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Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Vaccines (Basel) 2021; 9:vaccines9070800. [PMID: 34358217 PMCID: PMC8310045 DOI: 10.3390/vaccines9070800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Influenza B virus (IBV) is a major respiratory pathogen of humans, particularly in the elderly and children, and vaccines are the most effective way to control it. In previous work, incorporation of two mutations (E580G, S660A) along with the addition of an HA epitope tag in the PB1 segment of B/Brisbane/60/2008 (B/Bris) resulted in an attenuated strain that was safe and effective as a live attenuated vaccine. A third attempted mutation (K391E) in PB1 was not always stable. Interestingly, viruses that maintained the K391E mutation were associated with the mutation E48K. To explore the contribution of the E48K mutation to stability of the K391E mutation, a vaccine candidate was generated by inserting both mutations, along with attenuating mutations E580G and S660A, in PB1 of B/Bris (B/Bris PB1att 4M). Serial passages of the B/Bris PB1att 4M vaccine candidate in eggs and MDCK indicated high stability. In silico structural analysis revealed a potential interaction between amino acids at positions 48 and 391. In mice, B/Bris PB1att 4M was safe and provided complete protection against homologous challenge. These results confirm the compensatory effect of mutation E48K to stabilize the K391E mutation, resulting in a safer, yet still protective, IBV LAIV vaccine.
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Phadte AS, Mahalingam S, Santhoshkumar P, Sharma KK. Functional Rescue of Cataract-Causing αA-G98R-Crystallin by Targeted Compensatory Suppressor Mutations in Human αA-Crystallin. Biochemistry 2019; 58:4148-4158. [PMID: 31523965 DOI: 10.1021/acs.biochem.9b00374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The G98R mutation in αA-crystallin is associated with the onset of presenile cataract and is characterized biochemically by an increased oligomeric mass, altered chaperone function, and loss of structural stability over time. Thus, far, it is not known whether the inherent instability caused by gain-of-charge mutation could be rescued by a compensatory loss of charge mutation elsewhere on the protein. To answer this question, we investigated whether αA-G98R-mediated instability could be rescued through suppressor mutations by introducing site-specific "compensatory" mutations in αA-G98R-crystallin, αA-R21Q/G98R, αA-G98R/R116C, and αA-R157Q/G98R. The recombinant proteins were expressed, purified, characterized, and evaluated by circular dichroism (CD), intrinsic fluorescence, and bis-ANS-binding studies. Chaperone-like activities of recombinant proteins were assessed using alcohol dehydrogenase (ADH) and insulin as unfolding substrates. Far-UV CD studies revealed an increased α-helical content in αA-G98R in comparison to αA-WT, αA-R21Q, R157Q, and the double mutants, αA-R21Q/G98R, and αA-R157Q/G98R. Compared to αA-WT, αA-R21Q, and αA-G98R, the double mutants showed an increased intrinsic tryptophan fluorescence, whereas the highest hydrophobicity (bis-ANS-binding) was shown by αA-G98R. Introduction of a second mutation in αA-G98R reduced its bis-ANS-binding activity. Both αA-R21Q/G98R and αA-R157Q/G98R showed greater chaperone-like activity against ADH aggregation than αA-G98R. However, among the three G98R mutants, only αA-R21Q/G98R protected ARPE-19 cells from H2O2-induced cytotoxicity. These results suggest that the lost chaperone-like activity of αA-G98R-crystallin can be rescued by another targeted mutation and that substitution of αA-R21Q-crystallin at the N-terminal region can rescue a deleterious mutation in the conserved α-crystallin domain of the protein.
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Affiliation(s)
- Ashutosh S Phadte
- Department of Ophthalmology , University of Missouri School of Medicine , Columbia , Missouri 65212 , United States.,Department of Biochemistry , University of Missouri , Columbia , Missouri 65212 , United States
| | - Sundararajan Mahalingam
- Department of Ophthalmology , University of Missouri School of Medicine , Columbia , Missouri 65212 , United States
| | - Puttur Santhoshkumar
- Department of Ophthalmology , University of Missouri School of Medicine , Columbia , Missouri 65212 , United States
| | - Krishna K Sharma
- Department of Ophthalmology , University of Missouri School of Medicine , Columbia , Missouri 65212 , United States.,Department of Biochemistry , University of Missouri , Columbia , Missouri 65212 , United States
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Cha HJ, Jang DS, Jin KS, Choi KY. Structural analyses combined with small-angle X-ray scattering reveals that the retention of heme is critical for maintaining the structure of horseradish peroxidase under denaturing conditions. Amino Acids 2017; 49:715-723. [PMID: 28144743 DOI: 10.1007/s00726-016-2372-3] [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: 09/02/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022]
Abstract
We analyzed the structure of horseradish peroxidase (HRP) under denaturing conditions of 9 M urea or 6 M guanidine hydrochloride (GdnHCl). Far-UV circular dichroism (CD) spectra indicated the existence of native-like secondary structure of holo-HRP in 9 M urea. In addition, slight changes in near-UV and Soret region CD spectra of holo-HRP in 9 M urea suggest that the tertiary structure of holo-HRP and the binding of heme remain partially intact in this condition. A transition in the thermal unfolding transition curve of holo-HRP in 9 M urea indicated the existence of a considerable amount of secondary structure. However, no secondary structure, tertiary structure, or interaction between heme and HRP were observed in holo-HRP in 6 M GdnHCl. Small-angle X-ray scattering indicated that although distal and proximal domains of holo-HRP in 9 M urea might be partially unfolded, the central region that contains the heme might maintain its tertiary structure. Our results suggest that retention of the heme is essential for maintenance of the structure of HRP under highly denaturing conditions.
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Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Do Soo Jang
- Department of Life Sciences, POSTECH, Pohang, Korea.,Huons Co., Ltd., Seongnam, Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Korea.
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Huang T, Chang CY, Lohman JR, Rudolf JD, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN, Shen B. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. J Antibiot (Tokyo) 2016; 69:731-740. [PMID: 27406907 PMCID: PMC5083130 DOI: 10.1038/ja.2016.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/30/2016] [Accepted: 06/15/2016] [Indexed: 12/28/2022]
Abstract
Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.
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Affiliation(s)
- Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Changsoo Chang
- Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Lance Bigelow
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Shonda Clancy
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA
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Cha HJ, Jang DS, Jeong JH, Hong BH, Yun YS, Shin EJ, Choi KY. Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1322-7. [PMID: 27375051 DOI: 10.1016/j.bbapap.2016.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 06/11/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
Abstract
Ketosteroid isomerase (3-oxosteroid Δ(5)-Δ(4)-isomerase, KSI) from Pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of Δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. The active site of KSI is formed by several hydrophobic residues and three catalytic residues (Tyr14, Asp38, and Asp99). In this study, we investigated the role of a hydrophobic Met112 residue near the active site in the catalysis, steroid binding, and stability of KSI. Replacing Met112 with alanine (yields M112A) or leucine (M112L) decreased the kcat by 20- and 4-fold, respectively. Compared with the wild type (WT), M112A and M112L KSIs showed increased KD values for equilenin, an intermediate analogue; these changes suggest that loss of packing at position 112 might lead to unfavorable steroid binding, thereby resulting in decreased catalytic activity. Furthermore, M112A and M112L mutations reduced melting temperature (Tm) by 6.4°C and 2.5°C, respectively. These changes suggest that favorable packing in the core is important for the maintenance of stability in KSI. The M112K mutation decreased kcat by 2000-fold, compared with the WT. In M112K KSI structure, a new salt bridge was formed between Asp38 and Lys112. This bridge could change the electrostatic potential of Asp38, and thereby contribute to the decreased catalytic activity. The M112K mutation also decreased the stability by reducing Tm by 4.1°C. Our data suggest that the Met112 residue may contribute to the catalytic activity and stability of KSI by providing favorable hydrophobic environments and compact packing in the catalytic core.
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Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Do Soo Jang
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Bee Hak Hong
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Young Sung Yun
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Eun Ju Shin
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kwan Yong Choi
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea.
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Jang DS, Choi G, Cha HJ, Shin S, Hong BH, Lee HJ, Lee HC, Choi KY. Contribution of a low-barrier hydrogen bond to catalysis is not significant in ketosteroid isomerase. Mol Cells 2015; 38:409-15. [PMID: 25947291 PMCID: PMC4443282 DOI: 10.14348/molcells.2015.2266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 02/14/2015] [Accepted: 02/16/2015] [Indexed: 11/27/2022] Open
Abstract
Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. Δ(5)-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Δ(5)-3-ketosteroid to its conjugated Δ(4)-isomers at a rate that approaches the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shift of a proton at 16.8 ppm in the nuclear magnetic resonance spectrum has been attributed to an LBHB between Tyr14 Oη and C3-O of equilenin, an intermediate analogue, in the active site of D38N KSI. This shift in the spectrum was not observed in Y30F/Y55F/D38N and Y30F/Y55F/Y115F/D38N mutant KSIs when each mutant was complexed with equilenin, suggesting that Tyr14 could not form LBHB with the intermediate analogue in these mutant KSIs. The crystal structure of Y30F/Y55F/Y115F/D38N-equilenin complex revealed that the distance between Tyr14 Oη and C3-O of the bound steroid was within a direct hydrogen bond. The conversion of LBHB to an ordinary hydrogen bond in the mutant KSI reduced the binding affinity for the steroid inhibitors by a factor of 8.1-11. In addition, the absence of LBHB reduced the catalytic activity by only a factor of 1.7-2. These results suggest that the amount of stabilization energy of the reaction intermediate provided by LBHB is small compared with that provided by an ordinary hydrogen bond in KSI.
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Affiliation(s)
- Do Soo Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Gildon Choi
- Korea Research Institute of Chemical Technology, Daejeon 305-343,
Korea
| | - Hyung Jin Cha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Sejeong Shin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115,
USA
| | - Bee Hak Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Hyeong Ju Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Hee Cheon Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Kwan Yong Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
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Cha HJ, Jeong JH, Rojviriya C, Kim YG. Structure of putrescine aminotransferase from Escherichia coli provides insights into the substrate specificity among class III aminotransferases. PLoS One 2014; 9:e113212. [PMID: 25423189 PMCID: PMC4244111 DOI: 10.1371/journal.pone.0113212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 10/20/2014] [Indexed: 11/21/2022] Open
Abstract
YgjG is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5′-phosphate (PLP) as a cofactor. Previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. To better understand the enzyme's substrate specificity, crystal structures of YgjG from Escherichia coli were determined at 2.3 and 2.1 Å resolutions for the free and putrescine-bound enzymes, respectively. Sequence and structural analyses revealed that YgjG forms a dimer that adopts a class III PLP-dependent aminotransferase fold. A structural comparison between YgjG and other class III aminotransferases revealed that their structures are similar. However, YgjG has an additional N-terminal helical structure that partially contributes to a dimeric interaction with the other subunit via a helix-helix interaction. Interestingly, the YgjG substrate-binding site entrance size and charge distribution are smaller and more hydrophobic than other class III aminotransferases, which suggest that YgjG has a unique substrate binding site that could accommodate primary aliphatic diamine substrates, including putrescine. The YgjG crystal structures provide structural clues to putrescine aminotransferase substrate specificity and binding.
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Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Korea
| | - Catleya Rojviriya
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Korea
- * E-mail:
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