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Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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Hikage R, Sekiya Y, Sawasato K, Nishiyama KI. CdsA, a CDP-diacylglycerol synthase involved in phospholipid and glycolipid MPIase biosynthesis, possesses multiple initiation codons. Genes Cells 2024; 29:347-355. [PMID: 38351722 DOI: 10.1111/gtc.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 04/04/2024]
Abstract
CdsA is a CDP-diacylglycerol synthase essential for phospholipid and glycolipid MPIase biosynthesis, and therefore for growth. The initiation codon of CdsA has been assigned as "TTG," while methionine at the 37th codon was reported to be an initiation codon in the original report. Since a vector containing the open reading frame starting with "TTG" under a controllable promoter complemented the cdsA knockout, "TTG" could function as an initiation codon. However, no evidence supporting that this "TTG" is the sole initiation codon has been reported. We determined the initiation codon by examining the ability of mutants around the N-terminal region to complement cdsA mutants. Even if the "TTG" was substituted with a stop codon, the clear complementation was observed. Moreover, the clones with multiple mutations of stop codons complemented the cdsA mutant up to the 37th codon, indicating that cdsA possesses multiple codons that can function as initiation codons. We constructed an experimental system in which the chromosomal expression of cdsA can be analyzed. By means of this system, we found that the cdsA mutant with substitution of "TTG" with a stop codon is fully functional. Thus, we concluded that CdsA contains multiple initiation codons.
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Affiliation(s)
- Runa Hikage
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yusei Sekiya
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Katsuhiro Sawasato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Ken-Ichi Nishiyama
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
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Sudha G, Bassot C, Lamb J, Shu N, Huang Y, Elofsson A. The evolutionary history of topological variations in the CPA/AT transporters. PLoS Comput Biol 2021; 17:e1009278. [PMID: 34403419 PMCID: PMC8396727 DOI: 10.1371/journal.pcbi.1009278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 08/27/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
CPA/AT transporters are made up of scaffold and a core domain. The core domain contains two non-canonical helices (broken or reentrant) that mediate the transport of ions, amino acids or other charged compounds. During evolution, these transporters have undergone substantial changes in structure, topology and function. To shed light on these structural transitions, we create models for all families using an integrated topology annotation method. We find that the CPA/AT transporters can be classified into four fold-types based on their structure; (1) the CPA-broken fold-type, (2) the CPA-reentrant fold-type, (3) the BART fold-type, and (4) a previously not described fold-type, the Reentrant-Helix-Reentrant fold-type. Several topological transitions are identified, including the transition between a broken and reentrant helix, one transition between a loop and a reentrant helix, complete changes of orientation, and changes in the number of scaffold helices. These transitions are mainly caused by gene duplication and shuffling events. Structural models, topology information and other details are presented in a searchable database, CPAfold (cpafold.bioinfo.se).
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Affiliation(s)
- Govindarajan Sudha
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Claudio Bassot
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - John Lamb
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Nanjiang Shu
- Bioinformatics Short-term Support and Infrastructure (BILS), Science for Life Laboratory, Sweden
| | - Yan Huang
- Science for Life Laboratory, Karolinska Institutet, Stockholm University, Solna, Sweden
| | - Arne Elofsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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Predicting Alpha Helical Transmembrane Proteins Using HMMs. Methods Mol Biol 2018; 1552:63-82. [PMID: 28224491 DOI: 10.1007/978-1-4939-6753-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Alpha helical transmembrane (TM) proteins constitute an important structural class of membrane proteins involved in a wide variety of cellular functions. The prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes, is of great importance for the elucidation of their structure and function. Several methods have been applied for the prediction of the transmembrane segments and the topology of alpha helical transmembrane proteins utilizing different algorithmic techniques. Hidden Markov Models (HMMs) have been efficiently used in the development of several computational methods used for this task. In this chapter we give a brief review of different available prediction methods for alpha helical transmembrane proteins pointing out sequence and structural features that should be incorporated in a prediction method. We then describe the procedure of the design and development of a Hidden Markov Model capable of predicting the transmembrane alpha helices in proteins and discriminating them from globular proteins.
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Kjaergaard M, Kragelund BB. Functions of intrinsic disorder in transmembrane proteins. Cell Mol Life Sci 2017; 74:3205-3224. [PMID: 28601983 PMCID: PMC11107515 DOI: 10.1007/s00018-017-2562-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine receptors. The functions of the disordered regions are many and varied. We will discuss selected examples including: (1) Organization of receptors, kinases, phosphatases and second messenger sources into signaling complexes. (2) Modulation of the membrane-embedded domain function by ball-and-chain like mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding protein disorder.
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Affiliation(s)
- Magnus Kjaergaard
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
- The Danish Research Institute of Translational Neuroscience (DANDRITE), Aarhus, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Tooke FJ, Babot M, Chandra G, Buchanan G, Palmer T. A unifying mechanism for the biogenesis of membrane proteins co-operatively integrated by the Sec and Tat pathways. eLife 2017; 6. [PMID: 28513434 PMCID: PMC5449189 DOI: 10.7554/elife.26577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
The majority of multi-spanning membrane proteins are co-translationally inserted into the bilayer by the Sec pathway. An important subset of membrane proteins have globular, cofactor-containing extracytoplasmic domains requiring the dual action of the co-translational Sec and post-translational Tat pathways for integration. Here, we identify further unexplored families of membrane proteins that are dual Sec-Tat-targeted. We establish that a predicted heme-molybdenum cofactor-containing protein, and a complex polyferredoxin, each require the concerted action of two translocases for their assembly. We determine that the mechanism of handover from Sec to Tat pathway requires the relatively low hydrophobicity of the Tat-dependent transmembrane domain. This, coupled with the presence of C-terminal positive charges, results in abortive insertion of this transmembrane domain by the Sec pathway and its subsequent release at the cytoplasmic side of the membrane. Together, our data points to a simple unifying mechanism governing the assembly of dual targeted membrane proteins.
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Affiliation(s)
- Fiona J Tooke
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Marion Babot
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Grant Buchanan
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Tracy Palmer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology. Proc Natl Acad Sci U S A 2016; 113:10340-5. [PMID: 27562165 DOI: 10.1073/pnas.1605888113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The energetics of membrane-protein interactions determine protein topology and structure: hydrophobicity drives the insertion of helical segments into the membrane, and positive charges orient the protein with respect to the membrane plane according to the positive-inside rule. Until recently, however, quantifying these contributions met with difficulty, precluding systematic analysis of the energetic basis for membrane-protein topology. We recently developed the dsTβL method, which uses deep sequencing and in vitro selection of segments inserted into the bacterial plasma membrane to infer insertion-energy profiles for each amino acid residue across the membrane, and quantified the insertion contribution from hydrophobicity and the positive-inside rule. Here, we present a topology-prediction algorithm called TopGraph, which is based on a sequence search for minimum dsTβL insertion energy. Whereas the average insertion energy assigned by previous experimental scales was positive (unfavorable), the average assigned by TopGraph in a nonredundant set is -6.9 kcal/mol. By quantifying contributions from both hydrophobicity and the positive-inside rule we further find that in about half of large membrane proteins polar segments are inserted into the membrane to position more positive charges in the cytoplasm, suggesting an interplay between these two energy contributions. Because membrane-embedded polar residues are crucial for substrate binding and conformational change, the results implicate the positive-inside rule in determining the architectures of membrane-protein functional sites. This insight may aid structure prediction, engineering, and design of membrane proteins. TopGraph is available online (topgraph.weizmann.ac.il).
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Thermo-responsive chiral column by scissoring motion from rigid–flexible aromatic rod assembly. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2015.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Peters C, Tsirigos KD, Shu N, Elofsson A. Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics 2015; 32:1158-62. [PMID: 26644416 DOI: 10.1093/bioinformatics/btv709] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/29/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The translocon recognizes sufficiently hydrophobic regions of a protein and inserts them into the membrane. Computational methods try to determine what hydrophobic regions are recognized by the translocon. Although these predictions are quite accurate, many methods still fail to distinguish marginally hydrophobic transmembrane (TM) helices and equally hydrophobic regions in soluble protein domains. In vivo, this problem is most likely avoided by targeting of the TM-proteins, so that non-TM proteins never see the translocon. Proteins are targeted to the translocon by an N-terminal signal peptide. The targeting is also aided by the fact that the N-terminal helix is more hydrophobic than other TM-helices. In addition, we also recently found that the C-terminal helix is more hydrophobic than central helices. This information has not been used in earlier topology predictors. RESULTS Here, we use the fact that the N- and C-terminal helices are more hydrophobic to develop a new version of the first-principle-based topology predictor, SCAMPI. The new predictor has two main advantages; first, it can be used to efficiently separate membrane and non-membrane proteins directly without the use of an extra prefilter, and second it shows improved performance for predicting the topology of membrane proteins that contain large non-membrane domains. AVAILABILITY AND IMPLEMENTATION The predictor, a web server and all datasets are available at http://scampi.bioinfo.se/ CONTACT arne@bioinfo.se SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christoph Peters
- Department of Biochemistry and Biophysics, Science for Life Laboratory and
| | | | - Nanjiang Shu
- Department of Biochemistry and Biophysics, Science for Life Laboratory and Sweden Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm University, Solna 17121, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory and
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