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Alanis E, Aguilar F, Banaei N, Dean FB, Villarreal A, Alanis M, Lozano K, Bullard JM, Zhang Y. A rationally designed antimicrobial peptide from structural and functional insights of Clostridioides difficile translation initiation factor 1. Microbiol Spectr 2024; 12:e0277323. [PMID: 38329351 PMCID: PMC10913371 DOI: 10.1128/spectrum.02773-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
A significant increase of hospital-acquired bacterial infections during the COVID-19 pandemic has become an urgent medical problem. Clostridioides difficile is an urgent antibiotic-resistant bacterial pathogen and a leading causative agent of nosocomial infections. The increasing recurrence of C. difficile infection and antibiotic resistance in C. difficile has led to an unmet need for the discovery of new compounds distinctly different from present antimicrobials, while antimicrobial peptides as promising alternatives to conventional antibiotics have attracted growing interest recently. Protein synthesis is an essential metabolic process in all bacteria and a validated antibiotic target. Initiation factor 1 from C. difficile (Cd-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis. Here, we report the solution nuclear magnetic resonance (NMR) structure of Cd-IF1 which adopts a typical β-barrel fold and consists of a five-stranded β-sheet and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5. The interaction of Cd-IF1 with the 30S ribosomal subunit was studied by NMR titration for the construction of a structural model of Cd-IF1 binding with the 30S subunit. The short α-helix in IF1 was found to be critical for IF1 ribosomal binding. A peptide derived from this α-helix was tested and displayed a high ability to inhibit the growth of C. difficile and other bacterial strains. These results provide a clue for the rational design of new antimicrobials.IMPORTANCEBacterial infections continue to represent a major worldwide health hazard due to the emergence of drug-resistant strains. Clostridioides difficile is a common nosocomial pathogen and the causative agent in many infections resulting in an increase in morbidity and mortality. Bacterial protein synthesis is an essential metabolic process and an important target for antibiotic development; however, the precise structural mechanism underlying the process in C. difficile remains unknown. This study reports the solution structure of C. difficile translation initiation factor 1 (IF1) and its interaction with the 30S ribosomal subunit. A short α-helix in IF1 structure was identified as critically important for ribosomal binding and function in regulating the translation initiation, which allowed a rational design of a new peptide. The peptide demonstrated a high ability to inhibit bacterial growth with broad-spectrum antibacterial activity. This study provides a new clue for the rational design of new antimicrobials against bacterial infections.
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Affiliation(s)
- Elvira Alanis
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Faith Aguilar
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Frank B. Dean
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Alexa Villarreal
- Department of Mechanical Engineering, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Miguel Alanis
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Karen Lozano
- Department of Mechanical Engineering, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - James M. Bullard
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Yonghong Zhang
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
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Aguilar F, Banaei N, Zhang Y. 1H, 13C and 15N resonance assignments and structure prediction of translation initiation factor 1 from Clostridium difficile. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:91-95. [PMID: 30370502 DOI: 10.1007/s12104-018-9858-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/24/2018] [Indexed: 06/08/2023]
Abstract
Clostridium difficile is a gram-positive, toxin-producing, anaerobic bacterium whose virulence factors and mechanisms of pathogenesis require further investigation. C. difficile infections (CDI) result in the severe and potentially fatal gastrointestinal diseases pseudomembranous colitis and toxic megacolon following extensive broad spectrum antibiotic treatment. The increasing C. difficile fatalities are a result of the bacteria's growing antibiotic resistance and consequential CDI recurrence, which led to the unmet need for new CDI treatment. Bacterial protein synthesis is an essential metabolic process and an effective target for antibacterial agents. Translation initiation factor 1 from C. difficile (Cd-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis. Here we report the complete NMR 1H, 13C and 15N chemical shift assignments of Cd-IF1 as the basis for NMR structure determination and interaction studies. Secondary structure analyses have identified five β-strands and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5, which is supported by 15N-{1H} heteroNOEs. The assigned chemical shifts were used to conduct structure prediction by CS-Rosetta. The predicted structure suggests that Cd-IF1 adopts the typical β-barrel structure and is composed of an oligomer-binding motif.
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Affiliation(s)
- Faith Aguilar
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA.
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Bernal A, Hu Y, Palmer SO, Silva A, Bullard J, Zhang Y. (1)H, (13)C and (15)N resonance assignments and secondary structure analysis of translation initiation factor 1 from Pseudomonas aeruginosa. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:249-252. [PMID: 26983940 PMCID: PMC5026565 DOI: 10.1007/s12104-016-9678-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/13/2016] [Indexed: 06/05/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen and a primary cause of infection in humans. P. aeruginosa can acquire resistance against multiple groups of antimicrobial agents, including β-lactams, aminoglycosides and fluoroquinolones, and multidrug resistance is increasing in this organism which makes treatment of the infections difficult and expensive. This has led to the unmet need for discovery of new compounds distinctly different from present antimicrobials. Protein synthesis is an essential metabolic process and a validated target for the development of new antibiotics. Translation initiation factor 1 from P. aeruginosa (Pa-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis, and its structure is unknown. Here we report the (1)H, (13)C and (15)N chemical shift assignments of Pa-IF1 as the basis for NMR structure determination and interaction studies. Secondary structure analyses deduced from the NMR chemical shift data have identified five β-strands with an unusually extended β-strand at the C-terminal end of the protein and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5. This is further supported by (15)N-{(1)H} hetero NOEs. These secondary structure elements suggest the Pa-IF1 adopts the typical β-barrel structure and is composed of an oligomer-binding motif.
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Affiliation(s)
- Alejandra Bernal
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Yanmei Hu
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Stephanie O Palmer
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Aaron Silva
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - James Bullard
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, TX, USA.
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Hu Y, Bernal A, Bullard JM, Zhang Y. Solution structure of protein synthesis initiation factor 1 from Pseudomonas aeruginosa. Protein Sci 2016; 25:2290-2296. [PMID: 27636899 DOI: 10.1002/pro.3042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/09/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen and a primary cause of nosocomial infection in humans. The rate of antibiotic resistance in P. aeruginosa is increasing worldwide leading to an unmet need for discovery of new chemical compounds distinctly different from present antimicrobials. Protein synthesis is an essential metabolic process and a validated target for the development of new antibiotics. Initiation factor 1 from P. aeruginosa (Pa-IF1) is the smallest of the three initiation factors that act to establish the 30S initiation complex during initiation of protein biosynthesis. Here we report the characterization and solution NMR structure of Pa-IF1. Pa-IF1 consists of a five-stranded β-sheet with an unusual extended β-strand at the C-terminus and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5. The structure adopts a typical β-barrel fold and contains an oligomer-binding motif. A cluster of basic residues (K39, R41, K42, K64, R66, R70, and R72) located on the surface of strands β4 and β5 near the short α-helix may compose the binding interface with the 30S subunit.
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Affiliation(s)
- Yanmei Hu
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
| | - Alejandra Bernal
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
| | - James M Bullard
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
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González M, Andrews E, Folch H, Sáez D, Cabrera A, Salgado P, Oñate A. Cloning, expression and immunogenicity of the translation initiation factor 3 homologue of Brucella abortus. Immunobiology 2008; 214:113-20. [PMID: 19167989 DOI: 10.1016/j.imbio.2008.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/05/2008] [Accepted: 07/03/2008] [Indexed: 10/21/2022]
Abstract
The infC gene of Brucella abortus encoding the translation initiation factor 3 (IF3) was cloned, sequenced and expressed in Escherichia coli. The amino acid sequence analysis predicted a product with 74-80% identity with the IF3 proteins from Mesorhizobium loti, Sinorhizobium meliloti, Aurantimona sp. and Mesorhizobium sp. This protein also show 54% amino acid sequence identity with the E. coli IF3, sharing most of the residues which were described as responsible for the biological activity of this protein. Since we have previously reported the immunoprotective capacity of this Brucella protein, we stimulated lymphoid cells from animals immunized with purified recombinant Brucella IF3 protein "in vitro" with this antigen. The lymphocytes were able to mount a strong proliferative response with concomitant production of gamma interferon, but without the secretion of either IL-4 or antibodies. Thus, immunization with the Brucella recombinant IF3 protein promotes a TH-1 polarized response, allowing us to propose it as a promising candidate antigen for the development of subunit vaccines against Brucella.
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Affiliation(s)
- Marcela González
- Department of Microbiology, Faculty of Biological Sciences, Molecular Immunology Laboratory, Universidad de Concepción, Concepción, Chile
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Brunelle JL, Youngman EM, Sharma D, Green R. The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA (NEW YORK, N.Y.) 2006; 12:33-9. [PMID: 16373492 PMCID: PMC1370883 DOI: 10.1261/rna.2256706] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ribosomal variants carrying mutations in active site nucleotides are severely compromised in their ability to catalyze peptide bond formation (PT) with minimal aminoacyl tRNA substrates such as puromycin. However, catalysis of PT by these same ribosomes with intact aminoacyl tRNA substrates is uncompromised. These data suggest that these active site nucleotides play an important role in the positioning of minimal aminoacyl tRNA substrates but are not essential for catalysis per se when aminoacyl tRNAs are positioned by more remote interactions with the ribosome. Previously reported biochemical studies and atomic resolution X-ray structures identified a direct Watson-Crick interaction between C75 of the A-site substrate and G2553 of the 23S rRNA. Here we show that the addition of this single cytidine residue (the C75 equivalent) to puromycin is sufficient to suppress the deficiencies of active site ribosomal variants, thus restoring "tRNA-like" behavior to this minimal substrate. Studies of the binding parameters and the pH-dependence of catalysis with this minimal substrate indicate that the interaction between C75 and the ribosomal A loop is an essential feature for robust catalysis and further suggest that the observed effects of C75 on peptidyl transfer activity reflect previously reported conformational rearrangements in this active site.
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Affiliation(s)
- Julie L Brunelle
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, 702A PCTB, Baltimore, MD 21205, USA
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Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU. Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 2005; 69:101-23. [PMID: 15755955 PMCID: PMC1082788 DOI: 10.1128/mmbr.69.1.101-123.2005] [Citation(s) in RCA: 418] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Valuable information on translation initiation is available from biochemical data and recently solved structures. We present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. The first section describes the ribosomal features relevant to the initiation process. Subsequent sections describe the structure, function, and interactions of the mRNA, the initiator tRNA, and the initiation factors IF1, IF2, and IF3. Finally, we provide an overview of mechanisms of regulation of the translation initiation event. Translation occurs on ribonucleoprotein complexes called ribosomes. The ribosome is composed of a large subunit and a small subunit that hold the activities of peptidyltransfer and decode the triplet code of the mRNA, respectively. Translation initiation is promoted by IF1, IF2, and IF3, which mediate base pairing of the initiator tRNA anticodon to the mRNA initiation codon located in the ribosomal P-site. The mechanism of translation initiation differs for canonical and leaderless mRNAs, since the latter is dependent on the relative level of the initiation factors. Regulation of translation occurs primarily in the initiation phase. Secondary structures at the mRNA ribosomal binding site (RBS) inhibit translation initiation. The accessibility of the RBS is regulated by temperature and binding of small metabolites, proteins, or antisense RNAs. The future challenge is to obtain atomic-resolution structures of complete initiation complexes in order to understand the mechanism of translation initiation in molecular detail.
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Affiliation(s)
- Brian Søgaard Laursen
- Department of Molecular Biology, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus C, Denmark
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Croitoru V, Bucheli-Witschel M, Hägg P, Abdulkarim F, Isaksson LA. Generation and characterization of functional mutants in the translation initiation factor IF1 of Escherichia coli. ACTA ACUST UNITED AC 2004; 271:534-44. [PMID: 14728680 DOI: 10.1046/j.1432-1033.2003.03954.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Three protein factors IF1, IF2 and IF3 are involved in the initiation of translation in prokaryotes. No clear function has been assigned to the smallest of these three factors, IF1. Therefore, to investigate the role of this protein in the initiation process in Escherichia coli we have mutated the corresponding gene infA. Because IF1 is essential for cell viability and no mutant selection has so far been described, the infA gene in a plasmid was mutated by site-directed mutagenesis in a strain with a chromosomal infA+ gene, followed by deletion of this infA+ gene. Using this approach, the six arginine residues of IF1 were altered to leucine or aspartate. Another set of plasmid-encoded IF1 mutants with a cold-sensitive phenotype was collected using localized random mutagenesis. All mutants with a mutated infA gene on a plasmid and a deletion of the chromosomal infA copy were viable, except for an R65D alteration. Differences in growth phenotypes of the mutants were observed in both minimal and rich media. Some of the mutated infA genes were successfully recombined into the chromosome thereby replacing the wild-type infA+ allele. Several of these recombinants showed reduced growth rate and a partial cold-sensitive phenotype. This paper presents a collection of IF1 mutants designed for in vivo and in vitro studies on the function of IF1.
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Askarian-Amiri ME, Pel HJ, Guévremont D, McCaughan KK, Poole ES, Sumpter VG, Tate WP. Functional characterization of yeast mitochondrial release factor 1. J Biol Chem 2000; 275:17241-8. [PMID: 10748224 DOI: 10.1074/jbc.m910448199] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast Saccharomyces cerevisiae mitochondrial release factor was expressed from the cloned MRF1 gene, purified from inclusion bodies, and refolded to give functional activity. The gene encoded a factor with release activity that recognized cognate stop codons in a termination assay with mitochondrial ribosomes and in an assay with Escherichia coli ribosomes. The noncognate stop codon, UGA, encoding tryptophan in mitochondria, was recognized weakly in the heterologous assay. The mitochondrial release factor 1 protein bound to bacterial ribosomes and formed a cross-link with the stop codon within a mRNA bound in a termination complex. The affinity was strongly dependent on the identity of stop signal. Two alleles of MRF1 that contained point mutations in a release factor 1 specific region of the primary structure and that in vivo compensated for mutations in the decoding site rRNA of mitochondrial ribosomes were cloned, and the expressed proteins were purified and refolded. The variant proteins showed impaired binding to the ribosome compared with mitochondrial release factor 1. This structural region in release factors is likely to be involved in codon-dependent specific ribosomal interactions.
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Affiliation(s)
- M E Askarian-Amiri
- Department of Biochemistry and Centre for Gene Research, University of Otago, P. O. Box 56, 9015 Dunedin, New Zealand
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Babic S, Hunter CN, Rakhlin NJ, Simons RW, Phillips-Jones MK. Molecular characterisation of the pifC gene encoding translation initiation factor 3, which is required for normal photosynthetic complex formation in Rhodobacter sphaeroides NCIB 8253. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:564-75. [PMID: 9370368 DOI: 10.1111/j.1432-1033.1997.t01-1-00564.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In order to determine whether translation initiation events play a selective role in regulating the expression of photosynthetic complexes in the photosynthetic bacterium Rhodobacter sphaeroides, we have undertaken an initial study to investigate the potential role of translation initiation factor IF3, which also behaves as a pleiotropic regulatory factor in some bacteria. Following the isolation and purification of a 24-kDa IF3-like protein (PifC) from R. sphaeroides, we used nested PCR to clone and characterise the encoding gene, pifC (photosynthesis-affecting initiation factor). The 545-bp pifC encodes a protein exhibiting 60% identity (78.6% similarity) with the Escherichia coli IF3 (InfC) protein and, in common with all other IF3 genes identified to date, pifC possesses a rare initiation codon (AUA). Furthermore, in common with IF3, PifC was shown here to perform a discriminatory function towards CUG start codons, confirming its role and function as an IF3 in R. sphaeroides. Insertion of a kanamycin resistance cassette into the 5' end of pifC resulted in a viable phenotype which exhibits growth rates similar to wild type but which possesses reduced bacteriochlorophyll and photosynthetic complexes in semi-aerobic cultures. It is shown here that the mutant is still able to produce a PifC protein but that it possesses reduced IF3 activity. This may account for the viable nature of the mutant strain, and may indicate that the effect of the mutation on photosynthesis can be more severe than shown in the present study. The mechanisms by which PifC may exert its selective regulatory effect on photosynthesis expression are discussed.
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Affiliation(s)
- S Babic
- Department of Microbiology, University of Leeds, UK
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Sette M, van Tilborg P, Spurio R, Kaptein R, Paci M, Gualerzi CO, Boelens R. The structure of the translational initiation factor IF1 from E.coli contains an oligomer-binding motif. EMBO J 1997; 16:1436-43. [PMID: 9135158 PMCID: PMC1169740 DOI: 10.1093/emboj/16.6.1436] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The structure of the translational initiation factor IF1 from Escherichia coli has been determined with multidimensional NMR spectroscopy. Using 1041 distance and 78 dihedral constraints, 40 distance geometry structures were calculated, which were refined by restrained molecular dynamics. From this set, 19 structures were selected, having low constraint energy and few constraint violations. The ensemble of 19 structures displays a root-mean-square deviation versus the average of 0.49 A for the backbone atoms and 1.12 A for all atoms for residues 6-36 and 46-67. The structure of IF1 is characterized by a five-stranded beta-barrel. The loop connecting strands three and four contains a short 3(10) helix but this region shows considerably higher flexibility than the beta-barrel. The fold of IF1 is very similar to that found in the bacterial cold shock proteins CspA and CspB, the N-terminal domain of aspartyl-tRNA synthetase and the staphylococcal nuclease, and can be identified as the oligomer-binding motif. Several proteins of this family are nucleic acid-binding proteins. This suggests that IF1 plays its role in the initiation of protein synthesis by nucleic acid interactions. Specific changes of NMR signals of IF1 upon titration with 30S ribosomal subunit identifies several residues that are involved in the interaction with ribosomes.
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Affiliation(s)
- M Sette
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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