1
|
Masse MM, Guzman-Luna V, Varela AE, Mahfuza Shapla U, Hutchinson RB, Srivastava A, Wei W, Fuchs AM, Cavagnero S. Nascent chains derived from a foldable protein sequence interact with specific ribosomal surface sites near the exit tunnel. Sci Rep 2024; 14:12324. [PMID: 38811604 PMCID: PMC11137106 DOI: 10.1038/s41598-024-61274-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
In order to become bioactive, proteins must be translated and protected from aggregation during biosynthesis. The ribosome and molecular chaperones play a key role in this process. Ribosome-bound nascent chains (RNCs) of intrinsically disordered proteins and RNCs bearing a signal/arrest sequence are known to interact with ribosomal proteins. However, in the case of RNCs bearing foldable protein sequences, not much information is available on these interactions. Here, via a combination of chemical crosslinking and time-resolved fluorescence-anisotropy, we find that nascent chains of the foldable globin apoHmp1-140 interact with ribosomal protein L23 and have a freely-tumbling non-interacting N-terminal compact region comprising 63-94 residues. Longer RNCs (apoHmp1-189) also interact with an additional yet unidentified ribosomal protein, as well as with chaperones. Surprisingly, the apparent strength of RNC/r-protein interactions does not depend on nascent-chain sequence. Overall, foldable nascent chains establish and expand interactions with selected ribosomal proteins and chaperones, as they get longer. These data are significant because they reveal the interplay between independent conformational sampling and nascent-protein interactions with the ribosomal surface.
Collapse
Affiliation(s)
- Meranda M Masse
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Angela E Varela
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ummay Mahfuza Shapla
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Rachel B Hutchinson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Aniruddha Srivastava
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- McGaw Medical Center, Northwestern University, Chicago, IL, 60611, USA
| | - Wanting Wei
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- AIDS Vaccine Research Laboratory, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Andrew M Fuchs
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| |
Collapse
|
2
|
Masse M, Hutchinson RB, Morgan CE, Allaman HJ, Guan H, Yu EW, Cavagnero S. Mapping Protein-Protein Interactions at Birth: Single-Particle Cryo-EM Analysis of a Ribosome-Nascent Globin Complex. ACS CENTRAL SCIENCE 2024; 10:385-401. [PMID: 38435509 PMCID: PMC10906257 DOI: 10.1021/acscentsci.3c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/05/2024]
Abstract
Interactions between ribosome-bound nascent chains (RNCs) and ribosomal components are critical to elucidate the mechanism of cotranslational protein folding. Nascent protein-ribosome contacts within the ribosomal exit tunnel were previously assessed mostly in the presence of C-terminal stalling sequences, yet little is known about contacts taking place in the absence of these strongly interacting motifs. Further, there is nearly no information about ribosomal proteins (r-proteins) interacting with nascent chains within the outer surface of the ribosome. Here, we combine chemical cross-linking, single-particle cryo-EM, and fluorescence anisotropy decays to determine the structural features of ribosome-bound apomyoglobin (apoMb). Within the ribosomal exit tunnel core, interactions are similar to those identified in previous reports. However, once the RNC enters the tunnel vestibule, it becomes more dynamic and interacts with ribosomal RNA (rRNA) and the L23 r-protein. Remarkably, on the outer surface of the ribosome, RNCs interact mainly with a highly conserved nonpolar patch of the L23 r-protein. RNCs also comprise a compact and dynamic N-terminal region lacking contact with the ribosome. In all, apoMb traverses the ribosome and interacts with it via its C-terminal region, while N-terminal residues sample conformational space and form a compact subdomain before the entire nascent protein sequence departs from the ribosome.
Collapse
Affiliation(s)
- Meranda
M. Masse
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Rachel B. Hutchinson
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Christopher E. Morgan
- Department
of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Heather J. Allaman
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Hongqing Guan
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Edward W. Yu
- Department
of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Silvia Cavagnero
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
3
|
Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
Collapse
Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| |
Collapse
|
4
|
Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure. Comput Struct Biotechnol J 2023; 21:1249-1261. [PMID: 36817958 PMCID: PMC9932298 DOI: 10.1016/j.csbj.2023.01.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/09/2023] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.
Collapse
|
5
|
Yang CI, Kim J, Shan SO. Ribosome-nascent chain interaction regulates N-terminal protein modification. J Mol Biol 2022; 434:167535. [PMID: 35278477 PMCID: PMC9126151 DOI: 10.1016/j.jmb.2022.167535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 01/02/2023]
Abstract
Numerous proteins initiate their folding, localization, and modifications early during translation, and emerging data show that the ribosome actively participates in diverse protein biogenesis pathways. Here we show that the ribosome imposes an additional layer of substrate selection during N-terminal methionine excision (NME), an essential protein modification in bacteria. Biochemical analyses show that cotranslational NME is exquisitely sensitive to a hydrophobic signal sequence or transmembrane domain near the N terminus of the nascent polypeptide. The ability of the nascent chain to access the active site of NME enzymes dictates NME efficiency, which is inhibited by confinement of the nascent chain on the ribosome surface and exacerbated by signal recognition particle. In vivo measurements corroborate the inhibition of NME by an N-terminal hydrophobic sequence, suggesting the retention of formylmethionine on a substantial fraction of the secretory and membrane proteome. Our work demonstrates how molecular features of a protein regulate its cotranslational modification and highlights the active participation of the ribosome in protein biogenesis pathways via interactions of the ribosome surface with the nascent protein.
Collapse
|
6
|
Common sequence motifs of nascent chains engage the ribosome surface and trigger factor. Proc Natl Acad Sci U S A 2021; 118:2103015118. [PMID: 34930833 PMCID: PMC8719866 DOI: 10.1073/pnas.2103015118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Proteins are produced by ribosomes in the cell, and during this process, can begin to adopt their biologically active forms assisted by molecular chaperones such as trigger factor. This fundamental cellular mechanism is crucial to maintaining a functional proteome and avoiding deleterious misfolding. Here, we study how disordered nascent chains emerge from the ribosome exit tunnel, and find that interactions with the ribosome surface dominate their dynamics in vitro and in vivo. Moreover, we show that the types of amino acids that mediate such interactions are also those that recruit trigger factor. This lays the foundation to describe how nascent chains are handed over from the ribosome surface to chaperones during biosynthesis within the crowded cytosol. In the cell, the conformations of nascent polypeptide chains during translation are modulated by both the ribosome and its associated molecular chaperone, trigger factor. The specific interactions that underlie these modulations, however, are still not known in detail. Here, we combine protein engineering, in-cell and in vitro NMR spectroscopy, and molecular dynamics simulations to explore how proteins interact with the ribosome during their biosynthesis before folding occurs. Our observations of α-synuclein nascent chains in living Escherichia coli cells reveal that ribosome surface interactions dictate the dynamics of emerging disordered polypeptides in the crowded cytosol. We show that specific basic and aromatic motifs drive such interactions and directly compete with trigger factor binding while biasing the direction of the nascent chain during its exit out of the tunnel. These results reveal a structural basis for the functional role of the ribosome as a scaffold with holdase characteristics and explain how handover of the nascent chain to specific auxiliary proteins occurs among a host of other factors in the cytosol.
Collapse
|
7
|
Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE. Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. Microbiol Spectr 2021; 9:e0178221. [PMID: 34908470 PMCID: PMC8672879 DOI: 10.1128/spectrum.01782-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: these were positively charged despite the halophilicity of the organisms. IMPORTANCE The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged, including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences cotranslational folding, the contrasting charges observed in the S10-spc cluster r-proteins have potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2, which lies in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.
Collapse
Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Sidharth Rajesh
- Clements High School (Class of 2023), Fort Bend Independent School District, Sugar Land, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| |
Collapse
|
8
|
Guzman-Luna V, Fuchs AM, Allen AJ, Staikos A, Cavagnero S. An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel. Commun Biol 2021; 4:1236. [PMID: 34716402 PMCID: PMC8556260 DOI: 10.1038/s42003-021-02752-4] [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: 05/21/2020] [Accepted: 10/05/2021] [Indexed: 12/11/2022] Open
Abstract
The influence of the ribosome on nascent chains is poorly understood, especially in the case of proteins devoid of signal or arrest sequences. Here, we provide explicit evidence for the interaction of specific ribosomal proteins with ribosome-bound nascent chains (RNCs). We target RNCs pertaining to the intrinsically disordered protein PIR and a number of mutants bearing a variable net charge. All the constructs analyzed in this work lack N-terminal signal sequences. By a combination chemical crosslinking and Western-blotting, we find that all RNCs interact with ribosomal protein L23 and that longer nascent chains also weakly interact with L29. The interacting proteins are spatially clustered on a specific region of the large ribosomal subunit, close to the exit tunnel. Based on chain-length-dependence and mutational studies, we find that the interactions with L23 persist despite drastic variations in RNC sequence. Importantly, we also find that the interactions are highly Mg+2-concentration-dependent. This work is significant because it unravels a novel role of the ribosome, which is shown to engage with the nascent protein chain even in the absence of signal or arrest sequences.
Collapse
Affiliation(s)
- Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Andrew M Fuchs
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Anna J Allen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
| |
Collapse
|
9
|
Hutchinson RB, Chen X, Zhou N, Cavagnero S. Fluorescence Anisotropy Decays and Microscale-Volume Viscometry Reveal the Compaction of Ribosome-Bound Nascent Proteins. J Phys Chem B 2021; 125:6543-6558. [PMID: 34110829 PMCID: PMC8741338 DOI: 10.1021/acs.jpcb.1c04473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This work introduces a technology that combines fluorescence anisotropy decay with microscale-volume viscometry to investigate the compaction and dynamics of ribosome-bound nascent proteins. Protein folding in the cell, especially when nascent chains emerge from the ribosomal tunnel, is poorly understood. Previous investigations based on fluorescence anisotropy decay determined that a portion of the ribosome-bound nascent protein apomyoglobin (apoMb) forms a compact structure. This work, however, could not assess the size of the compact region. The combination of fluorescence anisotropy with microscale-volume viscometry, presented here, enables identifying the size of compact nascent-chain subdomains using a single fluorophore label. Our results demonstrate that the compact region of nascent apoMb contains 57-83 amino acids and lacks residues corresponding to the two native C-terminal helices. These amino acids are necessary for fully burying the nonpolar residues in the native structure, yet they are not available for folding before ribosome release. Therefore, apoMb requires a significant degree of post-translational folding for the generation of its native structure. In summary, the combination of fluorescence anisotropy decay and microscale-volume viscometry is a powerful approach to determine the size of independently tumbling compact regions of biomolecules. This technology is of general applicability to compact macromolecules linked to larger frameworks.
Collapse
Affiliation(s)
| | - Xi Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ningkun Zhou
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| |
Collapse
|
10
|
Abstract
Folding of polypeptides begins during their synthesis on ribosomes. This process has evolved as a means for the cell to maintain proteostasis, by mitigating the risk of protein misfolding and aggregation. The capacity to now depict this cellular feat at increasingly higher resolution is providing insight into the mechanistic determinants that promote successful folding. Emerging from these studies is the intimate interplay between protein translation and folding, and within this the ribosome particle is the key player. Its unique structural properties provide a specialized scaffold against which nascent polypeptides can begin to form structure in a highly coordinated, co-translational manner. Here, we examine how, as a macromolecular machine, the ribosome modulates the intrinsic dynamic properties of emerging nascent polypeptide chains and guides them toward their biologically active structures.
Collapse
Affiliation(s)
- Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| |
Collapse
|
11
|
Leeb S, Yang F, Oliveberg M, Danielsson J. Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR. J Phys Chem B 2020; 124:10698-10707. [PMID: 33179918 PMCID: PMC7735724 DOI: 10.1021/acs.jpcb.0c08274] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/22/2020] [Indexed: 12/26/2022]
Abstract
In the cytosolic environment, protein crowding and Brownian motions result in numerous transient encounters. Each such encounter event increases the apparent size of the interacting molecules, leading to slower rotational tumbling. The extent of transient protein complexes formed in live cells can conveniently be quantified by an apparent viscosity, based on NMR-detected spin-relaxation measurements, that is, the longitudinal (T1) and transverse (T2) relaxation. From combined analysis of three different proteins and surface mutations thereof, we find that T2 implies significantly higher apparent viscosity than T1. At first sight, the effect on T1 and T2 seems thus nonunifiable, consistent with previous reports on other proteins. We show here that the T1 and T2 deviation is actually not a inconsistency but an expected feature of a system with fast exchange between free monomers and transient complexes. In this case, the deviation is basically reconciled by a model with fast exchange between the free-tumbling reporter protein and a transient complex with a uniform 143 kDa partner. The analysis is then taken one step further by accounting for the fact that the cytosolic content is by no means uniform but comprises a wide range of molecular sizes. Integrating over the complete size distribution of the cytosolic interaction ensemble enables us to predict both T1 and T2 from a single binding model. The result yields a bound population for each protein variant and provides a quantification of the transient interactions. We finally extend the approach to obtain a correction term for the shape of a database-derived mass distribution of the interactome in the mammalian cytosol, in good accord with the existing data of the cellular composition.
Collapse
Affiliation(s)
- Sarah Leeb
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Fan Yang
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| |
Collapse
|
12
|
Poitevin F, Kushner A, Li X, Dao Duc K. Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM. Molecules 2020; 25:E4262. [PMID: 32957592 PMCID: PMC7570653 DOI: 10.3390/molecules25184262] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal motion at the single particle level, specialization at the cellular and subcellular scale, or evolutionary differences across species. Upon solving the ribosome atomic structure at medium to high resolution, cryogenic electron microscopy (cryo-EM) has enabled investigating all these forms of heterogeneity. In this review, we present some recent advances in quantifying ribosome heterogeneity, with a focus on the conformational and evolutionary variations of the ribosome and their functional implications. These efforts highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data, which would more generally benefit the study of molecular dynamics and evolution of proteins and other complexes.
Collapse
Affiliation(s)
- Frédéric Poitevin
- Department of LCLS Data Analytics, Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
| | - Artem Kushner
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (A.K.); (X.L.)
- Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xinpei Li
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (A.K.); (X.L.)
- Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (A.K.); (X.L.)
- Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
13
|
Grishin SY, Deryusheva EI, Machulin AV, Selivanova OM, Glyakina AV, Gorbunova EY, Mustaeva LG, Azev VN, Rekstina VV, Kalebina TS, Surin AK, Galzitskaya OV. Amyloidogenic Propensities of Ribosomal S1 Proteins: Bioinformatics Screening and Experimental Checking. Int J Mol Sci 2020; 21:E5199. [PMID: 32707977 PMCID: PMC7432502 DOI: 10.3390/ijms21155199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
Structural S1 domains belong to the superfamily of oligosaccharide/oligonucleotide-binding fold domains, which are highly conserved from prokaryotes to higher eukaryotes and able to function in RNA binding. An important feature of this family is the presence of several copies of the structural domain, the number of which is determined in a strictly limited range from one to six. Despite the strong tendency for the aggregation of several amyloidogenic regions in the family of the ribosomal S1 proteins, their fibril formation process is still poorly understood. Here, we combined computational and experimental approaches for studying some features of the amyloidogenic regions in this protein family. The FoldAmyloid, Waltz, PASTA 2.0 and Aggrescan programs were used to assess the amyloidogenic propensities in the ribosomal S1 proteins and to identify such regions in various structural domains. The thioflavin T fluorescence assay and electron microscopy were used to check the chosen amyloidogenic peptides' ability to form fibrils. The bioinformatics tools were used to study the amyloidogenic propensities in 1331 ribosomal S1 proteins. We found that amyloidogenicity decreases with increasing sizes of proteins. Inside one domain, the amyloidogenicity is higher in the terminal parts. We selected and synthesized 11 amyloidogenic peptides from the Escherichia coli and Thermus thermophilus ribosomal S1 proteins and checked their ability to form amyloids using the thioflavin T fluorescence assay and electron microscopy. All 11 amyloidogenic peptides form amyloid-like fibrils. The described specific amyloidogenic regions are actually responsible for the fibrillogenesis process and may be potential targets for modulating the amyloid properties of bacterial ribosomal S1 proteins.
Collapse
Affiliation(s)
- Sergei Y Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Evgeniya I Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Andrey V Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Elena Y Gorbunova
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Leila G Mustaeva
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Vyacheslav N Azev
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Valentina V Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Tatyana S Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, Obolensk 142279, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| |
Collapse
|
14
|
Addabbo RM, Dalphin MD, Mecha MF, Liu Y, Staikos A, Guzman-Luna V, Cavagnero S. Complementary Role of Co- and Post-Translational Events in De Novo Protein Biogenesis. J Phys Chem B 2020; 124:6488-6507. [DOI: 10.1021/acs.jpcb.0c03039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yue Liu
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
15
|
Leeb S, Sörensen T, Yang F, Mu X, Oliveberg M, Danielsson J. Diffusive protein interactions in human versus bacterial cells. Curr Res Struct Biol 2020; 2:68-78. [PMID: 34235470 PMCID: PMC8244477 DOI: 10.1016/j.crstbi.2020.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 01/14/2023] Open
Abstract
Random encounters between proteins in crowded cells are by no means passive, but found to be under selective control. This control enables proteome solubility, helps to optimise the diffusive search for interaction partners, and allows for adaptation to environmental extremes. Interestingly, the residues that modulate the encounters act mesoscopically through protein surface hydrophobicity and net charge, meaning that their detailed signatures vary across organisms with different intracellular constraints. To examine such variations, we use in-cell NMR relaxation to compare the diffusive behaviour of bacterial and human proteins in both human and Escherichia coli cytosols. We find that proteins that ‘stick’ in E. coli are generally less restricted in mammalian cells. Furthermore, the rotational diffusion in the mammalian cytosol is less sensitive to surface-charge mutations. This implies that, in terms of protein motions, the mammalian cytosol is more forgiving to surface alterations than E. coli cells. The cellular differences seem not linked to the proteome properties per se, but rather to a 6-fold difference in protein concentrations. Our results outline a scenario in which the tolerant cytosol of mammalian cells, found in long-lived multicellular organisms, provides an enlarged evolutionary playground, where random protein-surface mutations are less deleterious than in short-generational bacteria. Random protein encounters and diffusibility in cells are controlled by surface charge. Protein rotational diffusion is less restricted in human cells than in E. coli. Human cells are less sensitive to alterations of protein charge than Escherichia coli cells.
Collapse
Affiliation(s)
- Sarah Leeb
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Therese Sörensen
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Fan Yang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Xin Mu
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| |
Collapse
|
16
|
Ando M, Sasaki Y, Akiyoshi K. Preparation of cationic proteoliposomes using cell-free membrane protein synthesis: the chaperoning effect of cationic liposomes. RSC Adv 2020; 10:28741-28745. [PMID: 35520093 PMCID: PMC9055869 DOI: 10.1039/d0ra05825d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Membrane protein reconstituted cationic liposomes are constructed using cell-free membrane protein synthesis in the presence of cationic liposomes. The chaperon effect of cationic liposomal membrane assists in folding the functional conformation of membrane protein. This preparation method enables the provision of the usage of proteoliposomes for drug delivery. The preparation method of cationic proteoliposomes is established using a cell-free membrane protein synthesis in the presence of cationic liposomes.![]()
Collapse
Affiliation(s)
- Mitsuru Ando
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| |
Collapse
|
17
|
Farías-Rico JA, Ruud Selin F, Myronidi I, Frühauf M, von Heijne G. Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome. Proc Natl Acad Sci U S A 2018; 115:E9280-E9287. [PMID: 30224455 PMCID: PMC6176590 DOI: 10.1073/pnas.1812756115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
During the last five decades, studies of protein folding in dilute buffer solutions have produced a rich picture of this complex process. In the cell, however, proteins can start to fold while still attached to the ribosome (cotranslational folding) and it is not yet clear how the ribosome affects the folding of protein domains of different sizes, thermodynamic stabilities, and net charges. Here, by using arrest peptides as force sensors and on-ribosome pulse proteolysis, we provide a comprehensive picture of how the distance from the peptidyl transferase center in the ribosome at which proteins fold correlates with protein size. Moreover, an analysis of a large collection of mutants of the Escherichia coli ribosomal protein S6 shows that the force exerted on the nascent chain by protein folding varies linearly with the thermodynamic stability of the folded state, and that the ribosome environment disfavors folding of domains of high net-negative charge.
Collapse
Affiliation(s)
| | - Frida Ruud Selin
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ioanna Myronidi
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marie Frühauf
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden
| |
Collapse
|
18
|
Fujiwara K, Ito K, Chiba S. MifM-instructed translation arrest involves nascent chain interactions with the exterior as well as the interior of the ribosome. Sci Rep 2018; 8:10311. [PMID: 29985442 PMCID: PMC6037786 DOI: 10.1038/s41598-018-28628-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/25/2018] [Indexed: 11/09/2022] Open
Abstract
Bacillus subtilis MifM is a monitoring substrate of the YidC pathways of protein integration into the membrane and controls the expression of the YidC2 (YqjG) homolog by undergoing regulated translational elongation arrest. The elongation arrest requires interactions between the MifM nascent polypeptide and the ribosomal components near the peptidyl transferase center (PTC) as well as at the constriction site of the ribosomal exit tunnel. Here, we addressed the roles played by more N-terminal regions of MifM and found that, in addition to the previously-identified arrest-provoking elements, the MifM residues 41-60 likely located at the tunnel exit and outside the ribosome contribute to the full induction of elongation arrest. Mutational effects of the cytosolically exposed part of the ribosomal protein uL23 suggested its involvement in the elongation arrest, presumably by interacting with the extra-ribosomal portion of MifM. In vitro translation with reconstituted translation components recapitulated the effects of the mutations at the 41-60 segment, reinforcing the importance of direct molecular interactions between the nascent chain and the ribosome. These results indicate that the nascent MifM polypeptide interacts extensively with the ribosome both from within and without to direct the elongation halt and consequent up-regulation of YidC2.
Collapse
Affiliation(s)
- Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
| | - Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan.
| |
Collapse
|
19
|
Abstract
Prion-like proteins overlap with intrinsically disordered and low-complexity sequence families. These proteins are widespread, especially among mRNA-binding proteins. A salient feature of these proteins is the ability to form protein assemblies with distinct biophysical and functional properties. While prion-like proteins are involved in myriad of cellular processes, we propose potential roles for protein assemblies in regulated protein synthesis. Since proteins are the ultimate functional output of gene expression, when, where, and how much of a particular protein is made dictates the functional state of a cell. Recent finding suggests that the prion-like proteins offer unique advantages in translation regulation and also raises questions regarding formation and regulation of protein assemblies.
Collapse
Affiliation(s)
- Liying Li
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA
| | - J P McGinnis
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA
| | - Kausik Si
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA.
| |
Collapse
|
20
|
Abstract
![]()
We review how major cell behaviors,
such as bacterial growth laws,
are derived from the physical chemistry of the cell’s proteins.
On one hand, cell actions depend on the individual biological functionalities
of their many genes and proteins. On the other hand, the common physics
among proteins can be as important as the unique biology that distinguishes
them. For example, bacterial growth rates depend strongly on temperature.
This dependence can be explained by the folding stabilities across
a cell’s proteome. Such modeling explains how thermophilic
and mesophilic organisms differ, and how oxidative damage of highly
charged proteins can lead to unfolding and aggregation in aging cells.
Cells have characteristic time scales. For example, E. coli can duplicate as fast as 2–3 times per hour. These time scales
can be explained by protein dynamics (the rates of synthesis and degradation,
folding, and diffusional transport). It rationalizes how bacterial
growth is slowed down by added salt. In the same way that the behaviors
of inanimate materials can be expressed in terms of the statistical
distributions of atoms and molecules, some cell behaviors can be expressed
in terms of distributions of protein properties, giving insights into
the microscopic basis of growth laws in simple cells.
Collapse
Affiliation(s)
- Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Adam M R de Graff
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lucas Sawle
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
| |
Collapse
|