1
|
White SH. Fifty Years of Biophysics at the Membrane Frontier. Annu Rev Biophys 2023; 52:21-67. [PMID: 36791747 DOI: 10.1146/annurev-biophys-051622-112341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The author first describes his childhood in the South and the ways in which it fostered the values he has espoused throughout his life, his development of a keen fascination with science, and the influences that supported his progress toward higher education. His experiences in ROTC as a student, followed by two years in the US Army during the Vietnam War, honed his leadership skills. The bulk of the autobiography is a chronological journey through his scientific career, beginning with arrival at the University of California, Irvine in 1972, with an emphasis on the postdoctoral students and colleagues who have contributed substantially to each phase of his lab's progress. White's fundamental findings played a key role in the development of membrane biophysics, helping establish it as fertile ground for research. A story gradually unfolds that reveals the deeply collaborative and painstakingly executed work necessary for a successful career in science.
Collapse
Affiliation(s)
- Stephen H White
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California, USA;
| |
Collapse
|
2
|
Ball HL, Said H, Chapman K, Fu R, Xiong Y, Burk JA, Rosenbaum D, Veneziano R, Cotten ML. Orexin A, an amphipathic α-helical neuropeptide involved in pleiotropic functions in the nervous and immune systems: Synthetic approach and biophysical studies of the membrane-bound state. Biophys Chem 2023; 297:107007. [PMID: 37037119 DOI: 10.1016/j.bpc.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
This research reports on the membrane interactions of orexin A (OXA), an α-helical and amphipathic neuropeptide that contains 33 residues and two disulfide bonds in the N-terminal region. OXA, which activates the orexins 1 and 2 receptors in neural and immune cell membranes, has essential pleiotropic physiological effects, including at the levels of arousal, sleep/wakefulness, energy balance, neuroprotection, lipid signaling, the inflammatory response, and pain. As a result, the orexin system has become a prominent target to treat diseases such as sleep disorders, drug addiction, and inflammation. While the high-resolution structure of OXA has been investigated in water and bound to micelles, there is a lack of information about its conformation bound to phospholipid membranes and its receptors. NMR is a powerful method to investigate peptide structures in a membrane environment. To facilitate the NMR structural studies of OXA exposed to membranes, we present a novel synthetic scheme, leading to the production of isotopically-labeled material at high purity. A receptor activation assay shows that the 15N-labeled peptide is biologically active. Biophysical studies are performed using surface plasmon resonance, circular dichroism, and NMR to investigate the interactions of OXA with phospholipid bilayers. The results demonstrate a strong interaction between the peptide and phospholipids, an increase in α-helical content upon membrane binding, and an in-plane orientation of the C-terminal region critical to function. This new knowledge about structure-activity relationships in OXA could inspire the design of novel therapeutics that leverage the anti-inflammatory and neuro-protective functions of OXA, and therefore could help address neuroinflammation, a major issue associated with neurological disorders such as Alzheimer's disease.
Collapse
Affiliation(s)
- Haydn L Ball
- Department of Chemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hooda Said
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Karen Chapman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA
| | - Joshua A Burk
- Department of Psychological Sciences, William & Mary, Williamsburg, VA 23185, USA
| | - Daniel Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Remi Veneziano
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Myriam L Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA.
| |
Collapse
|
3
|
Steinkühler J, Jacobs ML, Boyd MA, Villaseñor CG, Loverde SM, Kamat NP. PEO- b-PBD Diblock Copolymers Induce Packing Defects in Lipid/Hybrid Membranes and Improve Insertion Rates of Natively Folded Peptides. Biomacromolecules 2022; 23:4756-4765. [PMID: 36318160 PMCID: PMC9667879 DOI: 10.1021/acs.biomac.2c00936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/10/2022] [Indexed: 11/15/2022]
Abstract
Hybrid membranes assembled from biological lipids and synthetic polymers are a promising scaffold for the reconstitution and utilization of membrane proteins. Recent observations indicate that inclusion of small fractions of polymer in lipid membranes can improve protein folding and function, but the exact structural and physical changes a given polymer sequence imparts on a membrane often remain unclear. Here, we use all-atom molecular dynamics simulations to study the structure of hybrid membranes assembled from DOPC phospholipids and PEO-b-PBD diblock copolymers. We verified our computational model using new and existing experimental data and obtained a detailed picture of the polymer conformations in the lipid membrane that we can relate to changes in membrane elastic properties. We find that inclusion of low polymer fractions induces transient packing defects into the membrane. These packing defects act as insertion sites for two model peptides, and in this way, small amounts of polymer content in lipid membranes can lead to large increases in peptide insertion rates. Additionally, we report the peptide conformational space in both pure lipid and hybrid membranes. Both membranes support similar alpha helical peptide structures, exemplifying the biocompatibility of hybrid membranes.
Collapse
Affiliation(s)
- Jan Steinkühler
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois60208, United States
| | - Miranda L. Jacobs
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois60208, United States
| | - Margrethe A. Boyd
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois60208, United States
| | - Citlayi G. Villaseñor
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois60208, United States
| | - Sharon M. Loverde
- Department
of Chemistry, College of Staten Island, The City University of New York, Staten Island, New York10314, United States
| | - Neha P. Kamat
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois60657, United States
| |
Collapse
|
4
|
Kawamala BK, Abrol R. Three-stage model of helical membrane protein folding: Role of membrane-water interface as the intermediate stage vestibule for TM helices during their in membrano assembly. Biochem Biophys Res Commun 2022; 624:1-7. [PMID: 35926384 PMCID: PMC10587497 DOI: 10.1016/j.bbrc.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/02/2022] [Indexed: 11/22/2022]
Abstract
Integral membrane proteins (MPs) are dominated by transmembrane α-helical (TMH) proteins playing critical roles in cellular signaling processes. These proteins display a wide range of sizes from one TMH domain to at least 26 TMH domains and diverse structural folds. A common feature of most of these folds is the TM orientation of the helical domains and the approximately parallel packing of these domains into helical bundles of varying stability, however, it has been challenging to study the folding of these proteins experimentally. The contribution of helix stabilization in membrane and interface to the folding energy landscape are investigated here for the full range of TMH protein sizes containing 1 TM domain (1-TMH protein) to 24 TM domains (24-TMH protein) for all TMH proteins with available structures using structural bioinformatics based hydropathy analysis. The TM helix insertion stabilization energies from Water to membrane-water Interface (WAT→INT energies) are on average half of those insertion energies from water to transmembrane orientation (WAT→TM energies) for the whole polytopic helical membrane proteome (1-TMH to 24-TMH proteins). This suggests a potentially dominant role of the membrane-water interface as a viable holding vestibule for the TM helices during their release from the translocon. This provides proteome-level evidence for the broadly applicable four-step thermodynamic framework by White and co-workers as well as a natural extension of Popot and Engelman's original two-stage model of helical MP folding to a three-stage model, where, in the new intermediate stage, the membrane-water interface acts as a holding vestibule for the translated TM helices, reconciling the interface's critical role in MP folding seen in many previous studies. Support for this model is provided by showing the stability of hydrophobic TM helices at the membrane-water interface through several microsecond long molecular dynamics simulations of five hydrophobic helical domains and a helical hairpin pre-folded from the ribosomal exit vestibule.
Collapse
Affiliation(s)
- Bridget-K Kawamala
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, USA
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, USA.
| |
Collapse
|
5
|
Brady R, Harris NJ, Pellowe GA, Gulaidi Breen S, Booth PJ. How lipids affect the energetics of co-translational alpha helical membrane protein folding. Biochem Soc Trans 2022; 50:555-567. [PMID: 35212365 PMCID: PMC9022994 DOI: 10.1042/bst20201063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 11/23/2022]
Abstract
Membrane proteins need to fold with precision in order to function correctly, with misfolding potentially leading to disease. The proteins reside within a hydrophobic lipid membrane and must insert into the membrane and fold correctly, generally whilst they are being translated by the ribosome. Favourable and unfavourable free energy contributions are present throughout each stage of insertion and folding. The unfavourable energy cost of transferring peptide bonds into the hydrophobic membrane interior is compensated for by the favourable hydrophobic effect of partitioning a hydrophobic transmembrane alpha-helix into the membrane. Native membranes are composed of many different types of lipids, but how these different lipids influence folding and the associated free energies is not well understood. Altering the lipids in the bilayer is known to affect the probability of transmembrane helix insertion into the membrane, and lipids also affect protein stability and can promote successful folding. This review will summarise the free energy contributions associated with insertion and folding of alpha helical membrane proteins, as well as how lipids can make these processes more or less favourable. We will also discuss the implications of this work for the free energy landscape during the co-translational folding of alpha helical membrane proteins.
Collapse
Affiliation(s)
- Ryan Brady
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Nicola J. Harris
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Grant A. Pellowe
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Samuel Gulaidi Breen
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Paula J. Booth
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| |
Collapse
|
6
|
Cotranslational recruitment of ribosomes in protocells recreates a translocon-independent mechanism of proteorhodopsin biogenesis. iScience 2021; 24:102429. [PMID: 33997704 PMCID: PMC8102411 DOI: 10.1016/j.isci.2021.102429] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 01/10/2023] Open
Abstract
The emergence of lipid membranes and embedded proteins was essential for the evolution of cells. Translocon complexes mediate cotranslational recruitment and membrane insertion of nascent proteins, but they already contain membrane-integral proteins. Therefore, a simpler mechanism must exist, enabling spontaneous membrane integration while preventing aggregation of unchaperoned protein in the aqueous phase. Here, we used giant unilamellar vesicles encapsulating minimal translation components to systematically interrogate the requirements for insertion of the model protein proteorhodopsin (PR) – a structurally ubiquitous membrane protein. We show that the N-terminal hydrophobic domain of PR is both necessary and sufficient for cotranslational recruitment of ribosomes to the membrane and subsequent membrane insertion of PR. Insertion of N-terminally truncated PR was restored by artificially attaching ribosomes to the membrane. Our findings offer a self-sufficient protein-inherent mechanism as a possible explanation for effective membrane protein biogenesis in a “pretranslocon” era, and they offer new opportunities for generating artificial cells. Generated a simple artificial cell model for membrane protein insertion We identified protein-inherent control of translational targeting without chaperones Ribosomes, artificially tethered to GUVs increased membrane protein insertion
Collapse
|
7
|
Vasquez-Montes V, Ladokhin AS. Expanding MPEx Hydropathy Analysis to Account for Electrostatic Contributions to Protein Interactions with Anionic Membranes. J Membr Biol 2021; 254:109-117. [PMID: 33564913 DOI: 10.1007/s00232-021-00170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022]
Abstract
Hydropathy plots are a crucial tool to guide experimental design, as they generate predictions of protein-membrane interactions and their bilayer topology. The predictions are based on experimentally determined hydrophobicity scales, which provide an estimate for the propensity and stability of these interactions. A significant improvement to the accuracy of hydropathy analyses was provided by the development of the popular Wimley-White interfacial and octanol hydrophobicity scales. These scales have been previously incorporated into the freely available MPEx (Membrane Protein Explorer) online application. Here, we introduce a substantial update to MPEx that allows for the consideration of electrostatic contributions to the bilayer partitioning free energy. This component originates from the Coulombic attraction or repulsion of charges between proteins and membranes. Its inclusion in hydropathy calculations increases the accuracy of hydropathy plot predictions and extends their use to more complex systems (i.e., anionic membranes). We illustrate the application of this analysis to studies on the membrane selectivity of antimicrobial peptides, the membrane partitioning of ion-channel gating modifiers, and the amyloid proteins α-synuclein and Tau, as well as pH-dependent bilayer interactions of diphtheria toxin and apoptotic inhibitor Bcl-xL.
Collapse
Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| |
Collapse
|
8
|
Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition. J Membr Biol 2021; 254:75-96. [PMID: 33564914 DOI: 10.1007/s00232-021-00174-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 12/16/2022]
Abstract
The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore-forming peptide into a selective pore-former for different lipid types. A library of 2916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.
Collapse
|
9
|
Marx DC, Fleming KG. Local Bilayer Hydrophobicity Modulates Membrane Protein Stability. J Am Chem Soc 2021; 143:764-772. [DOI: 10.1021/jacs.0c09412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Dagan C. Marx
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Karen G. Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
10
|
McKay MJ, Fu R, Greathouse DV, Koeppe RE. Breaking the Backbone: Central Arginine Residues Induce Membrane Exit and Helix Distortions within a Dynamic Membrane Peptide. J Phys Chem B 2019; 123:8034-8047. [PMID: 31483653 DOI: 10.1021/acs.jpcb.9b06034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane domains of membrane proteins sometimes contain conserved charged or ionizable residues which may be essential for protein function and regulation. This work examines the molecular interactions of single Arg residues within a highly dynamic transmembrane peptide helix. To this end, we have modified the GW4,20ALP23 (acetyl-GGAW4(AL)7AW20AGA-amide) model peptide framework to incorporate Arg residues near the center of the peptide. Peptide helix formation, orientation and dynamics were analyzed by means of solid-state NMR spectroscopy to monitor specific 2H- or 15N-labeled residues. GW4,20ALP23 itself adopts a tilted orientation within lipid bilayer membranes. Nevertheless, the GW4,20ALP23 helix exhibits moderate to high dynamic averaging of NMR observables, such as 2H quadrupolar splittings or 15N-1H dipolar couplings, due to competition between the interfacial Trp residues on opposing helix faces. Here we examine how the helix dynamics are impacted by the introduction of a single Arg residue at position 12 or 14. Residue R14 restricts the helix to low dynamic averaging and a well-defined tilt that varies inversely with the lipid bilayer thickness. To compensate for the dominance of R14, the competing Trp residues cause partial unwinding of the helix at the C-terminal. By contrast, R12GW4,20ALP23 exits the DOPC bilayer to an interfacial surface-bound location. Interestingly, multiple orientations are exhibited by a single residue, Ala-9. Quadrupolar splittings generated by 2H-labeled residues A3, A5, A7, and A9 do not fit to the α-helical quadrupolar wave plot defined by residues A11, A13, A15, A17, A19, and A21. The discontinuity at residue A9 implicates a helical swivel distortion and an apparent 310-helix involving the N-terminal residues preceding A11. These molecular features suggest that, while arginine residues are prominent factors controlling transmembrane helix dynamics, the influence of interfacial tryptophan residues cannot be ignored.
Collapse
Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University , Tallahassee , Florida 32310 , United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| |
Collapse
|