1
|
Saha N, Tomar RS. Copper inhibits protein maturation in the secretory pathway by targeting the Sec61 translocon in Saccharomyces cerevisiae. J Biol Chem 2022; 298:102170. [PMID: 35738397 PMCID: PMC9304788 DOI: 10.1016/j.jbc.2022.102170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
In Saccharomyces cerevisiae, proteins destined for secretion utilize the post-translational translocon machinery to gain entry into the endoplasmic reticulum. These proteins then mature by undergoing a number of post-translational modifications in different compartments of the secretory pathway. While these modifications have been well established for many proteins, to date only a few studies have been conducted regarding the conditions and factors affecting maturation of these proteins before entering into the endoplasmic reticulum. Here, using immunoblotting, microscopy, and spot test assays, we show that excess copper inhibits the Sec61 translocon function and causes accumulation of two well-known post-translationally translocated proteins, Gas1 (glycophospholipid-anchored surface protein) and CPY (carboxypeptidase Y), in the cytosol. We further show that the copper-sensitive phenotype of sec61-deficient yeast cells is ameliorated by restoring the levels of SEC61 through plasmid transformation. Furthermore, screening of translocation-defective Sec61 mutants revealed that sec61-22, bearing L80M, V134I, M248V, and L342S mutations, is resistant to copper, suggesting that copper might be inflicting toxicity through one of these residues. In conclusion, these findings imply that copper-mediated accumulation of post-translationally translocated proteins is due to the inhibition of Sec61.
Collapse
Affiliation(s)
- Nitu Saha
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, 462066, Madhya Pradesh, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, 462066, Madhya Pradesh, India.
| |
Collapse
|
2
|
Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
Collapse
Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| |
Collapse
|
3
|
Whitley P, Grau B, Gumbart JC, Martínez-Gil L, Mingarro I. Folding and Insertion of Transmembrane Helices at the ER. Int J Mol Sci 2021; 22:ijms222312778. [PMID: 34884581 PMCID: PMC8657811 DOI: 10.3390/ijms222312778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023] Open
Abstract
In eukaryotic cells, the endoplasmic reticulum (ER) is the entry point for newly synthesized proteins that are subsequently distributed to organelles of the endomembrane system. Some of these proteins are completely translocated into the lumen of the ER while others integrate stretches of amino acids into the greasy 30 Å wide interior of the ER membrane bilayer. It is generally accepted that to exist in this non-aqueous environment the majority of membrane integrated amino acids are primarily non-polar/hydrophobic and adopt an α-helical conformation. These stretches are typically around 20 amino acids long and are known as transmembrane (TM) helices. In this review, we will consider how transmembrane helices achieve membrane integration. We will address questions such as: Where do the stretches of amino acids fold into a helical conformation? What is/are the route/routes that these stretches take from synthesis at the ribosome to integration through the ER translocon? How do these stretches ‘know’ to integrate and in which orientation? How do marginally hydrophobic stretches of amino acids integrate and survive as transmembrane helices?
Collapse
Affiliation(s)
- Paul Whitley
- Department of Biology and Biochemistry, Centre for Regenerative Medicine, University of Bath, Bath BA2 7AY, UK;
| | - Brayan Grau
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - James C. Gumbart
- School of Physics, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Luis Martínez-Gil
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
- Correspondence: ; Tel.: +34-963543796
| |
Collapse
|
4
|
Efficient integration of transmembrane domains depends on the folding properties of the upstream sequences. Proc Natl Acad Sci U S A 2021; 118:2102675118. [PMID: 34373330 PMCID: PMC8379923 DOI: 10.1073/pnas.2102675118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The topology of membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. For each polypeptide segment of ∼20 residues entering the translocon, their combined hydrophobicities were previously shown to define membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect the hydrophobicity threshold. Sequences that are rapidly folding, intrinsically disordered, very short, or strongly binding chaperones allow efficient integration at low hydrophobicity. Folding deficient mutant domains and artificial sequences not binding chaperones interfered with membrane integration likely by remaining partially unfolded and exposing hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. Rapid folding or strong chaperone binding thus promote efficient integration. The topology of most membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. The translocon provides a pore for the transfer of polypeptide segments across the membrane while giving them lateral access to the lipid. For each polypeptide segment of ∼20 residues, the combined hydrophobicities of its constituent amino acids were previously shown to define the extent of membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect its hydrophobicity requirement for integration. Rapidly folding domains, sequences that are intrinsically disordered or very short or capable of binding chaperones with high affinity, allow for efficient transmembrane integration with low-hydrophobicity thresholds for both orientations in the membrane. In contrast, long protein fragments, folding-deficient mutant domains, and artificial sequences not binding chaperones interfered with membrane integration, requiring higher hydrophobicity. We propose that the latter sequences, as they compact on their hydrophobic residues, partially folded but unable to reach a native state, expose hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. The results suggest that rapid folding or strong chaperone binding is required for efficient transmembrane integration.
Collapse
|
5
|
Bhadra P, Yadhanapudi L, Römisch K, Helms V. How does Sec63 affect the conformation of Sec61 in yeast? PLoS Comput Biol 2021; 17:e1008855. [PMID: 33780447 PMCID: PMC8031780 DOI: 10.1371/journal.pcbi.1008855] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/08/2021] [Accepted: 03/05/2021] [Indexed: 12/31/2022] Open
Abstract
The Sec complex catalyzes the translocation of proteins of the secretory pathway into the endoplasmic reticulum and the integration of membrane proteins into the endoplasmic reticulum membrane. Some substrate peptides require the presence and involvement of accessory proteins such as Sec63. Recently, a structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins was determined by cryo-electron microscopy (cryo-EM). Here, we show by co-precipitation that the Sec61 channel subunit Sbh1 is not required for formation of stable Sec63-Sec61 contacts. Molecular dynamics simulations started from the cryo-EM conformation of Sec61 bound to Sec63 and of unbound Sec61 revealed how Sec63 affects the conformation of Sec61 lateral gate, plug, pore region and pore ring diameter via three intermolecular contact regions. Molecular docking of SRP-dependent vs. SRP-independent signal peptide chains into the Sec61 channel showed that the pore regions affected by presence/absence of Sec63 play a crucial role in positioning the signal anchors of SRP-dependent substrates nearby the lateral gate.
Collapse
Affiliation(s)
- Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Saarland, Germany
| | - Lalitha Yadhanapudi
- Faculty of Natural Sciences and Technology, Saarland University, Saarbrücken, Saarland, Germany
| | - Karin Römisch
- Faculty of Natural Sciences and Technology, Saarland University, Saarbrücken, Saarland, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Saarland, Germany
| |
Collapse
|
6
|
Niesen MJM, Zimmer MH, Miller TF. Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon. J Am Chem Soc 2020; 142:5449-5460. [PMID: 32130863 PMCID: PMC7338273 DOI: 10.1021/jacs.9b07820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An important aspect of cellular function is the correct targeting and delivery of newly synthesized proteins. Central to this task is the machinery of the Sec translocon, a transmembrane channel that is involved in both the translocation of nascent proteins across cell membranes and the integration of proteins into the membrane. Considerable experimental and computational effort has focused on the Sec translocon and its role in nascent protein biosynthesis, including the correct folding and expression of integral membrane proteins. However, the use of molecular simulation methods to explore Sec-facilitated protein biosynthesis is hindered by the large system sizes and long (i.e., minute) time scales involved. In this work, we describe the development and application of a coarse-grained simulation approach that addresses these challenges and allows for direct comparison with both in vivo and in vitro experiments. The method reproduces a wide range of experimental observations, providing new insights into the underlying molecular mechanisms, predictions for new experiments, and a strategy for the rational enhancement of membrane protein expression levels.
Collapse
Affiliation(s)
- Michiel J M Niesen
- Department of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Matthew H Zimmer
- Department of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F Miller
- Department of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
7
|
Wang Z, Chen C, Liu H, Hrynshpan D, Savitskaya T, Chen J, Chen J. Effects of carbon nanotube on denitrification performance of Alcaligenes sp. TB: Promotion of electron generation, transportation and consumption. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 183:109507. [PMID: 31386942 DOI: 10.1016/j.ecoenv.2019.109507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/14/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Multi-walled carbon nanotubes (MWCNTs) promote biodegradation in water treatment, but the effect of MWCNT on denitrification under aerobic conditions is still unclear. This investigation focused on the denitrification performance of MWCNT and its toxic effects on Alcaligenes sp. TB which showed that 30 mg/L MWCNTs increased NO3- removal efficiency from 84% to 100% and decreased the NO2-and N2O accumulation rates by 36% and 17.5%, respectively. Nitrite reductase and nitrous oxide reductase activities were further increased by 19.5% and 7.5%, respectively. The mechanism demonstrated that electron generation (NADH yield) and electron transportation system activity increased by 14.5% and 104%, respectively. Cell membrane analysis found that MWCNT caused an increase in polyunsaturated fatty acids, which had positive effects on electron transportation and membrane fluidity at a low concentration of 96 mg/kg but caused membrane lipid peroxidation and impaired membrane integrity at a high concentration of 115 mg/L. These findings confirmed that MWCNT affects the activity of Alcaligenes sp. TB and consequently enhances denitrification performance.
Collapse
Affiliation(s)
- Zeyu Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Cong Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Huan Liu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Dzmitry Hrynshpan
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus
| | - Tatsiana Savitskaya
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jun Chen
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310021, PR China.
| |
Collapse
|
8
|
Guerriero CJ, Gomez YK, Daskivich GJ, Reutter KR, Augustine AA, Weiberth KF, Nakatsukasa K, Grabe M, Brodsky JL. Harmonizing Experimental Data with Modeling to Predict Membrane Protein Insertion in Yeast. Biophys J 2019; 117:668-678. [PMID: 31399214 DOI: 10.1016/j.bpj.2019.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins must adopt their proper topologies within biological membranes, but achieving the correct topology is compromised by the presence of marginally hydrophobic transmembrane helices (TMHs). In this study, we report on a new model membrane protein in yeast that harbors two TMHs fused to an unstable nucleotide-binding domain. Because the second helix (TMH2) in this reporter has an unfavorable predicted free energy of insertion, we employed established methods to generate variants that alter TMH2 insertion free energy. We first found that altering TMH2 did not significantly affect the extent of protein degradation by the cellular quality control machinery. Next, we correlated predicted insertion free energies from a knowledge-based energy scale with the measured apparent free energies of TMH2 insertion. Although the predicted and apparent insertion energies showed a similar trend, the predicted free-energy changes spanned an unanticipated narrow range. By instead using a physics-based model, we obtained a broader range of free energies that agreed considerably better with the magnitude of the experimentally derived values. Nevertheless, some variants still inserted better in yeast than predicted from energy-based scales. Therefore, molecular dynamics simulations were performed and indicated that the corresponding mutations induced conformational changes within TMH2, which altered the number of stabilizing hydrogen bonds. Together, our results offer insight into the ability of the cellular quality control machinery to recognize conformationally distinct misfolded topomers, provide a model to assess TMH insertion in vivo, and indicate that TMH insertion energy scales may be limited depending on the specific protein and the mutation present.
Collapse
Affiliation(s)
| | - Yessica K Gomez
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Grant J Daskivich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Karl-Richard Reutter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew A Augustine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kurt F Weiberth
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kunio Nakatsukasa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
9
|
Spiess M, Junne T, Janoschke M. Membrane Protein Integration and Topogenesis at the ER. Protein J 2019; 38:306-316. [DOI: 10.1007/s10930-019-09827-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
10
|
Kida Y, Sakaguchi M. Interaction mapping of the Sec61 translocon identifies two Sec61α regions interacting with hydrophobic segments in translocating chains. J Biol Chem 2018; 293:17050-17060. [PMID: 30213864 DOI: 10.1074/jbc.ra118.003219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/26/2018] [Indexed: 01/09/2023] Open
Abstract
Many proteins in organelles of the secretory pathway, as well as secretory proteins, are translocated across and inserted into the endoplasmic reticulum membrane by the Sec61 translocon, a protein-conducting channel. The channel consists of 10 transmembrane (TM) segments of the Sec61α subunit and possesses an opening between TM2b and TM7, termed the lateral gate. Structural and biochemical analyses of complexes of Sec61 and its ortholog SecY have revealed that the lateral gate is the exit for signal sequences and TM segments of translocating polypeptides to the lipid bilayer and also involved in the recognition of such hydrophobic sequences. Moreover, even marginally hydrophobic (mH) segments insufficient for membrane integration can be transiently stalled in surrounding Sec61α regions and cross-linked to them, but how the Sec61 translocon accommodates these mH segments remains unclear. Here, we used Cys-scanned variants of human Sec61α expressed in cultured 293-H cells to examine which channel regions associate with mH segments. A TM segment in a ribosome-associated polypeptide was mainly cross-linked to positions at the lateral gate, whereas an mH segment in a nascent chain was cross-linked to the Sec61α pore-interior positions at TM5 and TM10, as well as the lateral gate. Of note, cross-linking at position 180 in TM5 of Sec61α was reduced by an I179A substitution. We therefore conclude that at least two Sec61α regions, the lateral gate and the pore-interior site around TM5, interact with mH segments and are involved in accommodating them.
Collapse
Affiliation(s)
- Yuichiro Kida
- From the Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
| | - Masao Sakaguchi
- From the Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
| |
Collapse
|
11
|
Niesen MJM, Müller-Lucks A, Hedman R, von Heijne G, Miller TF. Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon. Biophys J 2018; 115:1885-1894. [PMID: 30366631 DOI: 10.1016/j.bpj.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/15/2018] [Accepted: 10/02/2018] [Indexed: 12/21/2022] Open
Abstract
During ribosomal translation, nascent polypeptide chains (NCs) undergo a variety of physical processes that determine their fate in the cell. This study utilizes a combination of arrest peptide experiments and coarse-grained molecular dynamics to measure and elucidate the molecular origins of forces that are exerted on NCs during cotranslational membrane insertion and translocation via the Sec translocon. The approach enables deconvolution of force contributions from NC-translocon and NC-ribosome interactions, membrane partitioning, and electrostatic coupling to the membrane potential. In particular, we show that forces due to NC-lipid interactions provide a readout of conformational changes in the Sec translocon, demonstrating that lateral gate opening only occurs when a sufficiently hydrophobic segment of NC residues reaches the translocon. The combination of experiment and theory introduced here provides a detailed picture of the molecular interactions and conformational changes during ribosomal translation that govern protein biogenesis.
Collapse
Affiliation(s)
- Michiel J M Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Annika Müller-Lucks
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rickard Hedman
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
| |
Collapse
|
12
|
Ulmschneider JP, Smith JC, White SH, Ulmschneider MB. The importance of the membrane interface as the reference state for membrane protein stability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2539-2548. [PMID: 30293965 DOI: 10.1016/j.bbamem.2018.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 11/26/2022]
Abstract
The insertion of nascent polypeptide chains into lipid bilayer membranes and the stability of membrane proteins crucially depend on the equilibrium partitioning of polypeptides. For this, the transfer of full sequences of amino-acid residues into the bilayer, rather than individual amino acids, must be understood. Earlier studies have revealed that the most likely reference state for partitioning very hydrophobic sequences is the membrane interface. We have used μs-scale simulations to calculate the interface-to-transmembrane partitioning free energies ΔGS→TM for two hydrophobic carrier sequences in order to estimate the insertion free energy for all 20 amino acid residues when bonded to the center of a partitioning hydrophobic peptide. Our results show that prior single-residue scales likely overestimate the partitioning free energies of polypeptides. The correlation of ΔGS→TM with experimental full-peptide translocon insertion data is high, suggesting an important role for the membrane interface in translocon-based insertion. The choice of carrier sequence greatly modulates the contribution of each single-residue mutation to the overall partitioning free energy. Our results demonstrate the importance of quantifying the observed full-peptide partitioning equilibrium, which is between membrane interface and transmembrane inserted, rather than combining individual water-to-membrane amino acid transfer free energies.
Collapse
Affiliation(s)
- Jakob P Ulmschneider
- School of Physics and Astronomy and the Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China.
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Biochemistry & Cellular Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Stephen H White
- Department of Physiology & Biophysics, University of California at Irvine, Irvine, CA, USA
| | | |
Collapse
|
13
|
Draycheva A, Lee S, Wintermeyer W. Cotranslational protein targeting to the membrane: Nascent-chain transfer in a quaternary complex formed at the translocon. Sci Rep 2018; 8:9922. [PMID: 29967439 PMCID: PMC6028451 DOI: 10.1038/s41598-018-28262-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/20/2018] [Indexed: 11/29/2022] Open
Abstract
Membrane proteins in bacteria are cotranslationally inserted into the plasma membrane through the SecYEG translocon. Ribosomes exposing the signal-anchor sequence (SAS) of a membrane protein are targeted to the translocon by the signal recognition particle (SRP) pathway. SRP scans translating ribosomes and forms high-affinity targeting complexes with those exposing a SAS. Recognition of the SAS activates SRP for binding to its receptor, FtsY, which, in turn, is primed for SRP binding by complex formation with SecYEG, resulting in a quaternary targeting complex. Here we examine the effect of SecYEG docking to ribosome-nascent-chain complexes (RNCs) on SRP binding and SAS transfer, using SecYEG embedded in phospholipid-containing nanodiscs and monitoring FRET between fluorescence-labeled constituents of the targeting complex. SecYEG–FtsY binding to RNC–SRP complexes lowers the affinity of SRP to both ribosome and FtsY, indicating a general weakening of the complex due to partial binding competition near the ribosomal peptide exit. The rearrangement of the quaternary targeting complex to the pre-transfer complex requires an at least partially exposed SAS. The presence of SecYEG-bound FtsY and the length of the nascent chain strongly influence nascent-chain transfer from SRP to the translocon and repositioning of SRP in the post-transfer complex.
Collapse
Affiliation(s)
- Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Sejeong Lee
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Chemistry Research Laboratory, University of Oxford, OX1 3TA, Oxford, UK
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| |
Collapse
|
14
|
Plasma cell deficiency in human subjects with heterozygous mutations in Sec61 translocon alpha 1 subunit (SEC61A1). J Allergy Clin Immunol 2017; 141:1427-1438. [PMID: 28782633 DOI: 10.1016/j.jaci.2017.06.042] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 05/30/2017] [Accepted: 06/20/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND Primary antibody deficiencies (PADs) are the most frequent primary immunodeficiencies in human subjects. The genetic causes of PADs are largely unknown. Sec61 translocon alpha 1 subunit (SEC61A1) is the major subunit of the Sec61 complex, which is the main polypeptide-conducting channel in the endoplasmic reticulum membrane. SEC61A1 is a target gene of spliced X-box binding protein 1 and strongly induced during plasma cell (PC) differentiation. OBJECTIVE We identified a novel genetic defect and studied its pathologic mechanism in 11 patients from 2 unrelated families with PADs. METHODS Whole-exome and targeted sequencing were conducted to identify novel genetic mutations. Functional studies were carried out ex vivo in primary cells of patients and in vitro in different cell lines to assess the effect of SEC61A1 mutations on B-cell differentiation and survival. RESULTS We investigated 2 families with patients with hypogammaglobulinemia, severe recurrent respiratory tract infections, and normal peripheral B- and T-cell subpopulations. On in vitro stimulation, B cells showed an intrinsic deficiency to develop into PCs. Genetic analysis and targeted sequencing identified novel heterozygous missense (c.254T>A, p.V85D) and nonsense (c.1325G>T, p.E381*) mutations in SEC61A1, segregating with the disease phenotype. SEC61A1-V85D was deficient in cotranslational protein translocation, and it disturbed the cellular calcium homeostasis in HeLa cells. Moreover, SEC61A1-V85D triggered the terminal unfolded protein response in multiple myeloma cell lines. CONCLUSION We describe a monogenic defect leading to a specific PC deficiency in human subjects, expanding our knowledge about the pathogenesis of antibody deficiencies.
Collapse
|
15
|
Abstract
Many proteins are translocated across the endoplasmic reticulum (ER) membrane in eukaryotes or the plasma membrane in prokaryotes. These proteins use hydrophobic signal sequences or transmembrane (TM) segments to trigger their translocation through the protein-conducting Sec61/SecY channel. Substrates are first directed to the channel by cytosolic targeting factors, which use hydrophobic pockets to bind diverse signal and TM sequences. Subsequently, these hydrophobic sequences insert into the channel, docking into a groove on the outside of the lateral gate of the channel, where they also interact with lipids. Structural data and biochemical experiments have elucidated how channel partners, the ribosome in cotranslational translocation, and the eukaryotic ER chaperone BiP or the prokaryotic cytosolic SecA ATPase in posttranslational translocation move polypeptides unidirectionally across the membrane. Structures of auxiliary components of the bacterial translocon, YidC and SecD/F, provide additional insight. Taken together, these recent advances result in mechanistic models of protein translocation.
Collapse
Affiliation(s)
- Tom A Rapoport
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Long Li
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Eunyong Park
- The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065;
| |
Collapse
|
16
|
Vitrac H, Dowhan W, Bogdanov M. Effects of mixed proximal and distal topogenic signals on the topological sensitivity of a membrane protein to the lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1291-1300. [PMID: 28432030 DOI: 10.1016/j.bbamem.2017.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
The final topology of membrane proteins is thought to be dictated primarily by the encoding sequence. However, according to the Charge Balance Rule the topogenic signals within nascent membrane proteins are interpreted in agreement with the Positive Inside Rule as influenced by the protein phospholipid environment. The role of long-range protein-lipid interactions in establishing a final uniform or dual topology is unknown. In order to address this role, we determined the positional dependence of the potency of charged residues as topological signals within Escherichia coli sucrose permease (CscB) in cells in which the zwitterionic phospholipid phosphatidylethanolamine (PE), acting as topological determinant, was either eliminated or tightly titrated. Although the position of a single or paired oppositely charged amino acid residues within an extramembrane domain (EMD), either proximal, central or distal to a transmembrane domain (TMD) end, does not appear to be important, the oppositely charged residues exert their topogenic effects separately only in the absence of PE. Thus, the Charge Balance Rule can be executed in a retrograde manner from any cytoplasmic EMD or any residue within an EMD most likely outside of the translocon. Moreover, CscB is inserted into the membrane in two opposite orientations at different ratios with the native orientation proportional to the mol % of PE. The results demonstrate how the cooperative contribution of lipid-protein interactions affects the potency of charged residues as topological signals, providing a molecular mechanism for the realization of single, equal or different amounts of oppositely oriented protein within the same membrane.
Collapse
Affiliation(s)
- Heidi Vitrac
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center McGovern Medical School, Houston, TX 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center McGovern Medical School, Houston, TX 77030, USA
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center McGovern Medical School, Houston, TX 77030, USA.
| |
Collapse
|
17
|
Niesen MJM, Wang CY, Van Lehn RC, Miller TF. Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration. PLoS Comput Biol 2017; 13:e1005427. [PMID: 28328943 PMCID: PMC5381951 DOI: 10.1371/journal.pcbi.1005427] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/05/2017] [Accepted: 02/28/2017] [Indexed: 01/05/2023] Open
Abstract
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency.
Collapse
Affiliation(s)
- Michiel J. M. Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Connie Y. Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Reid C. Van Lehn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
| |
Collapse
|
18
|
Vitrac H, MacLean DM, Karlstaedt A, Taegtmeyer H, Jayaraman V, Bogdanov M, Dowhan W. Dynamic Lipid-dependent Modulation of Protein Topology by Post-translational Phosphorylation. J Biol Chem 2016; 292:1613-1624. [PMID: 27974465 DOI: 10.1074/jbc.m116.765719] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/13/2016] [Indexed: 01/01/2023] Open
Abstract
Membrane protein topology and folding are governed by structural principles and topogenic signals that are recognized and decoded by the protein insertion and translocation machineries at the time of initial membrane insertion and folding. We previously demonstrated that the lipid environment is also a determinant of initial protein topology, which is dynamically responsive to post-assembly changes in membrane lipid composition. However, the effect on protein topology of post-assembly phosphorylation of amino acids localized within initially cytoplasmically oriented extramembrane domains has never been investigated. Here, we show in a controlled in vitro system that phosphorylation of a membrane protein can trigger a change in topological arrangement. The rate of change occurred on a scale of seconds, comparable with the rates observed upon changes in the protein lipid environment. The rate and extent of topological rearrangement were dependent on the charges of extramembrane domains and the lipid bilayer surface. Using model membranes mimicking the lipid compositions of eukaryotic organelles, we determined that anionic lipids, cholesterol, sphingomyelin, and membrane fluidity play critical roles in these processes. Our results demonstrate how post-translational modifications may influence membrane protein topology in a lipid-dependent manner, both along the organelle trafficking pathway and at their final destination. The results provide further evidence that membrane protein topology is dynamic, integrating for the first time the effect of changes in lipid composition and regulators of cellular processes. The discovery of a new topology regulatory mechanism opens additional avenues for understanding unexplored structure-function relationships and the development of optimized topology prediction tools.
Collapse
Affiliation(s)
- Heidi Vitrac
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
| | - David M MacLean
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Anja Karlstaedt
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Heinrich Taegtmeyer
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Vasanthi Jayaraman
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Mikhail Bogdanov
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - William Dowhan
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
| |
Collapse
|
19
|
Römisch K. A Case for Sec61 Channel Involvement in ERAD. Trends Biochem Sci 2016; 42:171-179. [PMID: 27932072 DOI: 10.1016/j.tibs.2016.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 11/25/2022]
Abstract
Proteins that misfold in the endoplasmic reticulum (ER) need to be transported back to the cytosol for degradation by proteasomes, a process known as ER-associated degradation (ERAD). The first candidate discussed as a retrograde protein transport conduit was the Sec61 channel which is responsible for secretory protein transport into the ER during biogenesis. The Sec61 channel binds the proteasome 19S regulatory particle which can extract an ERAD substrate from the ER. Nevertheless its role as a general export channel has been dismissed, and Hrd1 and Der1 have been proposed as alternatives. The discovery of export-specific sec61 mutants and of mammalian ERAD substrates whose export is dependent on the 19S regulatory particle suggest that dismissal of a role of Sec61 in export may have been premature.
Collapse
Affiliation(s)
- Karin Römisch
- Department of Biology, Naturwissenschaftlich-technische Fakultät 8, Saarland University, 66123 Saarbruecken, Germany.
| |
Collapse
|
20
|
Stone TA, Schiller N, Workewych N, von Heijne G, Deber CM. Hydrophobic Clusters Raise the Threshold Hydrophilicity for Insertion of Transmembrane Sequences in Vivo. Biochemistry 2016; 55:5772-5779. [PMID: 27620701 DOI: 10.1021/acs.biochem.6b00650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Insertion of a nascent membrane protein segment by the translocon channel into the bilayer is naturally promoted by high segmental hydrophobicity, but its selection as a transmembrane (TM) segment is complicated by the diverse environments (aqueous vs lipidic) the protein encounters and by the fact that most TM segments contain a substantial amount (∼30%) of polar residues, as required for protein structural stabilization and/or function. To examine the contributions of these factors systematically, we designed and synthesized a peptide library consisting of pairs of compositionally identical, but sequentially different, peptides with 19-residue core sequences varying (i) in Leu positioning (with five or seven Leu residues clustered into a contiguous "block" in the middle of the segment or "scrambled" throughout the sequence) and (ii) in Ser content (0-6 residues). The library was analyzed by a combination of biophysical and biological techniques, including HPLC retention times, circular dichroism measurements of helicity in micelle and phospholipid bilayer media, and relative blue shifts in Trp fluorescence maxima, as well as by the extent of membrane insertion in a translocon-mediated assay using microsomal membranes from dog pancreas endoplasmic reticulum. We found that local blocks of high hydrophobicity heighten the translocon's propensity to insert moderately hydrophilic sequences, until a "threshold hydrophilicity" is surpassed whereby segments no longer insert even in the presence of Leu blocks. This study codifies the prerequisites of apolar/polar content and residue positioning that define nascent TM segments, illustrates the accuracy in their prediction, and highlights how a single disease-causing mutation can tip the balance toward anomalous translocation/insertion.
Collapse
Affiliation(s)
- Tracy A Stone
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children , Toronto M5G 0A4, Ontario, Canada.,Department of Biochemistry, University of Toronto , Toronto M5S 1A8, Ontario, Canada
| | - Nina Schiller
- Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden.,Science for Life Laboratory, Stockholm University , Box 1031, SE-171 21 Solna, Sweden
| | - Natalie Workewych
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children , Toronto M5G 0A4, Ontario, Canada
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden.,Science for Life Laboratory, Stockholm University , Box 1031, SE-171 21 Solna, Sweden
| | - Charles M Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children , Toronto M5G 0A4, Ontario, Canada.,Department of Biochemistry, University of Toronto , Toronto M5S 1A8, Ontario, Canada
| |
Collapse
|
21
|
Bolar N, Golzio C, Živná M, Hayot G, Van Hemelrijk C, Schepers D, Vandeweyer G, Hoischen A, Huyghe J, Raes A, Matthys E, Sys E, Azou M, Gubler MC, Praet M, Van Camp G, McFadden K, Pediaditakis I, Přistoupilová A, Hodaňová K, Vyleťal P, Hartmannová H, Stránecký V, Hůlková H, Barešová V, Jedličková I, Sovová J, Hnízda A, Kidd K, Bleyer A, Spong R, Vande Walle J, Mortier G, Brunner H, Van Laer L, Kmoch S, Katsanis N, Loeys B. Heterozygous Loss-of-Function SEC61A1 Mutations Cause Autosomal-Dominant Tubulo-Interstitial and Glomerulocystic Kidney Disease with Anemia. Am J Hum Genet 2016; 99:174-87. [PMID: 27392076 PMCID: PMC5005467 DOI: 10.1016/j.ajhg.2016.05.028] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/30/2016] [Indexed: 02/08/2023] Open
Abstract
Autosomal-dominant tubulo-interstitial kidney disease (ADTKD) encompasses a group of disorders characterized by renal tubular and interstitial abnormalities, leading to slow progressive loss of kidney function requiring dialysis and kidney transplantation. Mutations in UMOD, MUC1, and REN are responsible for many, but not all, cases of ADTKD. We report on two families with ADTKD and congenital anemia accompanied by either intrauterine growth retardation or neutropenia. Ultrasound and kidney biopsy revealed small dysplastic kidneys with cysts and tubular atrophy with secondary glomerular sclerosis, respectively. Exclusion of known ADTKD genes coupled with linkage analysis, whole-exome sequencing, and targeted re-sequencing identified heterozygous missense variants in SEC61A1-c.553A>G (p.Thr185Ala) and c.200T>G (p.Val67Gly)-both affecting functionally important and conserved residues in SEC61. Both transiently expressed SEC6A1A variants are delocalized to the Golgi, a finding confirmed in a renal biopsy from an affected individual. Suppression or CRISPR-mediated deletions of sec61al2 in zebrafish embryos induced convolution defects of the pronephric tubules but not the pronephric ducts, consistent with the tubular atrophy observed in the affected individuals. Human mRNA encoding either of the two pathogenic alleles failed to rescue this phenotype as opposed to a complete rescue by human wild-type mRNA. Taken together, these findings provide a mechanism by which mutations in SEC61A1 lead to an autosomal-dominant syndromic form of progressive chronic kidney disease. We highlight protein translocation defects across the endoplasmic reticulum membrane, the principal role of the SEC61 complex, as a contributory pathogenic mechanism for ADTKD.
Collapse
|
22
|
Trovato F, O'Brien EP. Insights into Cotranslational Nascent Protein Behavior from Computer Simulations. Annu Rev Biophys 2016; 45:345-69. [PMID: 27297399 DOI: 10.1146/annurev-biophys-070915-094153] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Regulation of protein stability and function in vivo begins during protein synthesis, when the ribosome translates a messenger RNA into a nascent polypeptide. Cotranslational processes involving a nascent protein include folding, binding to other macromolecules, enzymatic modification, and secretion through membranes. Experiments have shown that the rate at which the ribosome adds amino acids to the elongating nascent chain influences the efficiency of these processes, with alterations to these rates possibly contributing to diseases, including some types of cancer. In this review, we discuss recent insights into cotranslational processes gained from molecular simulations, how different computational approaches have been combined to understand cotranslational processes at multiple scales, and the new scenarios illuminated by these simulations. We conclude by suggesting interesting questions that computational approaches in this research area can address over the next few years.
Collapse
Affiliation(s)
- Fabio Trovato
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802;
| |
Collapse
|
23
|
Junne T, Spiess M. Integration of transmembrane domains is regulated by their downstream sequences. J Cell Sci 2016; 130:372-381. [DOI: 10.1242/jcs.194472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/10/2016] [Indexed: 12/31/2022] Open
Abstract
The Sec61 translocon catalyzes translocation of proteins into the endoplasmic reticulum and the lateral integration of transmembrane segments into the lipid bilayer. Integration is mediated by the hydrophobicity of a polypeptide segment consistent with thermodynamic equilibration between the translocon and the lipid membrane. Integration efficiency of a generic series of increasingly hydrophobic sequences (H-segments) was found to diverge significantly in different reporter constructs as a function of the ∼100 residues carboxyterminal of the H-segments. The hydrophobicity threshold of integration was considerably lowered by insertion of generic ∼20-residue peptides either made of flexible glycine-serine repeats, containing multiple negative charges, or consisting of an oligo-proline stretch. A highly flexible, 100-residue glycine-serine stretch maximally enhanced this effect. The apparent free energy of integration was found to be changed by more than 3 kcal/mol with the downstream sequences tested. The C-terminal sequences could also be shown to affect integration of natural mildly hydrophobic sequences. The results suggest that the conformation of the nascent polypeptide in the protected cavity between ribosome and translocon significantly influences the release of the H-segment into the bilayer.
Collapse
Affiliation(s)
- Tina Junne
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Martin Spiess
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| |
Collapse
|
24
|
De Marothy MT, Elofsson A. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding. Protein Sci 2015; 24:1057-74. [PMID: 25970811 DOI: 10.1002/pro.2698] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/24/2015] [Indexed: 01/12/2023]
Abstract
Cells have developed an incredible machinery to facilitate the insertion of membrane proteins into the membrane. While we have a fairly good understanding of the mechanism and determinants of membrane integration, more data is needed to understand the insertion of membrane proteins with more complex insertion and folding pathways. This review will focus on marginally hydrophobic transmembrane helices and their influence on membrane protein folding. These weakly hydrophobic transmembrane segments are by themselves not recognized by the translocon and therefore rely on local sequence context for membrane integration. How can such segments reside within the membrane? We will discuss this in the light of features found in the protein itself as well as the environment it resides in. Several characteristics in proteins have been described to influence the insertion of marginally hydrophobic helices. Additionally, the influence of biological membranes is significant. To begin with, the actual cost for having polar groups within the membrane may not be as high as expected; the presence of proteins in the membrane as well as characteristics of some amino acids may enable a transmembrane helix to harbor a charged residue. The lipid environment has also been shown to directly influence the topology as well as membrane boundaries of transmembrane helices-implying a dynamic relationship between membrane proteins and their environment.
Collapse
Affiliation(s)
- Minttu T De Marothy
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
| |
Collapse
|
25
|
Stone TA, Schiller N, von Heijne G, Deber CM. Hydrophobic blocks facilitate lipid compatibility and translocon recognition of transmembrane protein sequences. Biochemistry 2015; 54:1465-73. [PMID: 25635746 PMCID: PMC4341838 DOI: 10.1021/bi5014886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Biophysical hydrophobicity scales
suggest that partitioning of
a protein segment from an aqueous phase into a membrane is governed
by its perceived segmental hydrophobicity but do not establish specifically
(i) how the segment is identified in vivo for translocon-mediated
insertion or (ii) whether the destination lipid bilayer is biochemically
receptive to the inserted sequence. To examine the congruence between
these dual requirements, we designed and synthesized a library of
Lys-tagged peptides of a core length sufficient to span a bilayer
but with varying patterns of sequence, each composed of nine Leu residues,
nine Ser residues, and one (central) Trp residue. We found that peptides
containing contiguous Leu residues (Leu-block peptides, e.g., LLLLLLLLLWSSSSSSSSS),
in comparison to those containing discontinuous stretches of Leu residues
(non-Leu-block peptides, e.g., SLSLLSLSSWSLLSLSLLS),
displayed greater helicity (circular dichroism spectroscopy), traveled
slower during sodium dodecyl sulfate–polyacrylamide gel electrophoresis,
had longer reverse phase high-performance liquid chromatography retention
times on a C-18 column, and were helical when reconstituted into 1-palmitoyl-2-oleoylglycero-3-phosphocholine
liposomes, each observation indicating superior lipid compatibility
when a Leu-block is present. These parameters were largely paralleled
in a biological membrane insertion assay using microsomal membranes
from dog pancreas endoplasmic reticulum, where we found only the Leu-block
sequences successfully inserted; intriguingly, an amphipathic peptide
(SLLSSLLSSWLLSSLLSSL;
Leu face, Ser face) with biophysical properties similar to those of
Leu-block peptides failed to insert. Our overall results identify
local sequence lipid compatibility rather than average hydrophobicity
as a principal determinant of transmembrane segment potential, while
demonstrating that further subtleties of hydrophobic and helical patterning,
such as circumferential hydrophobicity in Leu-block segments, promote
translocon-mediated insertion.
Collapse
Affiliation(s)
- Tracy A Stone
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children , Toronto M5G 0A4, Ontario, Canada
| | | | | | | |
Collapse
|
26
|
Junne T, Wong J, Studer C, Aust T, Bauer BW, Beibel M, Bhullar B, Bruccoleri R, Eichenberger J, Estoppey D, Hartmann N, Knapp B, Krastel P, Melin N, Oakeley EJ, Oberer L, Riedl R, Roma G, Schuierer S, Petersen F, Tallarico JA, Rapoport TA, Spiess M, Hoepfner D. Decatransin, a new natural product inhibiting protein translocation at the Sec61/SecYEG translocon. J Cell Sci 2015; 128:1217-29. [PMID: 25616894 DOI: 10.1242/jcs.165746] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A new cyclic decadepsipeptide was isolated from Chaetosphaeria tulasneorum with potent bioactivity on mammalian and yeast cells. Chemogenomic profiling in S. cerevisiae indicated that the Sec61 translocon complex, the machinery for protein translocation and membrane insertion at the endoplasmic reticulum, is the target. The profiles were similar to those of cyclic heptadepsipeptides of a distinct chemotype (including HUN-7293 and cotransin) that had previously been shown to inhibit cotranslational translocation at the mammalian Sec61 translocon. Unbiased, genome-wide mutagenesis followed by full-genome sequencing in both fungal and mammalian cells identified dominant mutations in Sec61p (yeast) or Sec61α1 (mammals) that conferred resistance. Most, but not all, of these mutations affected inhibition by both chemotypes, despite an absence of structural similarity. Biochemical analysis confirmed inhibition of protein translocation into the endoplasmic reticulum of both co- and post-translationally translocated substrates by both chemotypes, demonstrating a mechanism independent of a translating ribosome. Most interestingly, both chemotypes were found to also inhibit SecYEG, the bacterial Sec61 translocon homolog. We suggest 'decatransin' as the name for this new decadepsipeptide translocation inhibitor.
Collapse
Affiliation(s)
- Tina Junne
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Joanne Wong
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Christian Studer
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Thomas Aust
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Benedikt W Bauer
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Martin Beibel
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Bhupinder Bhullar
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | | | - Jürg Eichenberger
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - David Estoppey
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Nicole Hartmann
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Britta Knapp
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Nicolas Melin
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Edward J Oakeley
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Ralph Riedl
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Frank Petersen
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - John A Tallarico
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Martin Spiess
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Dominic Hoepfner
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| |
Collapse
|
27
|
Ge Y, Draycheva A, Bornemann T, Rodnina MV, Wintermeyer W. Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion. Nat Commun 2014; 5:5263. [PMID: 25314960 PMCID: PMC4218953 DOI: 10.1038/ncomms6263] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/12/2014] [Indexed: 01/05/2023] Open
Abstract
Proteins are co-translationally inserted into the bacterial plasma membrane via the SecYEG translocon by lateral release of hydrophobic transmembrane segments into the phospholipid bilayer. The trigger for lateral opening of the translocon is not known. Here we monitor lateral opening by photo-induced electron transfer (PET) between two fluorophores attached to the two SecY helices at the rim of the gate. In the resting translocon, the fluorescence is quenched, consistent with a closed conformation. Ribosome binding to the translocon diminishes PET quenching, indicating opening of the gate. The effect is larger with ribosomes exposing hydrophobic transmembrane segments and vanishes at low temperature. We propose a temperature-dependent dynamic equilibrium between closed and open conformations of the translocon that is shifted towards partially and fully open by ribosome binding and insertion of a hydrophobic peptide, respectively. The combined effects of ribosome and peptide binding allow for co-translational membrane insertion of successive transmembrane segments. Integral membrane proteins laterally partition from the SecYEG translocon into the phospholipid bilayer. Here, the authors use photo-induced electron transfer to show that ribosome binding induces the opening of the lateral gate, and demonstrate that lateral opening does not happen at low temperature.
Collapse
Affiliation(s)
- Yan Ge
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Albena Draycheva
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Thomas Bornemann
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| |
Collapse
|
28
|
Cymer F, von Heijne G, White SH. Mechanisms of integral membrane protein insertion and folding. J Mol Biol 2014; 427:999-1022. [PMID: 25277655 DOI: 10.1016/j.jmb.2014.09.014] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/13/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
The biogenesis, folding, and structure of α-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, as well as the transport of solutes and signals across membranes. Nearly all MPs require translocons--often referred to as protein-conducting channels--for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here, we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of MP insertion and the folding of polytopic MPs in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion.
Collapse
Affiliation(s)
- Florian Cymer
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm.,Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
| | - Stephen H White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems University of California, Irvine Irvine, CA 92697
| |
Collapse
|
29
|
Dou D, da Silva DV, Nordholm J, Wang H, Daniels R. Type II transmembrane domain hydrophobicity dictates the cotranslational dependence for inversion. Mol Biol Cell 2014; 25:3363-74. [PMID: 25165139 PMCID: PMC4214783 DOI: 10.1091/mbc.e14-04-0874] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The cellular hydrophobicity threshold for the inversion of Sec-dependent Nin-Cout (type II) transmembrane domains is dictated by whether their membrane integration occurs cotranslationally or posttranslationally. Membrane insertion by the Sec61 translocon in the endoplasmic reticulum (ER) is highly dependent on hydrophobicity. This places stringent hydrophobicity requirements on transmembrane domains (TMDs) from single-spanning membrane proteins. On examining the single-spanning influenza A membrane proteins, we found that the strict hydrophobicity requirement applies to the Nout-Cin HA and M2 TMDs but not the Nin-Cout TMDs from the type II membrane protein neuraminidase (NA). To investigate this discrepancy, we analyzed NA TMDs of varying hydrophobicity, followed by increasing polypeptide lengths, in mammalian cells and ER microsomes. Our results show that the marginally hydrophobic NA TMDs (ΔGapp > 0 kcal/mol) require the cotranslational insertion process for facilitating their inversion during translocation and a positively charged N-terminal flanking residue and that NA inversion enhances its plasma membrane localization. Overall the cotranslational inversion of marginally hydrophobic NA TMDs initiates once ∼70 amino acids past the TMD are synthesized, and the efficiency reaches 50% by ∼100 amino acids, consistent with the positioning of this TMD class in type II human membrane proteins. Inversion of the M2 TMD, achieved by elongating its C-terminus, underscores the contribution of cotranslational synthesis to TMD inversion.
Collapse
Affiliation(s)
- Dan Dou
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Diogo V da Silva
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Johan Nordholm
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Hao Wang
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Robert Daniels
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| |
Collapse
|
30
|
Hausrath AC. Model for coupled insertion and folding of membrane-spanning proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022707. [PMID: 25215758 DOI: 10.1103/physreve.90.022707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 06/03/2023]
Abstract
Current understanding of the forces directing the folding of integral membrane proteins is very limited compared to the detailed picture available for water-soluble proteins. While mechanistic studies of the folding process in vitro have been conducted for only a small number of membrane proteins, the available evidence indicates that their folding process is thermodynamically driven like that of soluble proteins. In vivo, however, the majority of integral membrane proteins are installed in membranes by dedicated machinery, suggesting that the cellular systems may act to facilitate and regulate the spontaneous physical process of folding. Both the in vitro folding process and the in vivo pathway must navigate an energy landscape dominated by the energetically favorable burial of hydrophobic segments in the membrane interior and the opposition to folding due to the need for passage of polar segments across the membrane. This manuscript describes a simple, exactly solvable model which incorporates these essential features of membrane protein folding. The model is used to compare the folding time under conditions which depict both the in vitro and in vivo pathways. It is proposed that the cellular complexes responsible for insertion of membrane proteins act by lowering the energy barrier for passage of polar regions through the membrane, thereby allowing the chain to more rapidly achieve the folded state.
Collapse
Affiliation(s)
- Andrew C Hausrath
- Department of Chemistry and Biochemistry and Program in Applied Mathematics, University of Arizona, Tucson, Arizona 85721, USA
| |
Collapse
|
31
|
Reithinger JH, Yim C, Kim S, Lee H, Kim H. Structural and functional profiling of the lateral gate of the Sec61 translocon. J Biol Chem 2014; 289:15845-55. [PMID: 24753257 PMCID: PMC4140938 DOI: 10.1074/jbc.m113.533794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/17/2014] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily conserved Sec61 translocon mediates the translocation and membrane insertion of proteins. For the integration of proteins into the membrane, the Sec61 translocon opens laterally to the lipid bilayer. Previous studies suggest that the lateral opening of the channel is mediated by the helices TM2b and TM7 of a pore-forming subunit of the Sec61 translocon. To map key residues in TM2b and TM7 in yeast Sec61 that modulate lateral gating activity, we performed alanine scanning and in vivo site-directed photocross-linking experiments. Alanine scanning identified two groups of critical residues in the lateral gate, one group that leads to defects in the translocation and membrane insertion of proteins and the other group that causes faster translocation and facilitates membrane insertion. Photocross-linking data show that the former group of residues is located at the interface of the lateral gate. Furthermore, different degrees of defects for the membrane insertion of single- and double-spanning membrane proteins were observed depending on whether the mutations were located in TM2b or TM7. These results demonstrate subtle differences in the molecular mechanism of the signal sequence binding/opening of the lateral gate and membrane insertion of a succeeding transmembrane segment in a polytopic membrane protein.
Collapse
Affiliation(s)
- Johannes H Reithinger
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Chewon Yim
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
| | - Sungmin Kim
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
| | - Hunsang Lee
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
| | - Hyun Kim
- From the School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea and
| |
Collapse
|
32
|
Fisher E, Lake E, McLeod RS. Apolipoprotein B100 quality control and the regulation of hepatic very low density lipoprotein secretion. J Biomed Res 2014; 28:178-93. [PMID: 25013401 PMCID: PMC4085555 DOI: 10.7555/jbr.28.20140019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 02/15/2014] [Indexed: 12/19/2022] Open
Abstract
Apolipoprotein B (apoB) is the main protein component of very low density lipoprotein (VLDL) and is necessary for the assembly and secretion of these triglyceride (TG)-rich particles. Following release from the liver, VLDL is converted to low density lipoprotein (LDL) in the plasma and increased production of VLDL can therefore play a detrimental role in cardiovascular disease. Increasing evidence has helped to establish VLDL assembly as a target for the treatment of dyslipidemias. Multiple factors are involved in the folding of the apoB protein and the formation of a secretion-competent VLDL particle. Failed VLDL assembly can initiate quality control mechanisms in the hepatocyte that target apoB for degradation. ApoB is a substrate for endoplasmic reticulum associated degradation (ERAD) by the ubiquitin proteasome system and for autophagy. Efficient targeting and disposal of apoB is a regulated process that modulates VLDL secretion and partitioning of TG. Emerging evidence suggests that significant overlap exists between these degradative pathways. For example, the insulin-mediated targeting of apoB to autophagy and postprandial activation of the unfolded protein response (UPR) may employ the same cellular machinery and regulatory cues. Changes in the quality control mechanisms for apoB impact hepatic physiology and pathology states, including insulin resistance and fatty liver. Insulin signaling, lipid metabolism and the hepatic UPR may impact VLDL production, particularly during the postprandial state. In this review we summarize our current understanding of VLDL assembly, apoB degradation, quality control mechanisms and the role of these processes in liver physiology and in pathologic states.
Collapse
Affiliation(s)
- Eric Fisher
- Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Elizabeth Lake
- Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Roger S McLeod
- Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| |
Collapse
|
33
|
Mackinnon AL, Paavilainen VO, Sharma A, Hegde RS, Taunton J. An allosteric Sec61 inhibitor traps nascent transmembrane helices at the lateral gate. eLife 2014; 3:e01483. [PMID: 24497544 PMCID: PMC3913039 DOI: 10.7554/elife.01483] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Membrane protein biogenesis requires the coordinated movement of hydrophobic transmembrane domains (TMD) from the cytosolic vestibule of the Sec61 channel into the lipid bilayer. Molecular insight into TMD integration has been hampered by the difficulty of characterizing intermediates during this intrinsically dynamic process. In this study, we show that cotransin, a substrate-selective Sec61 inhibitor, traps nascent TMDs in the cytosolic vestibule, permitting detailed interrogation of an early pre-integration intermediate. Site-specific crosslinking revealed the pre-integrated TMD docked to Sec61 near the cytosolic tip of the lateral gate. Escape from cotransin-arrest depends not only on cotransin concentration, but also on the biophysical properties of the TMD. Genetic selection of cotransin-resistant cancer cells uncovered multiple mutations clustered near the lumenal plug of Sec61α, thus revealing cotransin’s likely site of action. Our results suggest that TMD/lateral gate interactions facilitate TMD transfer into the membrane, a process that is allosterically modulated by cotransin binding to the plug. DOI:http://dx.doi.org/10.7554/eLife.01483.001 Cells are surrounded by a plasma membrane that acts like a barrier around the cell—keeping the cell’s boundaries distinct from surrounding cells and helping to regulate the contents of the cell. This plasma membrane is made up mostly of two layers of fatty molecules, and is also studded with proteins. Some of these membrane proteins act as channels that allow nutrients and other chemicals to enter and leave the cell, while others allow the cell to communicate with other cells and the outside environment. Like all proteins, membrane proteins are chains of amino acids that are linked together by a molecular machine called a ribosome. The ribosomes that make membrane proteins are located on the outside of a membrane-enclosed compartment within the cell called the endoplasmic reticulum. To eventually become embedded within a membrane, a new protein must—at the same time as it is being built—enter a channel within the membrane of the endoplasmic reticulum. The newly synthesized protein chain enters this channel, called Sec61, via an entrance near the ribosome and then threads its way toward the inside of the endoplasmic reticulum. However, there is also a ‘side-gate’ in Sec61 that allows specific segments the new protein to escape the channel and become embedded within the membrane. From here, the membrane protein can be trafficked to other destinations within the cell, including the plasma membrane. However, how the newly forming protein chain passes through the side-gate of Sec61 is not well understood. Now MacKinnon, Paavilainen et al. have used a small molecule called cotransin—which is known to interfere with the passage of proteins through Sec61—to observe the interactions between the Sec61 channel and the new protein. Cotransin appears to trap the new protein chain within the Sec61 channel by essentially ‘locking’ the side-gate. MacKinnon, Paavilainen et al. observed that the trapped protein interacts with the inside of the channel at the end closest to the ribosome—which is the likely location of the side-gate. In contrast, cotransin likely binds at the other end of the channel, to a piece of Sec61 that serves to plug the exit into the endoplasmic reticulum; and this plug is directly connected to the side-gate. By preventing the plug from moving out of the way, cotransin can somehow stop the new protein from passing through the side-gate. However, MacKinnon, Paavilainen et al. did find that some membrane proteins with certain physical and chemical properties could get through the gate, despite the presence of cotransin. The next challenge is to resolve exactly how interactions between cotransin and the Sec61 plug can block the escape of new proteins into the membrane. DOI:http://dx.doi.org/10.7554/eLife.01483.002
Collapse
Affiliation(s)
- Andrew L Mackinnon
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | | | | | | | | |
Collapse
|
34
|
Sommer N, Junne T, Kalies KU, Spiess M, Hartmann E. TRAP assists membrane protein topogenesis at the mammalian ER membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3104-3111. [DOI: 10.1016/j.bbamcr.2013.08.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 01/03/2023]
|
35
|
Abstract
The Sec61 translocon forms a pore to translocate polypeptide sequences across the membrane and offers a lateral gate for membrane integration of hydrophobic (H) segments. A central constriction of six apolar residues has been shown to form a seal, but also to determine the hydrophobicity threshold for membrane integration: Mutation of these residues in yeast Sec61p to glycines, serines, aspartates, or lysines lowered the hydrophobicity required for integration; mutation to alanines increased it. Whereas four leucines distributed in an oligo-alanine H segment were sufficient for 50% integration, we now find four leucines in the N-terminal half of the H segment to produce significantly more integration than in the C-terminal half, suggesting functional asymmetry within the translocon. Scanning a cluster of three leucines through an oligo-alanine H segment showed high integration levels, except around the position matching that of the hydrophobic constriction in the pore where integration was strongly reduced. Both asymmetry and the position effect of H-segment integration disappeared upon mutation of the constriction residues to glycines or serines, demonstrating that hydrophobicity at this position within the translocon is responsible for the phenomenon. Asymmetry was largely retained, however, when constriction residues were replaced by alanines. These results reflect on the integration mechanism of transmembrane domains and show that membrane insertion of H segments strongly depends not only on their intrinsic hydrophobicity but also on the local conditions in the translocon interior. Thus, the contribution of hydrophobic residues in the H segment is not simply additive and displays cooperativeness depending on their relative position.
Collapse
|
36
|
Co-translational targeting and translocation of proteins to the endoplasmic reticulum. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2392-402. [DOI: 10.1016/j.bbamcr.2013.02.021] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 12/16/2022]
|
37
|
Rychkova A, Warshel A. On the nature of the apparent free energy of inserting amino acids into membrane through the translocon. J Phys Chem B 2013; 117:13748-54. [PMID: 24087983 DOI: 10.1021/jp406925y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The nature of the biological free energy scale (ΔGapp), obtained from translocon mediated insertion studies, has been a major puzzle and the subject of major controversies. Part of the problem has been the complexity of the insertion process that discouraged workers from considering the feasible kinetics schemes and left the possible impression that ΔGapp presents some simple partition. Here we extend and clarify our recent analysis of the insertion problem using well-defined kinetics schemes and a free energy profile. We point out that although the rate constants of some steps are far from being obvious, it is essential to consider explicitly such schemes in order to advance in analyzing the meaning of ΔGapp. It is then shown that under some equilibrium conditions the kinetics scheme leads to a simple formula that allows one to relate ΔGapp to the actual free energy of partitioning between the water, the membrane, and the translocon. Other options are also considered (including limits with irreversible transitions that can be described by linear free energy relationships (LFERs)). It is concluded that it is unlikely that a kinetics plus thermodynamic based analysis can lead to a result that identifies ΔGapp with the partition between the membrane and the translocon. Thus, we argue that unless such analysis is presented, it is unjustified to assume that ΔGapp corresponds to the membrane translocon equilibrium or to some other arbitrary definition. Furthermore, we point out that the presumption that it is sufficient to just calculate the PMF for going from the translocon (TR) to the membrane and then to assume irreversible diffusive motion to water and for further entrance to the membrane is not a valid analysis. Overall, we point out that it is important to try to relate ΔGapp to a well-defined kinetics scheme (regardless of the complication of the system) in order to determine whether the energies of inserting positively charged residues to the membrane are related to the corresponding ΔGapp. It is also suggested that deviations from our simple formula for equilibrium conditions can help in identifying and analyzing kinetics barriers.
Collapse
Affiliation(s)
- Anna Rychkova
- Department of Genetics, Stanford University , 365 Lasuen Street, Littlefield Center, MC2069, Stanford, California 94305, United States
| | | |
Collapse
|
38
|
Onishi Y, Yamagishi M, Imai K, Fujita H, Kida Y, Sakaguchi M. Stop-and-Move of a Marginally Hydrophobic Segment Translocating across the Endoplasmic Reticulum Membrane. J Mol Biol 2013; 425:3205-16. [PMID: 23747484 DOI: 10.1016/j.jmb.2013.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/28/2013] [Accepted: 05/30/2013] [Indexed: 10/26/2022]
|
39
|
Abstract
SecY and Sec61 translocons mediate the orderly insertion of transmembrane segments into the lipid bilayer during membrane-protein biogenesis. Reporting in this issue, Ismail et al. now use a SecM-based molecular force sensor to show that the translocon exerts a pulling force on the nascent chain that is capable of mechanical action at two distinct stages of the insertion process.
Collapse
Affiliation(s)
- Soo Jung Kim
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, USA
| | | |
Collapse
|
40
|
Mandon EC, Trueman SF, Gilmore R. Protein translocation across the rough endoplasmic reticulum. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a013342. [PMID: 23251026 DOI: 10.1101/cshperspect.a013342] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The rough endoplasmic reticulum is a major site of protein biosynthesis in all eukaryotic cells, serving as the entry point for the secretory pathway and as the initial integration site for the majority of cellular integral membrane proteins. The core components of the protein translocation machinery have been identified, and high-resolution structures of the targeting components and the transport channel have been obtained. Research in this area is now focused on obtaining a better understanding of the molecular mechanism of protein translocation and membrane protein integration.
Collapse
Affiliation(s)
- Elisabet C Mandon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-2324, USA
| | | | | |
Collapse
|
41
|
Kocik L, Junne T, Spiess M. Orientation of Internal Signal-Anchor Sequences at the Sec61 Translocon. J Mol Biol 2012; 424:368-78. [DOI: 10.1016/j.jmb.2012.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/10/2012] [Accepted: 10/12/2012] [Indexed: 11/29/2022]
|
42
|
Mades A, Gotthardt K, Awe K, Stieler J, Döring T, Füser S, Prange R. Role of human sec63 in modulating the steady-state levels of multi-spanning membrane proteins. PLoS One 2012; 7:e49243. [PMID: 23166619 PMCID: PMC3499540 DOI: 10.1371/journal.pone.0049243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 10/08/2012] [Indexed: 12/31/2022] Open
Abstract
The Sec61 translocon of the endoplasmic reticulum (ER) membrane forms an aqueous pore, allowing polypeptides to be transferred across or integrated into membranes. Protein translocation into the ER can occur co- and posttranslationally. In yeast, posttranslational translocation involves the heptameric translocase complex including its Sec62p and Sec63p subunits. The mammalian ER membrane contains orthologs of yeast Sec62p and Sec63p, but their function is poorly understood. Here, we analyzed the effects of excess and deficit Sec63 on various ER cargoes using human cell culture systems. The overexpression of Sec63 reduces the steady-state levels of viral and cellular multi-spanning membrane proteins in a cotranslational mode, while soluble and single-spanning ER reporters are not affected. Consistent with this, the knock-down of Sec63 increases the steady-state pools of polytopic ER proteins, suggesting a substrate-specific and regulatory function of Sec63 in ER import. Overexpressed Sec63 exerts its down-regulating activity on polytopic protein levels independent of its Sec62-interacting motif, indicating that it may not act in conjunction with Sec62 in human cells. The specific action of Sec63 is further sustained by our observations that the up-regulation of either Sec62 or two other ER proteins with lumenal J domains, like ERdj1 and ERdj4, does not compromise the steady-state level of a multi-spanning membrane reporter. A J domain-specific mutation of Sec63, proposed to weaken its interaction with the ER resident BiP chaperone, reduces the down-regulating capacity of excess Sec63, suggesting an involvement of BiP in this process. Together, these results suggest that Sec63 may perform a substrate-selective quantity control function during cotranslational ER import.
Collapse
Affiliation(s)
- Andreas Mades
- Department of Medicine III, Hematology and Oncology, Johannes Gutenberg-University School of Medicine, Mainz, Germany
| | - Katherina Gotthardt
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Karin Awe
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jens Stieler
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tatjana Döring
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sabine Füser
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Reinhild Prange
- Department of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- * E-mail:
| |
Collapse
|
43
|
Abstract
Peroxisomes are remarkably versatile cell organelles whose size, shape, number, and protein content can vary greatly depending on the organism, the developmental stage of the organism’s life cycle, and the environment in which the organism lives. The main functions usually associated with peroxisomes include the metabolism of lipids and reactive oxygen species. However, in recent years, it has become clear that these organelles may also act as intracellular signaling platforms that mediate developmental decisions by modulating extraperoxisomal concentrations of several second messengers. To fulfill their functions, peroxisomes physically and functionally interact with other cell organelles, including mitochondria and the endoplasmic reticulum. Defects in peroxisome dynamics can lead to organelle dysfunction and have been associated with various human disorders. The purpose of this paper is to thoroughly summarize and discuss the current concepts underlying peroxisome formation, multiplication, and degradation. In addition, this paper will briefly highlight what is known about the interplay between peroxisomes and other cell organelles and explore the physiological and pathological implications of this interorganellar crosstalk.
Collapse
Affiliation(s)
- Marc Fransen
- Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, P.O. Box 601, 3000 Leuven, Belgium
| |
Collapse
|
44
|
Zhang B, Miller TF. Long-timescale dynamics and regulation of Sec-facilitated protein translocation. Cell Rep 2012; 2:927-37. [PMID: 23084746 PMCID: PMC3483636 DOI: 10.1016/j.celrep.2012.08.039] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/21/2012] [Accepted: 08/31/2012] [Indexed: 01/11/2023] Open
Abstract
We present a coarse-grained modeling approach that spans the nanosecond- to minute-timescale dynamics of cotranslational protein translocation. The method enables direct simulation of both integral membrane protein topogenesis and transmembrane domain (TM) stop-transfer efficiency. Simulations reveal multiple kinetic pathways for protein integration, including a mechanism in which the nascent protein undergoes slow-timescale reorientation, or flipping, in the confined environment of the translocon channel. Competition among these pathways gives rise to the experimentally observed dependence of protein topology on ribosomal translation rate and protein length. We further demonstrate that sigmoidal dependence of stop-transfer efficiency on TM hydrophobicity arises from local equilibration of the TM across the translocon lateral gate, and it is predicted that slowing ribosomal translation yields decreased stop-transfer efficiency in long proteins. This work reveals the balance between equilibrium and nonequilibrium processes in protein targeting, and it provides insight into the molecular regulation of the Sec translocon.
Collapse
Affiliation(s)
- Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | |
Collapse
|
45
|
Zhang B, Miller TF. Direct simulation of early-stage Sec-facilitated protein translocation. J Am Chem Soc 2012; 134:13700-7. [PMID: 22852862 DOI: 10.1021/ja3034526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Direct simulations reveal key mechanistic features of early-stage protein translocation and membrane integration via the Sec-translocon channel. We present a novel computational protocol that combines non-equilibrium growth of the nascent protein with microsecond timescale molecular dynamics trajectories. Analysis of multiple, long timescale simulations elucidates molecular features of protein insertion into the translocon, including signal-peptide docking at the translocon lateral gate (LG), large lengthscale conformational rearrangement of the translocon LG helices, and partial membrane integration of hydrophobic nascent-protein sequences. Furthermore, the simulations demonstrate the role of specific molecular interactions in the regulation of protein secretion, membrane integration, and integral membrane protein topology. Salt-bridge contacts between the nascent-protein N-terminus, cytosolic translocon residues, and phospholipid head groups are shown to favor conformations of the nascent protein upon early-stage insertion that are consistent with the Type II (N(cyt)/C(exo)) integral membrane protein topology, and extended hydrophobic contacts between the nascent protein and the membrane lipid bilayer are shown to stabilize configurations that are consistent with the Type III (N(exo)/C(cyt)) topology. These results provide a detailed, mechanistic basis for understanding experimentally observed correlations between integral membrane protein topology, translocon mutagenesis, and nascent-protein sequence.
Collapse
Affiliation(s)
- Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
| | | |
Collapse
|
46
|
The predicted N-terminal signal sequence of the human α2C-adrenoceptor does not act as a functional cleavable signal peptide. Eur J Pharmacol 2012; 684:51-8. [DOI: 10.1016/j.ejphar.2012.03.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 03/13/2012] [Accepted: 03/23/2012] [Indexed: 11/21/2022]
|
47
|
Yamamoto H, Fujita H, Kida Y, Sakaguchi M. Pleiotropic effects of membrane cholesterol upon translocation of protein across the endoplasmic reticulum membrane. Biochemistry 2012; 51:3596-605. [PMID: 22493992 DOI: 10.1021/bi2018915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various proteins are translocated through and inserted into the endoplasmic reticulum membrane via translocon channels. The hydrophobic segments of signal sequences initiate translocation, and those on translocating polypeptides interrupt translocation to be inserted into the membrane. Positive charges suppress translocation to regulate the orientation of the signal sequences. Here, we investigated the effect of membrane cholesterol on the translocational behavior of nascent chains in a cell-free system. We found that the three distinct translocation processes were sensitive to membrane cholesterol. Cholesterol inhibited the initiation of translocation by the signal sequence, and the extent of inhibition depended on the signal sequence. Even when initiation was not inhibited, cholesterol impeded the movement of the positively charged residues of the translocating polypeptide chain. In surprising contrast, cholesterol enhanced the translocation of hydrophobic sequences through the translocon. On the basis of these findings, we propose that membrane cholesterol greatly affects partitioning of hydrophobic segments into the membrane and impedes the movement of positive charges.
Collapse
Affiliation(s)
- Hitoshi Yamamoto
- Graduate School of Life Science, University of Hyogo, Kouto 3-2-1, Ako-gun, Hyogo 678-1297, Japan
| | | | | | | |
Collapse
|
48
|
Abstract
The Sec61 or SecY channel, a universally conserved protein-conducting channel, translocates proteins across and integrates proteins into the eukaryotic endoplasmic reticulum (ER) membrane and the prokaryotic plasma membrane. Depending on channel-binding partners, polypeptides are moved by different mechanisms. In cotranslational translocation, the ribosome feeds the polypeptide chain directly into the channel. In posttranslational translocation, a ratcheting mechanism is used by the ER-lumenal chaperone BiP in eukaryotes, and a pushing mechanism is utilized by the SecA ATPase in bacteria. In prokaryotes, posttranslational translocation is facilitated through the function of the SecD/F protein. Recent structural and biochemical data show how the channel opens during translocation, translocates soluble proteins, releases hydrophobic segments of membrane proteins into the lipid phase, and maintains the barrier for small molecules.
Collapse
Affiliation(s)
- Eunyong Park
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
49
|
Ulmschneider JP, Smith JC, White SH, Ulmschneider MB. In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions. J Am Chem Soc 2011; 133:15487-95. [PMID: 21861483 PMCID: PMC3191535 DOI: 10.1021/ja204042f] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nascent transmembrane (TM) polypeptide segments are recognized and inserted into the lipid bilayer by the cellular translocon machinery. The recognition rules, described by a biological hydrophobicity scale, correlate strongly with physical hydrophobicity scales that describe the free energy of insertion of TM helices from water. However, the exact relationship between the physical and biological scales is unknown, because solubility problems limit our ability to measure experimentally the direct partitioning of hydrophobic peptides across lipid membranes. Here we use microsecond molecular dynamics (MD) simulations in which monomeric polyleucine segments of different lengths are allowed to partition spontaneously into and out of lipid bilayers. This approach directly reveals all states populated at equilibrium. For the hydrophobic peptides studied here, only surface-bound and transmembrane-inserted helices are found. The free energy of insertion is directly obtained from the relative occupancy of these states. A water-soluble state was not observed, consistent with the general insolubility of hydrophobic peptides. The approach further allows determination of the partitioning pathways and kinetics. Surprisingly, the transfer free energy appears to be independent of temperature, which implies that surface-to-bilayer peptide insertion is a zero-entropy process. We find that the partitioning free energy of the polyleucine segments correlates strongly with values from translocon experiments but reveals a systematic shift favoring shorter peptides, suggesting that translocon-to-bilayer partitioning is not equivalent but related to spontaneous surface-to-bilayer partitioning.
Collapse
Affiliation(s)
| | - Jeremy C. Smith
- IWR, University of Heidelberg, Germany
- Oak Ridge National Laboratory, Oak Ridge TN, USA
| | - Stephen H. White
- Department of Physiology & Biophysics, University of California at Irvine, Irvine CA, USA
| | - Martin B. Ulmschneider
- Department of Physiology & Biophysics, University of California at Irvine, Irvine CA, USA
| |
Collapse
|
50
|
MacCallum JL, Tieleman DP. Hydrophobicity scales: a thermodynamic looking glass into lipid-protein interactions. Trends Biochem Sci 2011; 36:653-62. [PMID: 21930386 DOI: 10.1016/j.tibs.2011.08.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/09/2011] [Accepted: 08/11/2011] [Indexed: 11/30/2022]
Abstract
The partitioning of amino acid sidechains into the membrane is a key aspect of membrane protein folding. However, lipid bilayers exhibit rapidly changing physicochemical properties over their nanometer-scale thickness, which complicates understanding the thermodynamics and microscopic details of membrane partitioning. Recent data from diverse approaches, including protein insertion by the Sec translocon, folding of a small beta-barrel membrane protein and computer simulations of the exact distribution of a variety of small molecules and peptides, have joined older hydrophobicity scales for membrane protein prediction. We examine the correlations among the scales and find that they are remarkably correlated even though there are large differences in magnitude. We discuss the implications of these scales for understanding membrane protein structure and function.
Collapse
Affiliation(s)
- Justin L MacCallum
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
| | | |
Collapse
|