical azimuthal rotations and flanking residues constrain the orientation of transmembrane helices. Biophys J 2013; 104:1508-16. [PMID: 23561527 DOI: 10.1016/j.bpj.2013.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/31/2013] [Accepted: 02/20/2013] [Indexed: 12/22/2022] Open
Abstract
In biological membranes the alignment of embedded proteins provides crucial structural information. The transmembrane (TM) parts have well-defined secondary structures, in most cases α-helices and their orientation is given by a tilt angle and an azimuthal rotation angle around the main axis. The tilt angle is readily visualized and has been found to be functionally relevant. However, there exist no general concepts on the corresponding azimuthal rotation. Here, we show that TM helices prefer discrete rotation angles. They arise from a combination of intrinsic properties of the helix geometry plus the influence of the position and type of flanking residues at both ends of the hydrophobic core. The helical geometry gives rise to canonical azimuthal angles for which the side chains of residues from the two ends of the TM helix tend to have maximum or minimum immersion within the membrane. This affects the preferential position of residues that fall near hydrophobic/polar interfaces of the membrane, depending on their hydrophobicity and capacity to form specific anchoring interactions. On this basis, we can explain the orientation and dynamics of TM helices and make accurate predictions, which correspond well to the experimental values of several model peptides (including dimers), and TM segments of polytopic membrane proteins.
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66
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Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers. Chem Phys Lipids 2013; 169:95-105. [DOI: 10.1016/j.chemphyslip.2013.02.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 11/23/2022]
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67
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Benjamini A, Smit B. Robust driving forces for transmembrane helix packing. Biophys J 2013; 103:1227-35. [PMID: 22995495 DOI: 10.1016/j.bpj.2012.08.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022] Open
Abstract
The packing structures of transmembrane helices are traditionally attributed to patterns in residues along the contact surface. In this view, besides keeping the helices confined in the membrane, the bilayer has only a minor effect on the helices structure. Here, we use two different approaches to show that the lipid environment has a crucial effect in determining the cross-angle distribution of packed helices. We analyzed structural data of a membrane proteins database. We show that the distribution of cross angles of helix pairs in this database is statistically indistinguishable from the cross-angle distribution of two noninteracting helices imbedded in the membrane. These results suggest that the cross angle is, to a large extent, determined by the tilt angle of the individual helices. We test this hypothesis using molecular simulations of a coarse-grained model that contains no specific residue interactions. These simulations reproduce the same cross-angle distribution as found in the database. As the tilt angle of a helix is dominated by hydrophobic mismatch between the protein and surrounding lipids, our results indicate that hydrophobic mismatch is the dominant factor guiding the transmembrane helix packing. Other short-range forces might then fine-tune the structure to its final configuration.
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Affiliation(s)
- Ayelet Benjamini
- Department of Chemistry, University of California, Berkeley, California, USA
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68
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Buried lysine, but not arginine, titrates and alters transmembrane helix tilt. Proc Natl Acad Sci U S A 2013; 110:1692-5. [PMID: 23319623 DOI: 10.1073/pnas.1215400110] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ionization states of individual amino acid residues of membrane proteins are difficult to decipher or assign directly in the lipid-bilayer membrane environment. We address this issue for lysines and arginines in designed transmembrane helices. For lysines (but not arginines) at two locations within dioleoyl-phosphatidylcholine bilayer membranes, we measure pK(a) values below 7.0. We find that buried charged lysine, in fashion similar to arginine, will modulate helix orientation to maximize its own access to the aqueous interface or, if occluded by aromatic rings, may cause a transmembrane helix to exit the lipid bilayer. Interestingly, the influence of neutral lysine (vis-à-vis leucine) upon helix orientation also depends upon its aqueous access. Our results suggest that changes in the ionization states of particular residues will regulate membrane protein function and furthermore illustrate the subtle complexity of ionization behavior with respect to the detailed lipid and protein environment.
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69
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Caputo GA. Analyzing the effects of hydrophobic mismatch on transmembrane α-helices using tryptophan fluorescence spectroscopy. Methods Mol Biol 2013; 1063:95-116. [PMID: 23975773 DOI: 10.1007/978-1-62703-583-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydrophobic matching between transmembrane protein segments and the lipid bilayer in which they are embedded is a significant factor in the behavior and orientation of such transmembrane segments. The condition of hydrophobic mismatch occurs when the hydrophobic thickness of a lipid bilayer is significantly different than the length of the membrane spanning segment of a protein, resulting in a mismatch. This mismatch can result in altered function of proteins as well as nonnative structural arrangements including effects on transmembrane α-helix tilt angles, oligomerization state, and/or the formation of non-transmembrane topographies. Here, a fluorescence-based protocol is described for testing model transmembrane α-helices and their sensitivity to hydrophobic mismatch by measuring the propensity of these helices to form non-transmembrane structures. Overall, good hydrophobic matching between the bilayer and transmembrane segments is an important factor that must be considered when designing membrane proteins or peptides.
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Affiliation(s)
- Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, USA
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70
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Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications. FROM SINGLE MOLECULES TO NANOSCOPICALLY STRUCTURED MATERIALS 2013. [DOI: 10.1007/12_2013_258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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71
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Ijäs HK, Lönnfors M, Nyholm TKM. Sterol affinity for phospholipid bilayers is influenced by hydrophobic matching between lipids and transmembrane peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:932-7. [PMID: 23220446 DOI: 10.1016/j.bbamem.2012.11.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 01/04/2023]
Abstract
Lipid self-organization is believed to be essential for shaping the lateral structure of membranes, but it is becoming increasingly clear that also membrane proteins can be involved in the maintenance of membrane architecture. Cholesterol is thought to be important for the lateral organization of eukaryotic cell membranes and has also been implicated to take part in the sorting of cellular transmembrane proteins. Hence, a good starting point for studying the influence of lipid-protein interactions on membrane trafficking is to find out how transmembrane proteins influence the lateral sorting of cholesterol in phospholipid bilayers. By measuring equilibrium partitioning of the fluorescent cholesterol analog cholestatrienol between large unilamellar vesicles and methyl-β-cyclodextrin the effect of hydrophobic matching on the affinity of sterols for phospholipid bilayers was determined. Sterol partitioning was measured in 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers with and without WALP19, WALP23 or WALP27 peptides. The results showed that the affinity of the sterol for the bilayers was affected by hydrophobic matching. An increasing positive hydrophobic mismatch led to stronger sterol binding to the bilayers (except in extreme situations), and a large negative hydrophobic mismatch decreased the affinity of the sterol for the bilayer. In addition, peptide insertion into the phospholipid bilayers was observed to depend on hydrophobic matching. In conclusion, the results showed that hydrophobic matching can affect lipid-protein interactions in a way that may facilitate the formation of lateral domains in cell membranes. This could be of importance in membrane trafficking.
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Affiliation(s)
- H Kristian Ijäs
- Department of Bioscience, Åbo Akademi University, Tykistökatu 6A, Turku, Finland
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72
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Rankenberg JM, Vostrikov VV, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Properties of membrane-incorporated WALP peptides that are anchored on only one end. Biochemistry 2012; 51:10066-74. [PMID: 23171005 DOI: 10.1021/bi301394z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides of the "WALP" family, acetyl-GWW(LA)(n)LWWA-[ethanol]amide, have proven to be opportune models for investigating lipid-peptide interactions. Because the average orientations and motional behavior of the N- and C-terminal Trp (W) residues differ, it is of interest to investigate how the positions of the tryptophans influence the properties of the membrane-incorporated peptides. To address this question, we synthesized acetyl-GGWW(LA)(n)-ethanolamide and acetyl-(AL)(n)WWG-ethanolamide, in which n = 4 or 8, which we designate as "N-anchored" and "C-anchored" peptides, respectively. Selected (2)H or (15)N labels were incorporated for solid-state nuclear magnetic resonance (NMR) spectroscopy. These peptides can be considered "half"-anchored WALP peptides, having only one pair of interfacial Trp residues near either the amino or the carboxyl terminus. The hydrophobic lengths of the (n = 8) peptides are similar to that of WALP23. These longer half-anchored WALP peptides incorporate into lipid bilayers as α-helices, as reflected in their circular dichroism spectra. Solid-state NMR experiments indicate that the longer peptide helices assume defined transmembrane orientations with small non-zero average tilt angles and moderate to high dynamic averaging in bilayer membranes of 1,2-dioleoylphosphatidylcholine, 1,2-dimyristoylphosphatidylcholine, and 1,2-dilauroylphosphatidylcholine. The intrinsically small apparent tilt angles suggest that interactions of aromatic residues with lipid headgroups may play an important role in determining the magnitude of the peptide tilt in the bilayer membrane. The shorter (n = 4) peptides, in stark contrast to the longer peptides, display NMR spectra that are characteristic of greatly reduced motional averaging, probably because of peptide aggregation in the bilayer environment, and CD spectra that are characteristic of β-structure.
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Affiliation(s)
- Johanna M Rankenberg
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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73
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Jämbeck JPM, Lyubartsev AP. An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. J Chem Theory Comput 2012; 8:2938-48. [PMID: 26592132 DOI: 10.1021/ct300342n] [Citation(s) in RCA: 346] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biological membranes are versatile in composition and host intriguing molecular processes. In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) is a necessity. Here, we report the results of our extension of earlier developed all-atomistic FF parameters for fully saturated phospholipids that complements an earlier parameter set for saturated phosphatidylcholine lipids (J. Phys. Chem. B, 2012, 116, 3164-3179). The FF, coined Slipids (Stockholm lipids), now also includes parameters for unsaturated phosphatidylcholine and phosphatidylethanolamine lipids, e.g., POPC, DOPC, SOPC, POPE, and DOPE. As the extended set of parameters is derived with the same philosophy as previously applied, the resulting FF has been developed in a fully consistent manner. The capabilities of Slipids are demonstrated by performing long simulations without applying any surface tension and using the correct isothermal-isobaric (NPT) ensemble for a range of temperatures and carefully comparing a number of properties with experimental findings. Results show that several structural properties are very well reproduced, such as scattering form factors, NMR order parameters, thicknesses, and area per lipid. Thermal dependencies of different thicknesses and area per lipid are reproduced as well. Lipid diffusion is systematically slightly underestimated, whereas the normalized lipid diffusion follows the experimental trends. This is believed to be due to the lack of collective movement in the relatively small bilayer patches used. Furthermore, the compatibility with amino acid FFs from the AMBER family is tested in explicit transmembrane complexes of the WALP23 peptide with DLPC and DOPC bilayers, and this shows that Slipids can be used to study more complex and biologically relevant systems.
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Affiliation(s)
- Joakim P M Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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Balleza D. Mechanical properties of lipid bilayers and regulation of mechanosensitive function: from biological to biomimetic channels. Channels (Austin) 2012; 6:220-33. [PMID: 22790280 DOI: 10.4161/chan.21085] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Material properties of lipid bilayers, including thickness, intrinsic curvature and compressibility regulate the function of mechanosensitive (MS) channels. This regulation is dependent on phospholipid composition, lateral packing and organization within the membrane. Therefore, a more complete framework to understand the functioning of MS channels requires insights into bilayer structure, thermodynamics and phospholipid structure, as well as lipid-protein interactions. Phospholipids and MS channels interact with each other mainly through electrostatic forces and hydrophobic matching, which are also crucial for antimicrobial peptides. They are excellent models for studying the formation and stabilization of membrane pores. Importantly, they perform equivalent responses as MS channels: (1) tilting in response to tension and (2) dissipation of osmotic gradients. Lessons learned from pore forming peptides could enrich our knowledge of mechanisms of action and evolution of these channels. Here, the current state of the art is presented and general principles of membrane regulation of mechanosensitive function are discussed.
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Affiliation(s)
- Daniel Balleza
- Unidad de Biofísica, CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain.
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Gofman Y, Haliloglu T, Ben-Tal N. The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation. J Chem Theory Comput 2012; 8:2896-2904. [PMID: 24932138 PMCID: PMC4053537 DOI: 10.1021/ct300128x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Indexed: 11/29/2022]
Abstract
Hydrophobic helical peptides interact with lipid bilayers
in various
modes, determined by the match between the length of the helix’s
hydrophobic core and the thickness of the hydrocarbon region of the
bilayer. For example, long helices may tilt with respect to the membrane
normal to bury their hydrophobic cores in the membrane, and the lipid
bilayer may stretch to match the helix length. Recent molecular dynamics
simulations and potential of mean force calculations have shown that
some TM helices whose lengths are equal to, or even shorter than,
the bilayer thickness may also tilt. The tilt is driven by a gain
in the helix precession entropy, which compensates for the free energy
penalty resulting from membrane deformation. Using this free energy
balance, we derived theoretically an equation of state, describing
the dependence of the tilt on the helix length and membrane thickness.
To this end, we conducted coarse-grained Monte Carlo simulations of
the interaction of helices of various lengths with lipid bilayers
of various thicknesses, reproducing and expanding the previous molecular
dynamics simulations. Insight from the simulations facilitated the
derivation of the theoretical model. The tilt angles calculated using
the theoretical model agree well with our simulations and with previous
calculations and measurements.
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Affiliation(s)
- Yana Gofman
- Helmholtz-Zentrum, 21502 Geesthacht, Germany ; The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Turkan Haliloglu
- Chemical Engineering Department, Polymer Research Center, Life Sciences and Technologies Research Center, Bogazici University, 34342 Bebek-Istanbul, Turkey
| | - Nir Ben-Tal
- The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
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Grage SL, Strandberg E, Wadhwani P, Esteban-Martín S, Salgado J, Ulrich AS. Comparative analysis of the orientation of transmembrane peptides using solid-state 2H- and 15N-NMR: mobility matters. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:475-82. [DOI: 10.1007/s00249-012-0801-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/23/2012] [Accepted: 03/06/2012] [Indexed: 02/01/2023]
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77
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Gleason NJ, Vostrikov VV, Greathouse DV, Grant CV, Opella SJ, Koeppe RE. Tyrosine replacing tryptophan as an anchor in GWALP peptides. Biochemistry 2012; 51:2044-53. [PMID: 22364236 DOI: 10.1021/bi201732e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic model peptides have proven useful for examining fundamental peptide-lipid interactions. A frequently employed peptide design consists of a hydrophobic core of Leu-Ala residues with polar or aromatic amino acids flanking each side at the interfacial positions, which serve to "anchor" a specific transmembrane orientation. For example, WALP family peptides (acetyl-GWW(LA)(n)LWWA-[ethanol]amide), anchored by four Trp residues, have received particular attention in both experimental and theoretical studies. A recent modification proved successful in reducing the number of Trp anchors to only one near each end of the peptide. The resulting GWALP23 (acetyl-GGALW(5)(LA)(6)LW(19)LAGA-[ethanol]amide) displays reduced dynamics and greater sensitivity to lipid-peptide hydrophobic mismatch than traditional WALP peptides. We have further modified GWALP23 to incorporate a single tyrosine, replacing W(5) with Y(5). The resulting peptide, Y(5)GWALP23 (acetyl-GGALY(5)(LA)(6)LW(19)LAGA-amide), has a single Trp residue that is sensitive to fluorescence experiments. By incorporating specific (2)H and (15)N labels in the core sequence of Y(5)GWALP23, we were able to use solid-state NMR spectroscopy to examine the peptide orientation in hydrated lipid bilayer membranes. The peptide orients well in membranes and gives well-defined (2)H quadrupolar splittings and (15)N/(1)H dipolar couplings throughout the core helical sequence between the aromatic residues. The substitution of Y(5) for W(5) has remarkably little influence on the tilt or dynamics of GWALP23 in bilayer membranes of the phospholipids DOPC, DMPC, or DLPC. A second analogue of the peptide with one Trp and two Tyr anchors, Y(4,5)GWALP23, is generally less responsive to the bilayer thickness and exhibits lower apparent tilt angles with evidence of more extensive dynamics. In general, the peptide behavior with multiple Tyr anchors appears to be quite similar to the situation when multiple Trp anchors are present, as in the original WALP series of model peptides.
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Affiliation(s)
- Nicholas J Gleason
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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