1
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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2
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Go YJ, Kalathingal M, Rhee YM. Elucidating activation and deactivation dynamics of VEGFR-2 transmembrane domain with coarse-grained molecular dynamics simulations. PLoS One 2023; 18:e0281781. [PMID: 36795710 PMCID: PMC9934429 DOI: 10.1371/journal.pone.0281781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
The vascular endothelial growth factor receptor 2 (VEGFR-2) is a member of receptor tyrosine kinases (RTKs) and is a dimeric membrane protein that functions as a primary regulator of angiogenesis. As is usual with RTKs, spatial alignment of its transmembrane domain (TMD) is essential toward VEGFR-2 activation. Experimentally, the helix rotations within TMD around their own helical axes are known to participate importantly toward the activation process in VEGFR-2, but the detailed dynamics of the interconversion between the active and inactive TMD forms have not been clearly elucidated at the molecular level. Here, we attempt to elucidate the process by using coarse grained (CG) molecular dynamics (MD) simulations. We observe that inactive dimeric TMD in separation is structurally stable over tens of microseconds, suggesting that TMD itself is passive and does not allow spontaneous signaling of VEGFR-2. By starting from the active conformation, we reveal the mechanism of TMD inactivation through analyzing the CG MD trajectories. We observe that interconversions between a left-handed overlay and a right-handed one are essential for the process of going from an active TMD structure to the inactive form. In addition, our simulations find that the helices can rotate properly when the overlaying structure of the helices interconverts and when the crossing angle of the two helices changes by larger than ~40 degrees. As the activation right after the ligand attachment on VEGFR-2 will take place in the reverse manner of this inactivation process, these structural aspects will also appear importantly for the activation process. The rather large change in helix configuration for activation also explains why VEGFR-2 rarely self-activate and how the activating ligand structurally drive the whole VEGFR-2. This mechanism of TMD activation / inactivation within VEGFR-2 may help in further understanding the overall activation processes of other RTKs.
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Affiliation(s)
- Yeon Ju Go
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Mahroof Kalathingal
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- * E-mail:
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3
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Mai H, Zimmer MH, Miller TF. Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods. J Phys Chem B 2023; 127:446-455. [PMID: 36607139 PMCID: PMC9869335 DOI: 10.1021/acs.jpcb.2c05795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/18/2022] [Indexed: 01/07/2023]
Abstract
Proteolysis targeting chimera (PROTAC) is a novel drug modality that facilitates the degradation of a target protein by inducing proximity with an E3 ligase. In this work, we present a new computational framework to model the cooperativity between PROTAC-E3 binding and PROTAC-target binding principally through protein-protein interactions (PPIs) induced by the PROTAC. Due to the scarcity and low resolution of experimental measurements, the physical and chemical drivers of these non-native PPIs remain to be elucidated. We develop a coarse-grained (CG) approach to model interactions in the target-PROTAC-E3 complexes, which enables converged thermodynamic estimations using alchemical free energy calculation methods despite an unconventional scale of perturbations. With minimal parametrization, we successfully capture fundamental principles of cooperativity, including the optimality of intermediate PROTAC linker lengths that originates from configurational entropy. We qualitatively characterize the dependency of cooperativity on PROTAC linker lengths and protein charges and shapes. Minimal inclusion of sequence- and conformation-specific features in our current force field, however, limits quantitative modeling to reproduce experimental measurements, but further development of the CG model may allow for efficient computational screening to optimize PROTAC cooperativity.
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Affiliation(s)
- Huanghao Mai
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Matthew H. Zimmer
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Thomas F. Miller
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California91125, United States
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4
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Berselli A, Benfenati F, Maragliano L, Alberini G. Multiscale modelling of claudin-based assemblies: a magnifying glass for novel structures of biological interfaces. Comput Struct Biotechnol J 2022; 20:5984-6010. [DOI: 10.1016/j.csbj.2022.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/03/2022] Open
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5
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Carmody PJ, Zimmer MH, Kuntz CP, Harrington HR, Duckworth K, Penn W, Mukhopadhyay S, Miller T, Schlebach J. Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning. Nucleic Acids Res 2021; 49:12943-12954. [PMID: 34871407 PMCID: PMC8682741 DOI: 10.1093/nar/gkab1172] [Citation(s) in RCA: 8] [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: 04/07/2021] [Revised: 10/22/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a translational recoding mechanism that enables the synthesis of multiple polypeptides from a single transcript. During translation of the alphavirus structural polyprotein, the efficiency of -1PRF is coordinated by a 'slippery' sequence in the transcript, an adjacent RNA stem-loop, and a conformational transition in the nascent polypeptide chain. To characterize each of these effectors, we measured the effects of 4530 mutations on -1PRF by deep mutational scanning. While most mutations within the slip-site and stem-loop reduce the efficiency of -1PRF, the effects of mutations upstream of the slip-site are far more variable. We identify several regions where modifications of the amino acid sequence of the nascent polypeptide impact the efficiency of -1PRF. Molecular dynamics simulations of polyprotein biogenesis suggest the effects of these mutations primarily arise from their impacts on the mechanical forces that are generated by the translocon-mediated cotranslational folding of the nascent polypeptide chain. Finally, we provide evidence suggesting that the coupling between cotranslational folding and -1PRF depends on the translation kinetics upstream of the slip-site. These findings demonstrate how -1PRF is coordinated by features within both the transcript and nascent chain.
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Affiliation(s)
- Patrick J Carmody
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Matthew H Zimmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Charles P Kuntz
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Kate E Duckworth
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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6
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Bhadra P, Helms V. Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes. Int J Mol Sci 2021; 22:10705. [PMID: 34639046 PMCID: PMC8509349 DOI: 10.3390/ijms221910705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Here, we review recent molecular modelling and simulation studies of the Sec translocon, the primary component/channel of protein translocation into the endoplasmic reticulum (ER) and bacterial periplasm, respectively. Our focus is placed on the eukaryotic Sec61, but we also mention modelling studies on prokaryotic SecY since both systems operate in related ways. Cryo-EM structures are now available for different conformational states of the Sec61 complex, ranging from the idle or closed state over an inhibited state with the inhibitor mycolactone bound near the lateral gate, up to a translocating state with bound substrate peptide in the translocation pore. For all these states, computational studies have addressed the conformational dynamics of the translocon with respect to the pore ring, the plug region, and the lateral gate. Also, molecular simulations are addressing mechanistic issues of insertion into the ER membrane vs. translocation into the ER, how signal-peptides are recognised at all in the translocation pore, and how accessory proteins affect the Sec61 conformation in the co- and post-translational pathways.
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Affiliation(s)
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Postfach 15 11 50, 66041 Saarbruecken, Germany;
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7
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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.
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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
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8
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Nicolaus F, Metola A, Mermans D, Liljenström A, Krč A, Abdullahi SM, Zimmer M, Miller Iii TF, von Heijne G. Residue-by-residue analysis of cotranslational membrane protein integration in vivo. eLife 2021; 10:64302. [PMID: 33554862 PMCID: PMC7886326 DOI: 10.7554/elife.64302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
We follow the cotranslational biosynthesis of three multispanning Escherichia coli inner membrane proteins in vivo using high-resolution force profile analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domain can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process. Our results support the 'sliding' model of translocon-mediated membrane protein integration, in which hydrophobic segments are continually exposed to the lipid bilayer during their passage through the SecYEG translocon.
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Affiliation(s)
- Felix Nicolaus
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ane Metola
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daphne Mermans
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Amanda Liljenström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ajda Krč
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Matthew Zimmer
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Thomas F Miller Iii
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory Stockholm University, Solna, Sweden
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9
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Samatova E, Daberger J, Liutkute M, Rodnina MV. Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding. Front Microbiol 2021; 11:619430. [PMID: 33505387 PMCID: PMC7829197 DOI: 10.3389/fmicb.2020.619430] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
Protein homeostasis of bacterial cells is maintained by coordinated processes of protein production, folding, and degradation. Translational efficiency of a given mRNA depends on how often the ribosomes initiate synthesis of a new polypeptide and how quickly they read the coding sequence to produce a full-length protein. The pace of ribosomes along the mRNA is not uniform: periods of rapid synthesis are separated by pauses. Here, we summarize recent evidence on how ribosome pausing affects translational efficiency and protein folding. We discuss the factors that slow down translation elongation and affect the quality of the newly synthesized protein. Ribosome pausing emerges as important factor contributing to the regulatory programs that ensure the quality of the proteome and integrate the cellular and environmental cues into regulatory circuits of the cell.
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Affiliation(s)
- Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jan Daberger
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marija Liutkute
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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10
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Mercier E, Wintermeyer W, Rodnina MV. Co-translational insertion and topogenesis of bacterial membrane proteins monitored in real time. EMBO J 2020; 39:e104054. [PMID: 32311161 PMCID: PMC7396858 DOI: 10.15252/embj.2019104054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 01/23/2023] Open
Abstract
Integral membrane proteins insert into the bacterial inner membrane co‐translationally via the translocon. Transmembrane (TM) segments of nascent proteins adopt their native topological arrangement with the N‐terminus of the first TM (TM1) oriented to the outside (type I) or the inside (type II) of the cell. Here, we study TM1 topogenesis during ongoing translation in a bacterial in vitro system, applying real‐time FRET and protease protection assays. We find that TM1 of the type I protein LepB reaches the translocon immediately upon emerging from the ribosome. In contrast, the type II protein EmrD requires a longer nascent chain before TM1 reaches the translocon and adopts its topology by looping inside the ribosomal peptide exit tunnel. Looping presumably is mediated by interactions between positive charges at the N‐terminus of TM1 and negative charges in the tunnel wall. Early TM1 inversion is abrogated by charge reversal at the N‐terminus. Kinetic analysis also shows that co‐translational membrane insertion of TM1 is intrinsically rapid and rate‐limited by translation. Thus, the ribosome has an important role in membrane protein topogenesis.
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Affiliation(s)
- Evan Mercier
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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11
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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.
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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
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12
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Harrington HR, Zimmer MH, Chamness LM, Nash V, Penn WD, Miller TF, Mukhopadhyay S, Schlebach JP. Cotranslational folding stimulates programmed ribosomal frameshifting in the alphavirus structural polyprotein. J Biol Chem 2020; 295:6798-6808. [PMID: 32169904 DOI: 10.1074/jbc.ra120.012706] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/04/2020] [Indexed: 11/06/2022] Open
Abstract
Viruses maximize their genetic coding capacity through a variety of biochemical mechanisms, including programmed ribosomal frameshifting (PRF), which facilitates the production of multiple proteins from a single mRNA transcript. PRF is typically stimulated by structural elements within the mRNA that generate mechanical tension between the transcript and ribosome. However, in this work, we show that the forces generated by the cotranslational folding of the nascent polypeptide chain can also enhance PRF. Using an array of biochemical, cellular, and computational techniques, we first demonstrate that the Sindbis virus structural polyprotein forms two competing topological isomers during its biosynthesis at the ribosome-translocon complex. We then show that the formation of one of these topological isomers is linked to PRF. Coarse-grained molecular dynamics simulations reveal that the translocon-mediated membrane integration of a transmembrane domain upstream from the ribosomal slip site generates a force on the nascent polypeptide chain that scales with observed frameshifting. Together, our results indicate that cotranslational folding of this viral protein generates a tension that stimulates PRF. To our knowledge, this constitutes the first example in which the conformational state of the nascent polypeptide chain has been linked to PRF. These findings raise the possibility that, in addition to RNA-mediated translational recoding, a variety of cotranslational folding or binding events may also stimulate PRF.
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Affiliation(s)
| | - Matthew H Zimmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Laura M Chamness
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Veronica Nash
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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13
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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14
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
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15
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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.
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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.
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16
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Popov N, Honaker LW, Popova M, Usol'tseva N, Mann EK, Jákli A, Popov P. Thermotropic Liquid Crystal-Assisted Chemical and Biological Sensors. MATERIALS (BASEL, SWITZERLAND) 2017; 11:E20. [PMID: 29295530 PMCID: PMC5793518 DOI: 10.3390/ma11010020] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 01/30/2023]
Abstract
In this review article, we analyze recent progress in the application of liquid crystal-assisted advanced functional materials for sensing biological and chemical analytes. Multiple research groups demonstrate substantial interest in liquid crystal (LC) sensing platforms, generating an increasing number of scientific articles. We review trends in implementing LC sensing techniques and identify common problems related to the stability and reliability of the sensing materials as well as to experimental set-ups. Finally, we suggest possible means of bridging scientific findings to viable and attractive LC sensor platforms.
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Affiliation(s)
- Nicolai Popov
- Department of Biology & Chemistry, Ivanovo State University, 153025 Ivanovo, Russia.
- Nanomaterials Research Institute, Ivanovo State University, 153025 Ivanovo, Russia.
| | - Lawrence W Honaker
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
| | - Maia Popova
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH 45056, USA.
| | - Nadezhda Usol'tseva
- Nanomaterials Research Institute, Ivanovo State University, 153025 Ivanovo, Russia.
| | | | - Antal Jákli
- Liquid Crystal Institute, Kent State University, Kent, OH 44242, USA.
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17
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Trovato F, Fumagalli G. Molecular simulations of cellular processes. Biophys Rev 2017; 9:941-958. [PMID: 29185136 DOI: 10.1007/s12551-017-0363-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/19/2017] [Indexed: 12/12/2022] Open
Abstract
It is, nowadays, possible to simulate biological processes in conditions that mimic the different cellular compartments. Several groups have performed these calculations using molecular models that vary in performance and accuracy. In many cases, the atomistic degrees of freedom have been eliminated, sacrificing both structural complexity and chemical specificity to be able to explore slow processes. In this review, we will discuss the insights gained from computer simulations on macromolecule diffusion, nuclear body formation, and processes involving the genetic material inside cell-mimicking spaces. We will also discuss the challenges to generate new models suitable for the simulations of biological processes on a cell scale and for cell-cycle-long times, including non-equilibrium events such as the co-translational folding, misfolding, and aggregation of proteins. A prominent role will be played by the wise choice of the structural simplifications and, simultaneously, of a relatively complex energetic description. These challenging tasks will rely on the integration of experimental and computational methods, achieved through the application of efficient algorithms. Graphical abstract.
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Affiliation(s)
- Fabio Trovato
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany.
| | - Giordano Fumagalli
- Nephrology and Dialysis Unit, USL Toscana Nord Ovest, 55041, Lido di Camaiore, Lucca, Italy
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18
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Niesen MJM, Marshall SS, Miller TF, Clemons WM. Improving membrane protein expression by optimizing integration efficiency. J Biol Chem 2017; 292:19537-19545. [PMID: 28918393 DOI: 10.1074/jbc.m117.813469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/12/2017] [Indexed: 12/22/2022] Open
Abstract
The heterologous overexpression of integral membrane proteins in Escherichia coli often yields insufficient quantities of purifiable protein for applications of interest. The current study leverages a recently demonstrated link between co-translational membrane integration efficiency and protein expression levels to predict protein sequence modifications that improve expression. Membrane integration efficiencies, obtained using a coarse-grained simulation approach, robustly predicted effects on expression of the integral membrane protein TatC for a set of 140 sequence modifications, including loop-swap chimeras and single-residue mutations distributed throughout the protein sequence. Mutations that improve simulated integration efficiency were 4-fold enriched with respect to improved experimentally observed expression levels. Furthermore, the effects of double mutations on both simulated integration efficiency and experimentally observed expression levels were cumulative and largely independent, suggesting that multiple mutations can be introduced to yield higher levels of purifiable protein. This work provides a foundation for a general method for the rational overexpression of integral membrane proteins based on computationally simulated membrane integration efficiencies.
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Affiliation(s)
- Michiel J M Niesen
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Stephen S Marshall
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Thomas F Miller
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - William M Clemons
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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