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2.
Front Bioinform ; 4: 1321508, 2024.
Article in English | MEDLINE | ID: mdl-38343649

ABSTRACT

The current richness of sequence data needs efficient methodologies to display and analyze the complexity of the information in a compact and readable manner. Traditionally, phylogenetic trees and sequence similarity networks have been used to display and analyze sequences of protein families. These methods aim to shed light on key computational biology problems such as sequence classification and functional inference. Here, we present a new methodology, AlignScape, based on self-organizing maps. AlignScape is applied to three large families of proteins: the kinases and GPCRs from human, and bacterial T6SS proteins. AlignScape provides a map of the similarity landscape and a tree representation of multiple sequence alignments These representations are useful to display, cluster, and classify sequences as well as identify functional trends. The efficient GPU implementation of AlignScape allows the analysis of large MSAs in a few minutes. Furthermore, we show how the AlignScape analysis of proteins belonging to the T6SS complex can be used to predict coevolving partners.

3.
Nat Commun ; 15(1): 429, 2024 Jan 10.
Article in English | MEDLINE | ID: mdl-38200008

ABSTRACT

The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.


Subject(s)
Type VI Secretion Systems , Type VI Secretion Systems/genetics , Membranes , Bacteroidetes , Cell Membrane , Cell Wall
4.
Chembiochem ; 25(1): e202300539, 2024 01 02.
Article in English | MEDLINE | ID: mdl-37837257

ABSTRACT

Chemical modification of aptamers is an important step to improve their performance and stability in biological media. This can be performed either during their identification (mod-SELEX) or after the in vitro selection process (post-SELEX). In order to reduce the complexity and workload of the post-SELEX modification of aptamers, we have evaluated the possibility of improving a previously reported, chemically modified aptamer by combining enzymatic synthesis and nucleotides bearing bioisosteres of the parent cubane side-chains or substituted cubane moieties. This method lowers the synthetic burden often associated with post-SELEX approaches and allowed to identify one additional sequence that maintains binding to the PvLDH target protein, albeit with reduced specificity. In addition, while bioisosteres often improve the potency of small molecule drugs, this does not extend to chemically modified aptamers. Overall, this versatile method can be applied for the post-SELEX modification of other aptamers and functional nucleic acids.


Subject(s)
Aptamers, Nucleotide , Nucleic Acids , SELEX Aptamer Technique/methods , Aptamers, Nucleotide/chemistry , DNA
5.
J Chem Inf Model ; 63(21): 6823-6833, 2023 11 13.
Article in English | MEDLINE | ID: mdl-37877240

ABSTRACT

Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.


Subject(s)
Proteins , Ubiquitin-Protein Ligases , Molecular Docking Simulation , Ligands , Proteolysis , Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism
6.
PLoS Pathog ; 19(9): e1011687, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37769028

ABSTRACT

A. baumannii can rapidly acquire new resistance mechanisms and persist on abiotic surface, enabling the colonization of asymptomatic human host. In Acinetobacter the type VI secretion system (T6SS) is involved in twitching, surface motility and is used for interbacterial competition allowing the bacteria to uptake DNA. A. baumannii possesses a T6SS that has been well studied for its regulation and specific activity, but little is known concerning its assembly and architecture. The T6SS nanomachine is built from three architectural sub-complexes. Unlike the baseplate (BP) and the tail-tube complex (TTC), which are inherited from bacteriophages, the membrane complex (MC) originates from bacteria. The MC is the most external part of the T6SS and, as such, is subjected to evolution and adaptation. One unanswered question on the MC is how such a gigantesque molecular edifice is inserted and crosses the bacterial cell envelope. The A. baumannii MC lacks an essential component, the TssJ lipoprotein, which anchors the MC to the outer membrane. In this work, we studied how A. baumannii compensates the absence of a TssJ. We have characterized for the first time the A. baumannii's specific T6SS MC, its unique characteristic, its membrane localization, and assembly dynamics. We also defined its composition, demonstrating that its biogenesis employs three Acinetobacter-specific envelope-associated proteins that define an intricate network leading to the assembly of a five-proteins membrane super-complex. Our data suggest that A. baumannii has divided the function of TssJ by (1) co-opting a new protein TsmK that stabilizes the MC and by (2) evolving a new domain in TssM for homo-oligomerization, a prerequisite to build the T6SS channel. We believe that the atypical species-specific features we report in this study will have profound implication in our understanding of the assembly and evolutionary diversity of different T6SSs, that warrants future investigation.

7.
J Mol Biol ; 435(2): 167918, 2023 01 30.
Article in English | MEDLINE | ID: mdl-36509161

ABSTRACT

The type VI secretion system (T6SS) is a multiprotein weapon evolved by Gram-negative bacteria to deliver effectors into eukaryotic cells or bacterial rivals. The T6SS uses a contractile mechanism to propel an effector-loaded needle into its target. The contractile tail is built on an assembly platform, the baseplate, which is anchored to a membrane complex. Baseplate-membrane complex interactions are mainly mediated by contacts between the C-terminal domain of the TssK baseplate component and the cytoplasmic domain of the TssL inner membrane protein. Currently, the structural details of this interaction are unknown due to the marginal stability of the TssK-TssL complex. Here we conducted a mutagenesis study based on putative TssK-TssL contact pairs identified by co-evolution analyses. We then evaluated the impact of these mutations on T6SS activity, TssK-TssL interaction and sheath assembly and dynamics in enteroaggregative Escherichia coli. Finally, we probed the TssK-TssL interface by disulfide cross-linking, allowing to propose a model for the baseplate-membrane complex interface.


Subject(s)
Escherichia coli Proteins , Escherichia coli , Membrane Proteins , Type VI Secretion Systems , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Membrane Proteins/chemistry , Membrane Proteins/genetics , Type VI Secretion Systems/chemistry , Type VI Secretion Systems/genetics , Mutagenesis , Protein Interaction Maps , Protein Interaction Domains and Motifs
8.
Anal Chem ; 94(51): 17751-17756, 2022 12 27.
Article in English | MEDLINE | ID: mdl-36510358

ABSTRACT

Cross-linking mass spectrometry (XL-MS) has become an indispensable tool for the emerging field of systems structural biology over the recent years. However, the confidence in individual protein-protein interactions (PPIs) depends on the correct assessment of individual inter-protein cross-links. In this article, we describe a mono- and intralink filter (mi-filter) that is applicable to any kind of cross-linking data and workflow. It stipulates that only proteins for which at least one monolink or intra-protein cross-link has been identified within a given data set are considered for an inter-protein cross-link and therefore participate in a PPI. We show that this simple and intuitive filter has a dramatic effect on different types of cross-linking data ranging from individual protein complexes over medium-complexity affinity enrichments to proteome-wide cell lysates and significantly reduces the number of false-positive identifications for inter-protein links in all these types of XL-MS data.


Subject(s)
Proteome , Mass Spectrometry , Proteome/chemistry , Cross-Linking Reagents/chemistry
9.
Biomolecules ; 12(9)2022 09 13.
Article in English | MEDLINE | ID: mdl-36139128

ABSTRACT

Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3-5 Å) cryo-EM density maps is a challenging task, in particular because poorly resolved side-chain densities hamper sequence assignment by automatic procedures at a lower resolution. Furthermore, segmentation of EM density maps into individual subunits remains a difficult problem when the structure of the subunits is not known, or when significant conformational rearrangement occurs between the isolated and associated form of the subunits. To tackle these issues, we have developed a graph-based method to thread most of the C-α trace of the protein backbone into the EM density map. The EM density is described as a weighted graph such that the resulting minimum spanning tree encompasses the high-density regions of the map. A pruning algorithm cleans the tree and finds the most probable positions of the C-α atoms, by using side-chain density when available, as a collection of C-α trace fragments. By complementing experimental EM maps with contact predictions from sequence co-evolutionary information, we demonstrate that this approach can correctly segment EM maps into individual subunits and assign amino acid sequences to backbone traces to generate atomic models.


Subject(s)
Proteins , Cryoelectron Microscopy/methods , Macromolecular Substances , Models, Molecular , Protein Conformation , Proteins/chemistry
10.
Anal Chem ; 93(9): 4166-4174, 2021 03 09.
Article in English | MEDLINE | ID: mdl-33617236

ABSTRACT

Chemical cross-linking (XL) coupled to mass spectrometry (MS) has become a powerful approach to probe the structure of protein assemblies. Although most of the applications concerned purified complexes, latest developments focus on large-scale in vivo studies. Pushing in this direction, we developed an advanced in vivo cross-linking mass spectrometry platform to study the cellular interactome of living bacterial cells. It is based on in vivo labeling and involves a one-step enrichment by click chemistry on a solid support. Our approach shows an impressive efficiency on Neisseria meningitidis, leading to the identification of about 3300 cross-links for the LC-MS/MS analysis of a biological triplicate using a benchtop high-resolution Orbitrap mass spectrometer. Highly dynamic multiprotein complexes were successfully captured and characterized in all bacterial compartments, showing the great potential and precision of our proteome-wide approach. Our workflow paves new avenues for the large-scale and nonbiased analysis of protein-protein interactions. All raw data, databases, and processing parameters are available on ProteomeXchange via PRIDE repository (data set identifier PXD021553).


Subject(s)
Proteome , Tandem Mass Spectrometry , Chromatography, Liquid , Cross-Linking Reagents , Multiprotein Complexes
11.
Science ; 370(6522)2020 12 11.
Article in English | MEDLINE | ID: mdl-33303586

ABSTRACT

Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.


Subject(s)
Multiprotein Complexes/chemistry , Multiprotein Complexes/genetics , Protein Interaction Maps/genetics , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/metabolism , Histones/chemistry , Histones/genetics , Mutation , Protein Conformation , Protein Interaction Mapping , Saccharomyces cerevisiae/genetics
12.
Methods Mol Biol ; 2022: 353-377, 2019.
Article in English | MEDLINE | ID: mdl-31396911

ABSTRACT

Integrative structure modeling provides 3D models of macromolecular systems that are based on information from multiple types of experiments, physical principles, statistical inferences, and prior structural models. Here, we provide a hands-on realistic example of integrative structure modeling of the quaternary structure of the actin, tropomyosin, and gelsolin protein assembly based on electron microscopy, solution X-ray scattering, and chemical crosslinking data for the complex as well as excluded volume, sequence connectivity, and rigid atomic X-ray structures of the individual subunits. We follow the general four-stage process for integrative modeling, including gathering the input information, converting the input information into a representation of the system and a scoring function, sampling alternative model configurations guided by the scoring function, and analyzing the results. The computational aspects of this approach are implemented in our open-source Integrative Modeling Platform (IMP), a comprehensive and extensible software package for integrative modeling ( https://integrativemodeling.org ). In particular, we rely on the Python Modeling Interface (PMI) module of IMP that provides facile mixing and matching of macromolecular representations, restraints based on different types of information, sampling algorithms, and analysis including validations of the input data and output models. Finally, we also outline how to deposit an integrative structure and corresponding experimental data into PDB-Dev, the nascent worldwide Protein Data Bank (wwPDB) resource for archiving and disseminating integrative structures ( https://pdb-dev.wwpdb.org ). The example application provides a starting point for a user interested in using IMP for integrative modeling of other biomolecular systems.


Subject(s)
Computational Biology/methods , Macromolecular Substances/chemistry , Databases, Protein , Models, Molecular , Protein Conformation , Software
13.
EMBO J ; 38(10)2019 05 15.
Article in English | MEDLINE | ID: mdl-30877094

ABSTRACT

Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to Myoviridae phages. It is composed of a phage tail-like structure inserted in the bacterial cell envelope by a membrane complex (MC) comprising the TssJ, TssL and TssM proteins. We previously reported the low-resolution negative-stain electron microscopy structure of the enteroaggregative Escherichia coli MC and proposed a rotational 5-fold symmetry with a TssJ:TssL:TssM stoichiometry of 2:2:2. Here, cryo-electron tomography analyses of the T6SS MC confirm the 5-fold symmetry in situ and identify the regions of the structure that insert into the bacterial membranes. A high-resolution model obtained by single-particle cryo-electron microscopy highlights new features: five additional copies of TssJ, yielding a TssJ:TssL:TssM stoichiometry of 3:2:2, an 11-residue loop in TssM, protruding inside the lumen of the MC and constituting a functionally important periplasmic gate, and hinge regions. Based on these data, we propose an updated model on MC structure and dynamics during T6SS assembly and function.


Subject(s)
Type VI Secretion Systems/chemistry , Type VI Secretion Systems/metabolism , Bacterial Secretion Systems/chemistry , Bacterial Secretion Systems/metabolism , Cell Membrane/chemistry , Cell Membrane/metabolism , Cryoelectron Microscopy , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Membrane Proteins/chemistry , Membrane Proteins/metabolism , Models, Molecular , Protein Binding , Protein Structure, Quaternary
14.
Methods ; 159-160: 4-22, 2019 04 15.
Article in English | MEDLINE | ID: mdl-30890443

ABSTRACT

Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microscopy maps, crystallographic structures, and other data by computational methods that integrate all known information and produce structural models at a level of resolution that is appropriate to the input data. The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the same protein, and structural and compositional heterogeneity. In recent years integrative structural biology approaches have been successfully applied to a range of RNA polymerase II complexes. Here we will provide a general background to integrative structural biology, a description of how it should be practically implemented and how it has furthered our understanding of the biology of large transcriptional assemblies. Finally, in the context of recent breakthroughs in microscope and direct electron detector technology, where increasingly EM is capable of resolving structural features directly without the aid of other structural techniques, we will discuss the future role of integrative structural techniques.


Subject(s)
Computational Biology/methods , Models, Molecular , RNA Polymerase II/metabolism , Transcription Initiation, Genetic , Animals , Cryoelectron Microscopy/methods , Eukaryota/genetics , Eukaryota/metabolism , Humans , Mass Spectrometry/methods , Molecular Conformation , Protein Conformation
15.
Structure ; 27(1): 175-188.e6, 2019 01 02.
Article in English | MEDLINE | ID: mdl-30393052

ABSTRACT

Cryo-electron microscopy (cryo-EM) has become a mainstream technique for determining the structures of complex biological systems. However, accurate integrative structural modeling has been hampered by the challenges in objectively weighing cryo-EM data against other sources of information due to the presence of random and systematic errors, as well as correlations, in the data. To address these challenges, we introduce a Bayesian scoring function that efficiently and accurately ranks alternative structural models of a macromolecular system based on their consistency with a cryo-EM density map as well as other experimental and prior information. The accuracy of this approach is benchmarked using complexes of known structure and illustrated in three applications: the structural determination of the GroEL/GroES, RNA polymerase II, and exosome complexes. The approach is implemented in the open-source Integrative Modeling Platform (http://integrativemodeling.org), thus enabling integrative structure determination by combining cryo-EM data with other sources of information.


Subject(s)
Cryoelectron Microscopy/methods , Molecular Dynamics Simulation , Bacterial Proteins/chemistry , Bayes Theorem , Chaperonin 10/chemistry , Chaperonin 60/chemistry , Mass Spectrometry/methods , RNA Polymerase II/chemistry
16.
Nat Microbiol ; 3(12): 1404-1416, 2018 12.
Article in English | MEDLINE | ID: mdl-30323254

ABSTRACT

To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among these multiprotein complexes, the type VI secretion system (T6SS) is a contractile nanomachine that targets both prokaryotic and eukaryotic cells. The T6SS comprises two functional subcomplexes: a bacteriophage-related tail structure anchored to the cell envelope by a membrane complex. As in other contractile injection systems, the tail is composed of an inner tube wrapped by a sheath and built on the baseplate. In the T6SS, the baseplate is not only the tail assembly platform, but also docks the tail to the membrane complex and hence serves as an evolutionary adaptor. Here we define the biogenesis pathway and report the cryo-electron microscopy (cryo-EM) structure of the wedge protein complex of the T6SS from enteroaggregative Escherichia coli (EAEC). Using an integrative approach, we unveil the molecular architecture of the whole T6SS baseplate and its interaction with the tail sheath, offering detailed insights into its biogenesis and function. We discuss architectural and mechanistic similarities but also reveal key differences with the T4 phage and Mu phage baseplates.


Subject(s)
Bacteriophages/metabolism , Escherichia coli/metabolism , Multiprotein Complexes/chemistry , Type VI Secretion Systems/chemistry , Type VI Secretion Systems/physiology , Cell Membrane , Cryoelectron Microscopy , Escherichia coli/genetics , Escherichia coli Proteins/chemistry , Models, Molecular , Protein Conformation , Protein Conformation, alpha-Helical , Protein Interaction Domains and Motifs , Type VI Secretion Systems/genetics
17.
Biophys J ; 114(7): 1604-1613, 2018 04 10.
Article in English | MEDLINE | ID: mdl-29642030

ABSTRACT

Cryo-electron microscopy is rapidly emerging as a powerful technique to determine the structures of complex macromolecular systems elusive to other techniques. Because many of these systems are highly dynamical, characterizing their movements is also a crucial step to unravel their biological functions. To achieve this goal, we report an integrative modeling approach to simultaneously determine structure and dynamics of macromolecular systems from cryo-electron microscopy density maps. By quantifying the level of noise in the data and dealing with their ensemble-averaged nature, this approach enables the integration of multiple sources of information to model ensembles of structures and infer their populations. We illustrate the method by characterizing structure and dynamics of the integral membrane receptor STRA6, thus providing insights into the mechanisms by which it interacts with retinol binding protein and translocates retinol across the membrane.


Subject(s)
Cryoelectron Microscopy , Proteins/chemistry , Proteins/metabolism , Cell Membrane/metabolism , Molecular Dynamics Simulation , Protein Conformation , Thermodynamics , Time Factors
18.
Nature ; 555(7697): 475-482, 2018 03 22.
Article in English | MEDLINE | ID: mdl-29539637

ABSTRACT

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.


Subject(s)
Nuclear Pore Complex Proteins/chemistry , Nuclear Pore Complex Proteins/metabolism , Nuclear Pore/chemistry , Nuclear Pore/metabolism , Saccharomyces cerevisiae/chemistry , Cross-Linking Reagents/chemistry , Mass Spectrometry , Models, Molecular , Protein Stability , Protein Transport , RNA Transport
19.
Protein Sci ; 27(1): 245-258, 2018 01.
Article in English | MEDLINE | ID: mdl-28960548

ABSTRACT

Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use.


Subject(s)
Computational Biology , Computer Simulation , Models, Molecular , Software
20.
Cell Rep ; 18(11): 2651-2663, 2017 03 14.
Article in English | MEDLINE | ID: mdl-28297669

ABSTRACT

During eukaryotic translation initiation, eIF3 binds the solvent-accessible side of the 40S ribosome and recruits the gate-keeper protein eIF1 and eIF5 to the decoding center. This is largely mediated by the N-terminal domain (NTD) of eIF3c, which can be divided into three parts: 3c0, 3c1, and 3c2. The N-terminal part, 3c0, binds eIF5 strongly but only weakly to the ribosome-binding surface of eIF1, whereas 3c1 and 3c2 form a stoichiometric complex with eIF1. 3c1 contacts eIF1 through Arg-53 and Leu-96, while 3c2 faces 40S protein uS15/S13, to anchor eIF1 to the scanning pre-initiation complex (PIC). We propose that the 3c0:eIF1 interaction diminishes eIF1 binding to the 40S, whereas 3c0:eIF5 interaction stabilizes the scanning PIC by precluding this inhibitory interaction. Upon start codon recognition, interactions involving eIF5, and ultimately 3c0:eIF1 association, facilitate eIF1 release. Our results reveal intricate molecular interactions within the PIC, programmed for rapid scanning-arrest at the start codon.


Subject(s)
Eukaryotic Initiation Factor-3/chemistry , Eukaryotic Initiation Factor-3/metabolism , Eukaryotic Initiation Factor-5/metabolism , Peptide Chain Initiation, Translational , RNA, Messenger/metabolism , Ribosomes/chemistry , Ribosomes/metabolism , Saccharomyces cerevisiae/metabolism , Amino Acid Sequence , Binding Sites , Eukaryotic Initiation Factor-1/metabolism , Magnetic Resonance Spectroscopy , Models, Molecular , Mutation/genetics , Protein Binding , Protein Subunits/metabolism , RNA, Messenger/genetics , Saccharomyces cerevisiae Proteins/metabolism
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