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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
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Jeckelmann JM, Erni B. Carbohydrate Transport by Group Translocation: The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System. Subcell Biochem 2019; 92:223-274. [PMID: 31214989 DOI: 10.1007/978-3-030-18768-2_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Bacterial Phosphoenolpyruvate (PEP) : Sugar Phosphotransferase System (PTS) mediates the uptake and phosphorylation of carbohydrates, and controls the carbon- and nitrogen metabolism in response to the availability of sugars. PTS occur in eubacteria and in a few archaebacteria but not in animals and plants. All PTS comprise two cytoplasmic phosphotransferase proteins (EI and HPr) and a species-dependent, variable number of sugar-specific enzyme II complexes (IIA, IIB, IIC, IID). EI and HPr transfer phosphorylgroups from PEP to the IIA units. Cytoplasmic IIA and IIB units sequentially transfer phosphates to the sugar, which is transported by the IIC and IICIID integral membrane protein complexes. Phosphorylation by IIB and translocation by IIC(IID) are tightly coupled. The IIC(IID) sugar transporters of the PTS are in the focus of this review. There are four structurally different PTS transporter superfamilies (glucose, glucitol, ascorbate, mannose) . Crystal structures are available for transporters of two superfamilies: bcIICmal (MalT, 5IWS, 6BVG) and bcIICchb (ChbC, 3QNQ) of B. subtilis from the glucose family, and IICasc (UlaA, 4RP9, 5ZOV) of E. coli from the ascorbate superfamily . They are homodimers and each protomer has an independent transport pathway which functions by an elevator-type alternating-access mechanism. bcIICmal and bcIICchb have the same fold, IICasc has a completely different fold. Biochemical and biophysical data accumulated in the past with the transporters for mannitol (IICBAmtl) and glucose (IICBglc) are reviewed and discussed in the context of the bcIICmal crystal structures. The transporters of the mannose superfamily are dimers of protomers consisting of a IIC and a IID protein chain. The crystal structure is not known and the topology difficult to predict. Biochemical data indicate that the IICIID complex employs a different transport mechanism . Species specific IICIID serve as a gateway for the penetration of bacteriophage lambda DNA across, and insertion of class IIa bacteriocins into the inner membrane. PTS transporters are inserted into the membrane by SecYEG translocon and have specific lipid requirements. Immunoelectron- and fluorescence microscopy indicate a non-random distribution and supramolecular complexes of PTS proteins.
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Affiliation(s)
- Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
| | - Bernhard Erni
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
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Ambroggio EE, Caruso B, Villarreal MA, Raussens V, Fidelio GD. Reversing the peptide sequence impacts on molecular surface behaviour. Colloids Surf B Biointerfaces 2015; 139:25-32. [PMID: 26700230 DOI: 10.1016/j.colsurfb.2015.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/20/2015] [Accepted: 12/02/2015] [Indexed: 01/01/2023]
Abstract
The protein's primary structure has all the information for specific protein/peptide folding and, in many cases, can define specific amphiphilic regions along molecules that are important for interaction with membranes. In order to shed light on how peptide sequence is important for the surface properties of amphiphilic peptides, we designed three pairs of peptides with the following characteristics: (1) all molecules have the same hydrophobic residues; (2) the couples differ from each other in their hydrophilic amino acids: positively, negatively and non-charged; (3) each pair has the same residues (same global molecular hydrophobicity) but the primary structure is reversed in comparison to its partner (retro-isomer), giving a molecule with a hydrophilic N or C-terminus and a hydrophobic C or N-terminus. Using the Langmuir monolayer approach, we observed that sequence reversal has a central role in the lateral stability of peptide monolayers, in the ability of the molecules to partition into the air-water interface and in the rheological properties of peptide films, whereas the peptide's secondary structure, determined by ATR-FTIR, was the same for all peptides. Reversing the sequence also gives a differential way of peptide/lipid interaction when peptides are in the presence of POPC lipid bilayers. Our results show how sequence inversion confers a distinctive peptide surface behaviour and lipid interaction for molecules with a similar structure.
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Affiliation(s)
- Ernesto E Ambroggio
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina.
| | - Benjamín Caruso
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina
| | - Marcos A Villarreal
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC), CONICET, Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Vincent Raussens
- Centre for Structural Biology and Bioinformatics, Laboratory for Structure and Function of Biological Membranes, Universit é Libre de Bruxelles, CP 206/02, Blvd. du Triomphe, B-1050 Brussels, Belgium
| | - Gerardo D Fidelio
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina
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Affiliation(s)
- Kevin R Mackenzie
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
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Meindl-Beinker NM, Lundin C, Nilsson I, White SH, von Heijne G. Asn- and Asp-mediated interactions between transmembrane helices during translocon-mediated membrane protein assembly. EMBO Rep 2006; 7:1111-6. [PMID: 17008929 PMCID: PMC1679787 DOI: 10.1038/sj.embor.7400818] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 09/04/2006] [Accepted: 09/04/2006] [Indexed: 11/09/2022] Open
Abstract
Inter-helix hydrogen bonding involving asparagine (Asn, N), glutamine (Gln, Q), aspartic acid (Asp, D) or glutamic acid (Glu, E) can drive efficient di- or trimerization of transmembrane helices in detergent micelles and lipid bilayers. Likewise, Asn-Asn and Asp-Asp pairs can promote the formation of helical hairpins during translocon-mediated membrane protein assembly in the endoplasmic reticulum. By in vitro translation of model integral membrane protein constructs in the presence of rough microsomes, we show that Asn- or Asp-mediated interactions with a neighbouring transmembrane helix can enhance the membrane insertion efficiency of a marginally hydrophobic transmembrane segment. Our observations suggest that inter-helix hydrogen bonds can form during Sec61 translocon-assisted insertion and thus could be important for membrane protein assembly.
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Affiliation(s)
- Nadja M Meindl-Beinker
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Carolina Lundin
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - IngMarie Nilsson
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Stephen H White
- Department of Physiology and Biophysics and the Program in Macromolecular Structure, University of California at Irvine, Irvine, California 92697-4560, USA
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
- Tel: +46 8 16 25 90; Fax: +46 8 15 36 79; E-mail:
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Abstract
The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd </=1.5 A), allowing 90% of the library to be assigned to clusters consisting of at least five members. Surprisingly, three quarters of the helical pairs belong to one of five tightly clustered motifs whose structural features can be understood in terms of simple principles of helix-helix packing. Thus, the universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.
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Affiliation(s)
| | - W. F. DeGrado
- Departments of *Biochemistry and Biophysics and
- Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6059
- To whom correspondence should be addressed at:
1009B Stellar–Chance Building, University of Pennsylvania, Philadelphia, PA 19104-6059.
E-mail:
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Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 2005; 433:377-81. [PMID: 15674282 DOI: 10.1038/nature03216] [Citation(s) in RCA: 745] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Accepted: 11/16/2004] [Indexed: 11/08/2022]
Abstract
Membrane proteins depend on complex translocation machineries for insertion into target membranes. Although it has long been known that an abundance of nonpolar residues in transmembrane helices is the principal criterion for membrane insertion, the specific sequence-coding for transmembrane helices has not been identified. By challenging the endoplasmic reticulum Sec61 translocon with an extensive set of designed polypeptide segments, we have determined the basic features of this code, including a 'biological' hydrophobicity scale. We find that membrane insertion depends strongly on the position of polar residues within transmembrane segments, adding a new dimension to the problem of predicting transmembrane helices from amino acid sequences. Our results indicate that direct protein-lipid interactions are critical during translocon-mediated membrane insertion.
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Affiliation(s)
- Tara Hessa
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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Abstract
The energetic cost of partitioning peptide bonds into membrane bilayers is prohibitive unless the peptide bonds participate in hydrogen bonds. However, even then there is a significant free energy penalty for dehydrating the peptide bonds that can only be overcome by favorable hydrophobic interactions. Membrane protein structure formation is thus dominated by hydrogen bonding interactions, which is the subject of this review.
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Affiliation(s)
- Stephen H White
- Department of Physiology and Biophysics, University of California at Irvine, Irvine, California 92697
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Senes A, Engel DE, DeGrado WF. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol 2004; 14:465-79. [PMID: 15313242 DOI: 10.1016/j.sbi.2004.07.007] [Citation(s) in RCA: 350] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Helical integral membrane proteins share several structural determinants that are widely conserved across their universe. The discovery of common motifs has furthered our understanding of the features that are important to stability in the membrane environment, while simultaneously providing clues about proteins that lack high-resolution structures. Motif analysis also helps to target mutagenesis studies, and other experimental and computational work. Three types of transmembrane motifs have recently seen interesting developments: the GxxxG motif and its like; polar and hydrogen bonding motifs; and proline motifs.
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Affiliation(s)
- Alessandro Senes
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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Hermansson M, von Heijne G. Inter-helical hydrogen bond formation during membrane protein integration into the ER membrane. J Mol Biol 2004; 334:803-9. [PMID: 14636604 DOI: 10.1016/j.jmb.2003.10.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recent work has shown that efficient di- or trimerization of hydrophobic transmembrane helices in detergent micelles or lipid bilayers can be driven by inter-helix hydrogen bonding involving polar residues such as Asn or Asp. Using in vitro translation in the presence of rough microsomes of a model integral membrane protein, we now show that the formation of so-called helical hairpins, two tightly spaced transmembrane helices connected by a short loop, can likewise be promoted by the introduction of Asn-Asn or Asp-Asp pairs in a long transmembrane hydrophobic segment. These observations suggest that inter-helix hydrogen bonds can form within the context of the Sec61 translocon in the endoplasmic reticulum, implying that hydrophobic segments in a nascent polypeptide chain in transit through the Sec61 channel have immediate access to a non-aqueous subcompartment within the translocon.
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Affiliation(s)
- Marika Hermansson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
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