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Günther J, Schuler G, Teppa E, Fürbass R. Charged Amino Acids in the Transmembrane Helix Strongly Affect the Enzyme Activity of Aromatase. Int J Mol Sci 2024; 25:1440. [PMID: 38338720 PMCID: PMC10855386 DOI: 10.3390/ijms25031440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Estrogens play critical roles in embryonic development, gonadal sex differentiation, behavior, and reproduction in vertebrates and in several human cancers. Estrogens are synthesized from testosterone and androstenedione by the endoplasmic reticulum membrane-bound P450 aromatase/cytochrome P450 oxidoreductase complex (CYP19/CPR). Here, we report the characterization of novel mammalian CYP19 isoforms encoded by CYP19 gene copies. These CYP19 isoforms are all defined by a combination of mutations in the N-terminal transmembrane helix (E42K, D43N) and in helix C of the catalytic domain (P146T, F147Y). The mutant CYP19 isoforms show increased androgen conversion due to the KN transmembrane helix. In addition, the TY substitutions in helix C result in a substrate preference for androstenedione. Our structural models suggest that CYP19 mutants may interact differently with the membrane (affecting substrate uptake) and with CPR (affecting electron transfer), providing structural clues for the catalytic differences.
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Affiliation(s)
- Juliane Günther
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Gerhard Schuler
- Veterinary Clinic for Reproductive Medicine and Neonatology, Faculty of Veterinary Medicine, Justus Liebig University, 35392 Giessen, Germany;
| | - Elin Teppa
- Université de Lille, CNRS, UMR 8576–UGDF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France;
| | - Rainer Fürbass
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
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2
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Slanina H, Madhugiri R, Wenk K, Reinke T, Schultheiß K, Schultheis J, Karl N, Linne U, Ziebuhr J. Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains. J Virol 2023; 97:e0046523. [PMID: 37199624 PMCID: PMC10308930 DOI: 10.1128/jvi.00465-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents the central functional subunit. It harbors the RNA-directed RNA polymerase (RdRp) domain and contains, at its N terminus, an additional domain called NiRAN which is widely conserved in coronaviruses and other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate and compare NiRAN-mediated NMPylation activities from representative alpha- and betacoronaviruses. We found that the four coronavirus NiRAN domains characterized to date have a number of conserved properties, including (i) robust nsp9-specific NMPylation activities that appear to operate largely independently of the C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed by ATP and other nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, and (iv) a key role of N-terminal residues (particularly Asn2) of nsp9 for efficient formation of a covalent phosphoramidate bond between NMP and the N-terminal amino group of nsp9. In this context, a mutational analysis confirmed the conservation and critical role of Asn2 across different subfamilies of the family Coronaviridae, as shown by studies using chimeric coronavirus nsp9 variants in which six N-terminal residues were replaced with those from other corona-, pito- and letovirus nsp9 homologs. The combined data of this and previous studies reveal a remarkable degree of conservation among coronavirus NiRAN-mediated NMPylation activities, supporting a key role of this enzymatic activity in viral RNA synthesis and processing. IMPORTANCE There is strong evidence that coronaviruses and other large nidoviruses evolved a number of unique enzymatic activities, including an additional RdRp-associated NiRAN domain, that are conserved in nidoviruses but not in most other RNA viruses. Previous studies of the NiRAN domain mainly focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and suggested different functions for this domain, such as NMPylation/RNAylation of nsp9, RNA guanylyltransferase activities involved in canonical and/or unconventional RNA capping pathways, and other functions. To help resolve partly conflicting information on substrate specificities and metal ion requirements reported previously for the SARS-CoV-2 NiRAN NMPylation activity, we extended these earlier studies by characterizing representative alpha- and betacoronavirus NiRAN domains. The study revealed that key features of NiRAN-mediated NMPylation activities, such as protein and nucleotide specificity and metal ion requirements, are very well conserved among genetically divergent coronaviruses, suggesting potential avenues for future antiviral drug development targeting this essential viral enzyme.
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Affiliation(s)
- Heiko Slanina
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - Kai Wenk
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Tess Reinke
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Karin Schultheiß
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Julia Schultheis
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Philipps University, Marburg, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
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3
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Bankapur S, Patil N. Enhanced Protein Structural Class Prediction Using Effective Feature Modeling and Ensemble of Classifiers. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:2409-2419. [PMID: 32149653 DOI: 10.1109/tcbb.2020.2979430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein Secondary Structural Class (PSSC) information is important in investigating further challenges of protein sequences like protein fold recognition, protein tertiary structure prediction, and analysis of protein functions for drug discovery. Identification of PSSC using biological methods is time-consuming and cost-intensive. Several computational models have been developed to predict the structural class; however, they lack in generalization of the model. Hence, predicting PSSC based on protein sequences is still proving to be an uphill task. In this article, we proposed an effective, novel and generalized prediction model consisting of a feature modeling and an ensemble of classifiers. The proposed feature modeling extracts discriminating information (features) by leveraging three techniques: (i) Embedding - features are extracted on the basis of spatial residue arrangements of the sequences using word embedding approaches; (ii) SkipXGram Bi-gram - various sets of skipped bi-gram features are extracted from the sequences; and (iii) General Statistical (GS) based features are extracted which covers the global information of structural sequences. The combined effective sets of features are trained and classified using an ensemble of three classifiers: Support Vector Machine (SVM), Random Forest (RF), and Gradient Boosting Machines (GBM). The proposed model when assessed on five benchmark datasets (high and low sequence similarity), viz. z277, z498, 25PDB, 1189, and FC699, reported an overall accuracy of 93.55, 97.58, 81.82, 81.11, and 93.93 percent respectively. The proposed model is further validated on a large-scale updated low similarity ( ≤ 25%) dataset, where it achieved an overall accuracy of 81.11 percent. The proposed generalized model is robust and consistently outperformed several state-of-the-art models on all the five benchmark datasets.
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4
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Taujale R, Zhou Z, Yeung W, Moremen KW, Li S, Kannan N. Mapping the glycosyltransferase fold landscape using interpretable deep learning. Nat Commun 2021; 12:5656. [PMID: 34580305 PMCID: PMC8476585 DOI: 10.1038/s41467-021-25975-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/31/2021] [Indexed: 12/28/2022] Open
Abstract
Glycosyltransferases (GTs) play fundamental roles in nearly all cellular processes through the biosynthesis of complex carbohydrates and glycosylation of diverse protein and small molecule substrates. The extensive structural and functional diversification of GTs presents a major challenge in mapping the relationships connecting sequence, structure, fold and function using traditional bioinformatics approaches. Here, we present a convolutional neural network with attention (CNN-attention) based deep learning model that leverages simple secondary structure representations generated from primary sequences to provide GT fold prediction with high accuracy. The model learns distinguishing secondary structure features free of primary sequence alignment constraints and is highly interpretable. It delineates sequence and structural features characteristic of individual fold types, while classifying them into distinct clusters that group evolutionarily divergent families based on shared secondary structural features. We further extend our model to classify GT families of unknown folds and variants of known folds. By identifying families that are likely to adopt novel folds such as GT91, GT96 and GT97, our studies expand the GT fold landscape and prioritize targets for future structural studies.
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Affiliation(s)
- Rahil Taujale
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Zhongliang Zhou
- Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Sheng Li
- Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
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5
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Song J, Castillo-González C, Ma Z, Shippen DE. Arabidopsis retains vertebrate-type telomerase accessory proteins via a plant-specific assembly. Nucleic Acids Res 2021; 49:9496-9507. [PMID: 34403479 PMCID: PMC8450087 DOI: 10.1093/nar/gkab699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
The recent discovery of the bona-fide telomerase RNA (TR) from plants reveals conserved and unique secondary structure elements and the opportunity for new insight into the telomerase RNP. Here we examine how two highly conserved proteins previously implicated in Arabidopsis telomere maintenance, AtPOT1a and AtNAP57 (dyskerin), engage plant telomerase. We report that AtPOT1a associates with Arabidopsis telomerase via interaction with TERT. While loss of AtPOT1a does not impact AtTR stability, the templating domain is more accessible in pot1a mutants, supporting the conclusion that AtPOT1a stimulates telomerase activity but does not facilitate telomerase RNP assembly. We also show, that despite the absence of a canonical H/ACA binding motif within AtTR, dyskerin binds AtTR with high affinity and specificity in vitro via a plant specific three-way junction (TWJ). A core element of the TWJ is the P1a stem, which unites the 5′ and 3′ ends of AtTR. P1a is required for dyskerin-mediated stimulation of telomerase repeat addition processivity in vitro, and for AtTR accumulation and telomerase activity in vivo. The deployment of vertebrate-like accessory proteins and unique RNA structural elements by Arabidopsis telomerase provides a new platform for exploring telomerase biogenesis and evolution.
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Affiliation(s)
- Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Zeyang Ma
- National Maize Improvement Center of China, China Agricultural University, 100193 Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, 100193 Beijing, China
| | - Dorothy E Shippen
- To whom correspondence should be addressed. Tel: +1 979 862 2342; Fax: +1 979 862 7638;
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6
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Lindquist P, Madsen JS, Bräuner-Osborne H, Rosenkilde MM, Hauser AS. Mutational Landscape of the Proglucagon-Derived Peptides. Front Endocrinol (Lausanne) 2021; 12:698511. [PMID: 34220721 PMCID: PMC8248487 DOI: 10.3389/fendo.2021.698511] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/24/2021] [Indexed: 12/18/2022] Open
Abstract
Strong efforts have been placed on understanding the physiological roles and therapeutic potential of the proglucagon peptide hormones including glucagon, GLP-1 and GLP-2. However, little is known about the extent and magnitude of variability in the amino acid composition of the proglucagon precursor and its mature peptides. Here, we identified 184 unique missense variants in the human proglucagon gene GCG obtained from exome and whole-genome sequencing of more than 450,000 individuals across diverse sub-populations. This provides an unprecedented source of population-wide genetic variation data on missense mutations and insights into the evolutionary constraint spectrum of proglucagon-derived peptides. We show that the stereotypical peptides glucagon, GLP-1 and GLP-2 display fewer evolutionary alterations and are more likely to be functionally affected by genetic variation compared to the rest of the gene products. Elucidating the spectrum of genetic variations and estimating the impact of how a peptide variant may influence human physiology and pathophysiology through changes in ligand binding and/or receptor signalling, are vital and serve as the first important step in understanding variability in glucose homeostasis, amino acid metabolism, intestinal epithelial growth, bone strength, appetite regulation, and other key physiological parameters controlled by these hormones.
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Affiliation(s)
- Peter Lindquist
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob S. Madsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette M. Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexander S. Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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7
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Irumagawa S, Kobayashi K, Saito Y, Miyata T, Umetsu M, Kameda T, Arai R. Rational thermostabilisation of four-helix bundle dimeric de novo proteins. Sci Rep 2021; 11:7526. [PMID: 33824364 PMCID: PMC8024369 DOI: 10.1038/s41598-021-86952-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
The stability of proteins is an important factor for industrial and medical applications. Improving protein stability is one of the main subjects in protein engineering. In a previous study, we improved the stability of a four-helix bundle dimeric de novo protein (WA20) by five mutations. The stabilised mutant (H26L/G28S/N34L/V71L/E78L, SUWA) showed an extremely high denaturation midpoint temperature (Tm). Although SUWA is a remarkably hyperstable protein, in protein design and engineering, it is an attractive challenge to rationally explore more stable mutants. In this study, we predicted stabilising mutations of WA20 by in silico saturation mutagenesis and molecular dynamics simulation, and experimentally confirmed three stabilising mutations of WA20 (N22A, N22E, and H86K). The stability of a double mutant (N22A/H86K, rationally optimised WA20, ROWA) was greatly improved compared with WA20 (ΔTm = 10.6 °C). The model structures suggested that N22A enhances the stability of the α-helices and N22E and H86K contribute to salt-bridge formation for protein stabilisation. These mutations were also added to SUWA and improved its Tm. Remarkably, the most stable mutant of SUWA (N22E/H86K, rationally optimised SUWA, ROSA) showed the highest Tm (129.0 °C). These new thermostable mutants will be useful as a component of protein nanobuilding blocks to construct supramolecular protein complexes.
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Affiliation(s)
- Shin Irumagawa
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano, 390-8621, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan
| | - Kaito Kobayashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
| | - Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, 169-8555, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Takeshi Miyata
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
| | - Ryoichi Arai
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan.
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano, 390-8621, Japan.
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan.
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8
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Jing X, Dong Q, Hong D, Lu R. Amino Acid Encoding Methods for Protein Sequences: A Comprehensive Review and Assessment. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:1918-1931. [PMID: 30998480 DOI: 10.1109/tcbb.2019.2911677] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
As the first step of machine-learning based protein structure and function prediction, the amino acid encoding play a fundamental role in the final success of those methods. Different from the protein sequence encoding, the amino acid encoding can be used in both residue-level and sequence-level prediction of protein properties by combining them with different algorithms. However, it has not attracted enough attention in the past decades, and there are no comprehensive reviews and assessments about encoding methods so far. In this article, we make a systematic classification and propose a comprehensive review and assessment for various amino acid encoding methods. Those methods are grouped into five categories according to their information sources and information extraction methodologies, including binary encoding, physicochemical properties encoding, evolution-based encoding, structure-based encoding, and machine-learning encoding. Then, 16 representative methods from five categories are selected and compared on protein secondary structure prediction and protein fold recognition tasks by using large-scale benchmark datasets. The results show that the evolution-based position-dependent encoding method PSSM achieved the best performance, and the structure-based and machine-learning encoding methods also show some potential for further application, the neural network based distributed representation of amino acids in particular may bring new light to this area. We hope that the review and assessment are useful for future studies in amino acid encoding.
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9
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Kulcsár PI, Tálas A, Tóth E, Nyeste A, Ligeti Z, Welker Z, Welker E. Blackjack mutations improve the on-target activities of increased fidelity variants of SpCas9 with 5'G-extended sgRNAs. Nat Commun 2020; 11:1223. [PMID: 32144253 PMCID: PMC7060260 DOI: 10.1038/s41467-020-15021-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/06/2020] [Indexed: 12/17/2022] Open
Abstract
Increased fidelity mutants of the SpCas9 nuclease constitute the most promising approach to mitigating its off-target effects. However, these variants are effective only in a restricted target space, and many of them are reported to work less efficiently when applied in clinically relevant, pre-assembled, ribonucleoprotein forms. The low tolerance to 5'-extended, 21G-sgRNAs contributes, to a great extent, to their decreased performance. Here, we report the generation of Blackjack SpCas9 variant that shows increased fidelity yet remain effective with 21G-sgRNAs. Introducing Blackjack mutations into previously reported increased fidelity variants make them effective with 21G-sgRNAs and increases their fidelity. Two "Blackjack" nucleases, eSpCas9-plus and SpCas9-HF1-plus are superior variants of eSpCas9 and SpCas9-HF1, respectively, possessing matching on-target activity and fidelity but retaining activity with 21G-sgRNAs. They facilitate the use of existing pooled sgRNA libraries with higher specificity and show similar activities whether delivered as plasmids or as pre-assembled ribonucleoproteins.
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Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary.
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary
- Gene Design Ltd, Szeged, H-6726, Hungary
| | | | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
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10
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Figiel M, Łakomska J, Dziedzicka-Wasylewska M, Górecki A. The effect of D380Y pathogenic mutation in human Yin Yang 1 on the protein's structure and function. Acta Biochim Pol 2020; 67:73-77. [PMID: 32077676 DOI: 10.18388/abp.2020_2911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/26/2020] [Indexed: 11/10/2022]
Abstract
Yin Yang 1 is a human transcription factor that controls a number of genes and takes part in the regulation of cell cycle, proliferation, differentiation, and neuronal development. Yin Yang 1 is composed of an N-terminal intrinsically disordered fragment and a C-terminal domain responsible for binding to DNA, composed of four zinc fingers. Recently, various alterations in the Yin Yang 1's DNA binding domain were linked with an unexplained intellectual disability named Gabriele-de Vries syndrome. In this paper, a repetitively occurring substitution of aspartate-380 for tyrosine was analyzed to assess its impact on Yin Yang 1's structure and DNA binding. The substitution was found to affect Yin Yang 1's secondary and tertiary structure to a limited extent and to impair the specificity of its interaction with DNA.
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Affiliation(s)
- Małgorzata Figiel
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Julia Łakomska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Andrzej Górecki
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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11
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Espasa A, Lang M, Aguiño CF, Sanchez-deAlcazar D, Fernández-Blázquez JP, Sonnewald U, Cortajarena AL, Coto PB, Costa RD. Long-living and highly efficient bio-hybrid light-emitting diodes with zero-thermal-quenching biophosphors. Nat Commun 2020; 11:879. [PMID: 32054851 PMCID: PMC7018753 DOI: 10.1038/s41467-020-14559-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023] Open
Abstract
Bio-hybrid light-emitting diodes (Bio-HLEDs) based on color down-converting filters with fluorescent proteins (FPs) have achieved moderate efficiencies (50 lm/W) and stabilities (300 h) due to both thermal- and photo-degradation. Here, we present a significant enhancement in efficiency (~130 lm/W) and stability (>150 days) using a zero-thermal-quenching bio-phosphor design. This is achieved shielding the FP surface with a hydrophilic polymer allowing their homogenous integration into the network of a light-guiding and hydrophobic host polymer. We rationalize how the control of the mechanical and optical features of this bio-phosphor is paramount towards highly stable and efficient Bio-HLEDs, regardless of the operation conditions. This is validated by the relationships between the stiffness of the FP-polymer phosphor and the maximum temperature reached under device operation as well as the transmittance of the filters and device efficiency.
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Affiliation(s)
- Anna Espasa
- IMDEA Materials Institute, Calle Eric Kandel 2, 28906, Getafe, Spain
| | - Martina Lang
- Department of Biology, Friedrich-Alexander-University of Erlangen-Nuremberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Carmen F Aguiño
- IMDEA Materials Institute, Calle Eric Kandel 2, 28906, Getafe, Spain
| | - Daniel Sanchez-deAlcazar
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Uwe Sonnewald
- Department of Biology, Friedrich-Alexander-University of Erlangen-Nuremberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, María Diaz de Haro 3, 48013, Bilbao, Spain
| | - Pedro B Coto
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julián Clavería 8, 33006, Oviedo, Spain
| | - Rubén D Costa
- IMDEA Materials Institute, Calle Eric Kandel 2, 28906, Getafe, Spain.
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12
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Anwar S, Kar RK, Haque MA, Dahiya R, Gupta P, Islam A, Ahmad F, Hassan MI. Effect of pH on the structure and function of pyruvate dehydrogenase kinase 3: Combined spectroscopic and MD simulation studies. Int J Biol Macromol 2020; 147:768-777. [PMID: 31982536 DOI: 10.1016/j.ijbiomac.2020.01.218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Pyruvate dehydrogenase kinase-3 (PDK3) plays important role in the glucose metabolism and is associated with cancer progression, and thus being considered as an attractive target for cancer therapy. In this study, we employed spectroscopic techniques to study the structural and conformational changes in the PDK3 at varying pH conditions ranging from pH 2.0 to 12.0. UV/Vis, fluorescence and circular dichroism spectroscopic measurements revealed that PDK3 maintains its native-like structure (both secondary and tertiary) in the alkaline conditions (pH 7.0-12.0). However, a significant loss in the structure was observed under acidic conditions (pH 2.0-6.0). The propensity of aggregate formation at pH 4.0 was estimated by thioflavin T fluorescence measurements. To further complement structural data, kinase activity assay was performed, and maximum activity of PDK3 was observed at pH 7.0-8.0 range; whereas, its activity was lost under acidic pH. To further see conformational changes at atomistic level we have performed all-atom molecular dynamics at different pH conditions for 150 ns. A well defined correlation was observed between experimental and computational studies. This work highlights the significance of structural dependence of pH for wide implications in protein-protein interaction, biological function and drug design procedures.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamic Research, Hebrew University of Jerusalem, Israel
| | - Md Anzarul Haque
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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13
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Abstract
A new paradigm has emerged that coding regions can regulate mRNA stability in model organisms. Here, due to differences in cognate tRNA abundance, synonymous codons are translated at different speeds, and slow codons then stimulate mRNA decay. To ask if this phenomenon also occurs in humans, we isolated RNA stability effects due to coding regions using the human ORFeome collection. We find that many open reading frame (ORF) characteristics, such as length and secondary structure, fail to provide explanations for how coding regions alter mRNA stability, and, instead, that the ORF relies on translation to impact mRNA stability. Consistent with what has been seen in other organisms, codon use is related to the effects of ORFs on transcript stability. Importantly, we found instability-associated codons have longer A-site dwell times, suggesting for the first time in humans a connection between elongation speed and mRNA decay. Thus, we propose that codon usage alters decoding speeds and so affects human mRNA stability.
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Affiliation(s)
- Ashrut Narula
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - James Ellis
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - J Matthew Taliaferro
- RNA Bioscience Initiative and Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Olivia S Rissland
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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14
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Guevara T, Körschgen H, Cuppari A, Schmitz C, Kuske M, Yiallouros I, Floehr J, Jahnen-Dechent W, Stöcker W, Gomis-Rüth FX. The C-terminal region of human plasma fetuin-B is dispensable for the raised-elephant-trunk mechanism of inhibition of astacin metallopeptidases. Sci Rep 2019; 9:14683. [PMID: 31604990 PMCID: PMC6789097 DOI: 10.1038/s41598-019-51095-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/24/2019] [Indexed: 01/07/2023] Open
Abstract
Human fetuin-B plays a key physiological role in human fertility through its inhibitory action on ovastacin, a member of the astacin family of metallopeptidases. The inhibitor consists of tandem cystatin-like domains (CY1 and CY2), which are connected by a linker containing a "CPDCP-trunk" and followed by a C-terminal region (CTR) void of regular secondary structure. Here, we solved the crystal structure of the complex of the inhibitor with archetypal astacin from crayfish, which is a useful model of human ovastacin. Two hairpins from CY2, the linker, and the tip of the "legumain-binding loop" of CY1 inhibit crayfish astacin following the "raised-elephant-trunk mechanism" recently reported for mouse fetuin-B. This inhibition is exerted by blocking active-site cleft sub-sites upstream and downstream of the catalytic zinc ion, but not those flanking the scissile bond. However, contrary to the mouse complex, which was obtained with fetuin-B nicked at a single site but otherwise intact, most of the CTR was proteolytically removed during crystallization of the human complex. Moreover, the two complexes present in the crystallographic asymmetric unit diverged in the relative arrangement of CY1 and CY2, while the two complexes found for the mouse complex crystal structure were equivalent. Biochemical studies in vitro confirmed the differential cleavage susceptibility of human and mouse fetuin-B in front of crayfish astacin and revealed that the cleaved human inhibitor blocks crayfish astacin and human meprin α and β only slightly less potently than the intact variant. Therefore, the CTR of animal fetuin-B orthologs may have a function in maintaining a particular relative orientation of CY1 and CY2 that nonetheless is dispensable for peptidase inhibition.
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Affiliation(s)
- Tibisay Guevara
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028, Barcelona, Catalonia, Spain
| | - Hagen Körschgen
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - Anna Cuppari
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028, Barcelona, Catalonia, Spain
| | - Carlo Schmitz
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstr. 30, D-52074, Aachen, Germany
| | - Michael Kuske
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - Julia Floehr
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstr. 30, D-52074, Aachen, Germany
| | - Willi Jahnen-Dechent
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstr. 30, D-52074, Aachen, Germany
| | - Walter Stöcker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028, Barcelona, Catalonia, Spain.
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15
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Naushad SM, Rama Devi AR, Hussain T, Alrokayan SA, Janaki Ramaiah M, Kutala VK. In silico analysis of the structural and functional implications of SLC19A1 R27H polymorphism. J Genet 2019; 98:85. [PMID: 31544789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In view of the documented association of solute carrier family 19 member 1 (SLC19A1) G80A (R27H) polymorphism with the risk for different types of cancers and systemic lupus erythematosus (SLE), we have reanalysed the case-control study on breast cancer to ascertain the conditions in which this polymorphic variant exerts the risk of breast cancer. Association statistics have revealed that this polymorphism exerts the risk for breast cancer under the conditions of low folate intake, and in the absence of well-documented protective polymorphism in cytosolic serine hydroxymethyltransferase. To substantiate this observation, we have developed a homology model of SLC19A1 using glycerol-3-phosphate transporter (d1pw4a) as a template where 73% of the residues were modelled at 90% confidence while 162 residues were modelled ab initio. The wild and mutant proteins shared same topology in S3, S5, S6, S7, S11 and S12 transmembrane domains. The topology varied at S1 (28-43 residue vs 28-44 residue), S2 (66-87 residue vs 69-87 residue), S4 (117-140 residue vs 117-139 residue), S8 (305-325 residue vs 305-324 residue), S9 (336-356 residue vs 336-355residue), and S10 (361-386 residue vs 361-385 residue) transmembrane domains between wild versus mutant proteins. S2 domain is shortened by three amino acid residues in the mutant while in other domains the difference corresponds to one amino acid residue. The 3DLigandSite analysis revealed that the metallic-ligand-binding sites at 273Trp, 277Asn, 379Leu, 439Phe and 442Leu are although unaffected, there is a loss of active sites corresponding to nonmetallic ligand binding. Tetrahydrofolate and methotrexate have lesser affinity towards the mutant protein than the wild protein. To conclude, the R27H polymorphism affects the secondary and tertiary structures of SLC19A1 with the significant loss in ligand-binding sites.
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Abstract
In the search for enzymatically processed RNA fragments, we found the novel three-way junction motif. The structure prediction suggested the arrangement of helices at acute angle approx. 60°. This allows the design of a trimeric RNA nanoparticle that can be functionalized with multiple regulatory fragments. Such RNA nano-object of equilateral triangular shape was applied for gene expression regulation studies in two independent cellular systems. Biochemical and functional studies confirmed the predicted shape and structure of the nanoparticle. The regulatory siRNA fragments incorporated into the nanoparticle were effectively released and triggered gene silencing. The regulatory effect was prolonged when induced with structuralized RNA compared to unstructured siRNAs. In these studies, the enzymatic processing of the motif was utilized for function release from the nanoparticle, enabling simultaneous delivery of different regulatory functions. This methodology of sequence search, RNA structural prediction, and application for rational design opens a new way for creating enzymatically processed RNA nanoparticles.
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Affiliation(s)
- Dominika Jedrzejczyk
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , 90-363 Lodz , Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , 90-363 Lodz , Poland
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17
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Banerjee A, Ray S. Molecular interactions and mutational impact upon rhodopsin (G90→D90) for hindering dark adaptation of eye: A comparative structural level outlook for signaling mechanism in night blindness. Mutat Res 2019; 814:7-14. [PMID: 30659944 DOI: 10.1016/j.mrfmmm.2019.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/17/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
For night blindness, a detailed structural exploration of the interactions among G-protein receptor rhodopsin, transducin and arrestin was performed. Rhodopsin is responsible for dim light vision while a point mutation (G90→D90) results in an adverse change in its photo-transduction. The validated 3D models of the three proteins were utilized, and upon mutation and interactions, rhodopsin attained higher stability (evaluated through thermodynamic energy calculations, electrostatic surface potential and solvent accessible area), thereby participating strongly with transducin. Conformational switches in mutated rhodopsin also depicted a firm conformation with few 310 helices accompanied by increased percentage of pure α-helices and sheets. All evaluations were corroborated through paired T-tests. Glu33 (glycosylated unit in the N-terminal zone) of rhodopsin plays a chief role in the overall interaction pattern. Arg69 and Glu33 from wild-type rhodopsin participated in ionic interactions, while the latter set of ionic interaction remained preserved even after mutation. Cys323 (C-terminal residue) and Arg69 formed H-bonds from the wild-type rhodopsin. Cys323 exceptionally supports cellular signaling pattern in the non-mutated situation and for the non-sufferers of night-blindness. Ser297 and Tyr43 from mutated rhodopsin reside in helices and interact with Thr32 of transducin, preserving the steady conformation in activated interacted state, even in the dark. Ser297 lies adjoined to Lys296 (retinal attachment site), which resides in NPXXY motif (an "activation switch" for signal transduction). Thus, the molecular facet for involvement of photo-transduction, which holds a paramount zone in ophthalmology, was dealt with. This might instigate the future prospect for drug discovery to prevent such mutations.
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Affiliation(s)
- Arundhati Banerjee
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India.
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18
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Ying L, Zhu H, Shoji S, Fredrick K. Roles of specific aminoglycoside-ribosome interactions in the inhibition of translation. RNA 2019; 25:247-254. [PMID: 30413565 PMCID: PMC6348987 DOI: 10.1261/rna.068460.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/06/2018] [Indexed: 05/18/2023]
Abstract
Aminoglycosides containing a 2-deoxystreptamine core (AGs) represent a large family of antibiotics that target the ribosome. These compounds promote miscoding, inhibit translocation, and inhibit ribosome recycling. AG binding to helix h44 of the small subunit induces rearrangement of A-site nucleotides A1492 and A1493, which promotes a key open-to-closed conformational change of the subunit and thereby increases miscoding. Mechanisms by which AGs inhibit translocation and recycling remain less clear. Structural studies have revealed a secondary AG binding site in H69 of the large subunit, and it has been proposed that interaction at this site is crucial for inhibition of translocation and recycling. Here, we analyze ribosomes with mutations targeting either or both AG binding sites. Assaying translocation, we find that ablation of the h44 site increases the IC50 values for AGs dramatically, while removal of the H69 site increases these values modestly. This suggests that the AG-h44 interaction is primarily responsible for inhibition, with H69 playing a minor role. Assaying recycling, we find that mutation of h44 has no effect on AG inhibition, consistent with a primary role for AG-H69 interaction. Collectively, these findings help clarify the roles of the two AG binding sites in mechanisms of inhibition by these compounds.
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Affiliation(s)
- Lanqing Ying
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hongkun Zhu
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shinichiro Shoji
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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19
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Semenyshyn R, Hentschel M, Stanglmair C, Teutsch T, Tarin C, Pacholski C, Giessen H, Neubrech F. In Vitro Monitoring Conformational Changes of Polypeptide Monolayers Using Infrared Plasmonic Nanoantennas. Nano Lett 2019; 19:1-7. [PMID: 30071729 DOI: 10.1021/acs.nanolett.8b02372] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proteins and peptides play a predominant role in biochemical reactions of living cells. In these complex environments, not only the constitution of the molecules but also their three-dimensional configuration defines their functionality. This so-called secondary structure of proteins is crucial for understanding their function in living matter. Misfolding, for example, is suspected as the cause of neurodegenerative diseases such as Alzheimer's and Parkinson's disease. Ultimately, it is necessary to study a single protein and its folding dynamics. Here, we report a first step in this direction, namely ultrasensitive detection and discrimination of in vitro polypeptide folding and unfolding processes using resonant plasmonic nanoantennas for surface-enhanced vibrational spectroscopy. We utilize poly-l-lysine as a model system which has been functionalized on the gold surface. By in vitro infrared spectroscopy of a single molecular monolayer at the amide I vibrations we directly monitor the reversible conformational changes between α-helix and β-sheet states induced by controlled external chemical stimuli. Our scheme in combination with advanced positioning of the peptides and proteins and more brilliant light sources is highly promising for ultrasensitive in vitro studies down to the single protein level.
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Affiliation(s)
- Rostyslav Semenyshyn
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Center for Integrated Quantum Science and Technology , IQST , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
| | - Mario Hentschel
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Center for Integrated Quantum Science and Technology , IQST , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
| | - Christoph Stanglmair
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 1 , 70569 Stuttgart , Germany
| | - Tanja Teutsch
- Institute for System Dynamics , University of Stuttgart , Waldburgstraße 17/19 , 70563 Stuttgart , Germany
| | - Cristina Tarin
- Institute for System Dynamics , University of Stuttgart , Waldburgstraße 17/19 , 70563 Stuttgart , Germany
| | - Claudia Pacholski
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 1 , 70569 Stuttgart , Germany
- Institute of Chemistry , University of Potsdam , Am Mühlenberg 3 , 14476 Potsdam OT Golm , Germany
| | - Harald Giessen
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Center for Integrated Quantum Science and Technology , IQST , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
| | - Frank Neubrech
- 4th Physics Institute and Research Center SCoPE , University of Stuttgart , Pfaffenwaldring 57 , 70569 Stuttgart , Germany
- Kirchhoff Institute for Physics , University of Heidelberg , Im Neuenheimer Feld 227 , 69120 Heidelberg , Germany
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20
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Cheng CW, Putaporntip C, Jongwutiwes S. Polymorphism in merozoite surface protein-7E of Plasmodium vivax in Thailand: Natural selection related to protein secondary structure. PLoS One 2018; 13:e0196765. [PMID: 29718980 PMCID: PMC5931635 DOI: 10.1371/journal.pone.0196765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/19/2018] [Indexed: 11/18/2022] Open
Abstract
Merozoite surface protein 7 (MSP-7) is a multigene family expressed during malaria blood-stage infection. MSP-7 forms complex with MSP-1 prior to merozoite egress from erythrocytes, and could affect merozoite invasion of erythrocytes. To characterize sequence variation in the orthologue in P. vivax (PvMSP-7), a gene member encoding PvMSP-7E was analyzed among 92 Thai isolates collected from 3 major endemic areas of Thailand (Northwest: Tak, Northeast: Ubon Ratchathani, and South: Yala and Narathiwat provinces). In total, 52 distinct haplotypes were found to circulate in these areas. Although population structure based on this locus was observed between each endemic area, no genetic differentiation occurred between populations collected from different periods in the same endemic area, suggesting spatial but not temporal genetic variation. Sequence microheterogeneity in both N- and C- terminal regions was predicted to display 4 and 6 α-helical domains, respectively. Signals of purifying selection were observed in α-helices II-X, suggesting structural or functional constraint in these domains. By contrast, α-helix-I spanning the putative signal peptide was under positive selection, in which amino acid substitutions could alter predicted CD4+ T helper cell epitopes. The central region of PvMSP-7E comprised the 5’-trimorphic and the 3’-dimorphic subregions. Positive selection was identified in the 3’ dimorphic subregion of the central domain. A consensus of intrinsically unstructured or disordered protein was predicted to encompass the entire central domain that contained a number of putative B cell epitopes and putative protein binding regions. Evidences of intragenic recombination were more common in the central region than the remainders of the gene. These results suggest that the extent of sequence variation, recombination events and selective pressures in the PvMSP-7E locus seem to be differentially affected by protein secondary structure.
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Affiliation(s)
- Chew Weng Cheng
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Somchai Jongwutiwes
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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21
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Frischauf I, Litviňuková M, Schober R, Zayats V, Svobodová B, Bonhenry D, Lunz V, Cappello S, Tociu L, Reha D, Stallinger A, Hochreiter A, Pammer T, Butorac C, Muik M, Groschner K, Bogeski I, Ettrich RH, Romanin C, Schindl R. Transmembrane helix connectivity in Orai1 controls two gates for calcium-dependent transcription. Sci Signal 2017; 10:eaao0358. [PMID: 29184031 PMCID: PMC6433236 DOI: 10.1126/scisignal.aao0358] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The channel Orai1 requires Ca2+ store depletion in the endoplasmic reticulum and an interaction with the Ca2+ sensor STIM1 to mediate Ca2+ signaling. Alterations in Orai1-mediated Ca2+ influx have been linked to several pathological conditions including immunodeficiency, tubular myopathy, and cancer. We screened large-scale cancer genomics data sets for dysfunctional Orai1 mutants. Five of the identified Orai1 mutations resulted in constitutively active gating and transcriptional activation. Our analysis showed that certain Orai1 mutations were clustered in the transmembrane 2 helix surrounding the pore, which is a trigger site for Orai1 channel gating. Analysis of the constitutively open Orai1 mutant channels revealed two fundamental gates that enabled Ca2+ influx: Arginine side chains were displaced so they no longer blocked the pore, and a chain of water molecules formed in the hydrophobic pore region. Together, these results enabled us to identify a cluster of Orai1 mutations that trigger Ca2+ permeation associated with gene transcription and provide a gating mechanism for Orai1.
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Affiliation(s)
- Irene Frischauf
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
| | - Monika Litviňuková
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Cardiovascular and Metabolic Sciences, Berlin D-13125, Germany
| | - Romana Schober
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
| | - Vasilina Zayats
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady CZ-373 33, Czech Republic
- Center of New Technologies, University of Warsaw, Warsaw 02-097, Poland
| | - Barbora Svobodová
- Institute for Biophysics, Medical University of Graz, Graz A-8010, Austria
| | - Daniel Bonhenry
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady CZ-373 33, Czech Republic
| | - Victoria Lunz
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
| | - Sabrina Cappello
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University Göttingen, Göttingen, Niedersachsen 37073, Germany
- Department of Biophysics, Center for Integrative Physiology and Molecular Medicine, Medical Faculty, Saarland University, Homburg D-66421, Germany
| | - Laura Tociu
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady CZ-373 33, Czech Republic
- University of Chicago, Chicago, IL 60637, USA
| | - David Reha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady CZ-373 33, Czech Republic
- Faculty of Sciences, University of South Bohemia, Nové Hrady CZ-373 33, Czech Republic
| | - Amrutha Stallinger
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Graz A-8010, Austria
| | - Anna Hochreiter
- Institute for Experimental and Clinical Cell Therapy, Paracelsus Medical University, Salzburg A-5020, Austria
| | - Teresa Pammer
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
| | - Carmen Butorac
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
| | - Martin Muik
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
| | - Klaus Groschner
- Institute for Biophysics, Medical University of Graz, Graz A-8010, Austria
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University Göttingen, Göttingen, Niedersachsen 37073, Germany
| | - Rüdiger H Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady CZ-373 33, Czech Republic
- Faculty of Sciences, University of South Bohemia, Nové Hrady CZ-373 33, Czech Republic
| | - Christoph Romanin
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz A-4020, Austria
| | - Rainer Schindl
- Institute for Biophysics, Medical University of Graz, Graz A-8010, Austria.
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22
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Kandoi G, Leelananda SP, Jernigan RL, Sen TZ. Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information. Methods Mol Biol 2017; 1484:35-44. [PMID: 27787818 DOI: 10.1007/978-1-4939-6406-2_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Predicting the secondary structure of a protein from its sequence still remains a challenging problem. The prediction accuracies remain around 80 %, and for very diverse methods. Using evolutionary information and machine learning algorithms in particular has had the most impact. In this chapter, we will first define secondary structures, then we will review the Consensus Data Mining (CDM) technique based on the robust GOR algorithm and Fragment Database Mining (FDM) approach. GOR V is an empirical method utilizing a sliding window approach to model the secondary structural elements of a protein by making use of generalized evolutionary information. FDM uses data mining from experimental structure fragments, and is able to successfully predict the secondary structure of a protein by combining experimentally determined structural fragments based on sequence similarities of the fragments. The CDM method combines predictions from GOR V and FDM in a hierarchical manner to produce consensus predictions for secondary structure. In other words, if sequence fragment are not available, then it uses GOR V to make the secondary structure prediction. The online server of CDM is available at http://gor.bb.iastate.edu/cdm/ .
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Affiliation(s)
- Gaurav Kandoi
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA
| | - Sumudu P Leelananda
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Taner Z Sen
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.
- Department of Genetics, Development and Cell Biology, Iowa State University, 1025 Crop Genome Informatics Lab, Ames, IA, 50011, USA.
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Zhao Z, Chen J, Yin X, Song H, Wang X. Study on the Function of Tumor Necrosis Factor α Before and After Mutation in Hepatitis B. Hepatogastroenterology 2015; 62:997-1001. [PMID: 26902044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND/AIMS To explore the cause of functional changes of TNF-α in removing hepatitis B virus (HBV) through the structural changes of each site in TNF-α before and after mutation. METHODOLOGY Three typical mutant sites (TNF-α-308G/A, 857C/T and 863C/A of TNF-α) were chosen and methods like ab initio modeling was adopted for 3D modeling of TNF-α before and after mutation. The structural changes were also analyzed. Then structural changes and functional changes were brought together for comparison to infer the root cause of the changes. RESULTS Mutation of TNF-α-308G/A led to the production of multiple helical structures and that of 863C/A caused the production of one helical structure in its adjacent region. Mutation of 857C/T, however, did not cause the change in the basic structure of TNF-α. CONCLUSIONS The helical structure of TNF-α may have a positive effect on the removal of hepatitis B virus.
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Abstract
An A81H variant of yeast iso-1-cytochrome c is prepared to test the hypothesis that the steric size of the amino acid at sequence position 81 of cytochrome c, which has evolved from Ala in yeast to Ile in mammals, slows the dynamics of the opening of the heme crevice. The A81H mutation is used both to increase steric size and to provide a probe of the dynamics of the heme crevice through measurement of the thermodynamics and kinetics of the His81-mediated alkaline conformational transition of A81H iso-1-cytochrome c. Thermodynamic measurements show that the native conformer is more stable than the His81-heme alkaline conformer for A81H iso-1-cytochrome c. ΔGu°(H2O) is approximately 1.9 kcal/mol for formation of the His81-heme alkaline conformer. By contrast, for K79H iso-1-cytochrome c, the native conformer is less stable than the His79-heme alkaline conformer. ΔGu°(H2O) is approximately -0.34 kcal/mol for formation of the His79-heme alkaline conformer. pH jump and gated electron transfer kinetics demonstrate that this stabilization of the native conformer in A81H iso-1-cytochrome c arises primarily from a decrease in the rate constant for formation of the His81-heme alkaline conformer, kf,His81, relative to kf,His79 for formation of the His79-heme alkaline conformer, which forms by a mechanism similar to that observed for the His81-heme alkaline conformer. The result is discussed in terms of the effect of global protein stability on protein dynamics and in terms of optimization of the sequence of cytochrome c for its role as a peroxidase in the early stages of apoptosis in higher eukaryotes.
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Affiliation(s)
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
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25
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Huang YMM, Chang CEA. Achieving peptide binding specificity and promiscuity by loops: case of the forkhead-associated domain. PLoS One 2014; 9:e98291. [PMID: 24870410 PMCID: PMC4037201 DOI: 10.1371/journal.pone.0098291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/30/2014] [Indexed: 11/18/2022] Open
Abstract
The regulation of a series of cellular events requires specific protein–protein interactions, which are usually mediated by modular domains to precisely select a particular sequence from diverse partners. However, most signaling domains can bind to more than one peptide sequence. How do proteins create promiscuity from precision? Moreover, these complex interactions typically occur at the interface of a well-defined secondary structure, α helix and β sheet. However, the molecular recognition primarily controlled by loop architecture is not fully understood. To gain a deep understanding of binding selectivity and promiscuity by the conformation of loops, we chose the forkhead-associated (FHA) domain as our model system. The domain can bind to diverse peptides via various loops but only interact with sequences containing phosphothreonine (pThr). We applied molecular dynamics (MD) simulations for multiple free and bound FHA domains to study the changes in conformations and dynamics. Generally, FHA domains share a similar folding structure whereby the backbone holds the overall geometry and the variety of sidechain atoms of multiple loops creates a binding surface to target a specific partner. FHA domains determine the specificity of pThr by well-organized binding loops, which are rigid to define a phospho recognition site. The broad range of peptide recognition can be attributed to different arrangements of the loop interaction network. The moderate flexibility of the loop conformation can help access or exclude binding partners. Our work provides insights into molecular recognition in terms of binding specificity and promiscuity and helpful clues for further peptide design.
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Affiliation(s)
- Yu-ming M. Huang
- Department of Chemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (YMH); (CAC)
| | - Chia-en A. Chang
- Department of Chemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (YMH); (CAC)
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Varghese LN, Ungureanu D, Liau NPD, Young SN, Laktyushin A, Hammaren H, Lucet IS, Nicola NA, Silvennoinen O, Babon JJ, Murphy JM. Mechanistic insights into activation and SOCS3-mediated inhibition of myeloproliferative neoplasm-associated JAK2 mutants from biochemical and structural analyses. Biochem J 2014; 458:395-405. [PMID: 24354892 PMCID: PMC4085142 DOI: 10.1042/bj20131516] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
JAK2 (Janus kinase 2) initiates the intracellular signalling cascade downstream of cell surface receptor activation by cognate haemopoietic cytokines, including erythropoietin and thrombopoietin. The pseudokinase domain (JH2) of JAK2 negatively regulates the catalytic activity of the adjacent tyrosine kinase domain (JH1) and mutations within the pseudokinase domain underlie human myeloproliferative neoplasms, including polycythaemia vera and essential thrombocytosis. To date, the mechanism of JH2-mediated inhibition of JH1 kinase activation as well as the susceptibility of pathological mutant JAK2 to inhibition by the physiological negative regulator SOCS3 (suppressor of cytokine signalling 3) have remained unclear. In the present study, using recombinant purified JAK2JH1-JH2 proteins, we demonstrate that, when activated, wild-type and myeloproliferative neoplasm-associated mutants of JAK2 exhibit comparable enzymatic activity and inhibition by SOCS3 in in vitro kinase assays. SAXS (small-angle X-ray scattering) showed that JAK2JH1-JH2 exists in an elongated configuration in solution with no evidence for interaction between JH1 and JH2 domains in cis. Collectively, these data are consistent with a model in which JAK2's pseudokinase domain does not influence the activity of JAK2 once it has been activated. Our data indicate that, in the absence of the N-terminal FERM domain and thus cytokine receptor association, the wild-type and pathological mutants of JAK2 are enzymatically equivalent and equally susceptible to inhibition by SOCS3.
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Affiliation(s)
- Leila N. Varghese
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Daniela Ungureanu
- School of Medicine, University of Tampere and Tampere University Hospital, Tampere 33014, Finland
| | - Nicholas P. D. Liau
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Samuel N. Young
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Artem Laktyushin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Henrik Hammaren
- School of Medicine, University of Tampere and Tampere University Hospital, Tampere 33014, Finland
| | - Isabelle S. Lucet
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Nicos A. Nicola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Olli Silvennoinen
- School of Medicine, University of Tampere and Tampere University Hospital, Tampere 33014, Finland
| | - Jeffrey J. Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - James M. Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
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Shafqat N, Kavanagh KL, Sass JO, Christensen E, Fukao T, Lee WH, Oppermann U, Yue WW. A structural mapping of mutations causing succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency. J Inherit Metab Dis 2013; 36:983-7. [PMID: 23420214 PMCID: PMC3825524 DOI: 10.1007/s10545-013-9589-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/08/2022]
Abstract
Succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency is a rare inherited metabolic disorder of ketone metabolism, characterized by ketoacidotic episodes and often permanent ketosis. To date there are ~20 disease-associated alleles on the OXCT1 gene that encodes the mitochondrial enzyme SCOT. SCOT catalyzes the first, rate-limiting step of ketone body utilization in peripheral tissues, by transferring a CoA moiety from succinyl-CoA to form acetoacetyl-CoA, for entry into the tricarboxylic acid cycle for energy production. We have determined the crystal structure of human SCOT, providing a molecular understanding of the reported mutations based on their potential structural effects. An interactive version of this manuscript (which may contain additional mutations appended after acceptance of this manuscript) may be found on the web address: http://www.thesgc.org/jimd/SCOT .
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Affiliation(s)
- Naeem Shafqat
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
| | - Kate L. Kavanagh
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
| | - Jörn Oliver Sass
- Zentrum für Kinder- und Jugendmedizin, Universitätsklinikum Freiburg, 79106 Freiburg, Germany
- Klinische Chemie & Biochemie, Universitäts-Kinderspital, 8032 Zürich, Switzerland
| | - Ernst Christensen
- Department of Clinical Genetics, Juliane Marie Centre, 2100 Copenhagen, Denmark
| | - Toshiyuki Fukao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, 501-1194 Japan
- Medical information Sciences Division, United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1194 Japan
| | - Wen Hwa Lee
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
- Botnar Research Centre, Oxford Biomedical Research Unit, OX3 7LD Oxford, UK
| | - Wyatt W. Yue
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
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Premkumar L, Heras B, Duprez W, Walden P, Halili M, Kurth F, Fairlie DP, Martin JL. Rv2969c, essential for optimal growth in Mycobacterium tuberculosis, is a DsbA-like enzyme that interacts with VKOR-derived peptides and has atypical features of DsbA-like disulfide oxidases. Acta Crystallogr D Biol Crystallogr 2013; 69:1981-94. [PMID: 24100317 PMCID: PMC3792642 DOI: 10.1107/s0907444913017800] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/28/2013] [Indexed: 12/16/2022]
Abstract
The bacterial disulfide machinery is an attractive molecular target for developing new antibacterials because it is required for the production of multiple virulence factors. The archetypal disulfide oxidase proteins in Escherichia coli (Ec) are DsbA and DsbB, which together form a functional unit: DsbA introduces disulfides into folding proteins and DsbB reoxidizes DsbA to maintain it in the active form. In Mycobacterium tuberculosis (Mtb), no DsbB homologue is encoded but a functionally similar but structurally divergent protein, MtbVKOR, has been identified. Here, the Mtb protein Rv2969c is investigated and it is shown that it is the DsbA-like partner protein of MtbVKOR. It is found that it has the characteristic redox features of a DsbA-like protein: a highly acidic catalytic cysteine, a highly oxidizing potential and a destabilizing active-site disulfide bond. Rv2969c also has peptide-oxidizing activity and recognizes peptide segments derived from the periplasmic loops of MtbVKOR. Unlike the archetypal EcDsbA enzyme, Rv2969c has little or no activity in disulfide-reducing and disulfide-isomerase assays. The crystal structure of Rv2969c reveals a canonical DsbA fold comprising a thioredoxin domain with an embedded helical domain. However, Rv2969c diverges considerably from other DsbAs, including having an additional C-terminal helix (H8) that may restrain the mobility of the catalytic helix H1. The enzyme is also characterized by a very shallow hydrophobic binding surface and a negative electrostatic surface potential surrounding the catalytic cysteine. The structure of Rv2969c was also used to model the structure of a paralogous DsbA-like domain of the Ser/Thr protein kinase PknE. Together, these results show that Rv2969c is a DsbA-like protein with unique properties and a limited substrate-binding specificity.
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Affiliation(s)
- Lakshmanane Premkumar
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Begoña Heras
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Wilko Duprez
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Patricia Walden
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Maria Halili
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Fabian Kurth
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Jennifer L. Martin
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
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Chen YR, Huang HB, Lo CJ, Wang CC, Ho LK, Liu HT, Shiao MS, Lin TH, Chen YC. Effect of alanine replacement of l17 and f19 on the aggregation and neurotoxicity of arctic-type aβ40. PLoS One 2013; 8:e61874. [PMID: 23634215 PMCID: PMC3636269 DOI: 10.1371/journal.pone.0061874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 03/15/2013] [Indexed: 01/18/2023] Open
Abstract
Alzheimer’s disease is the most common form of neurodegenerative disease. Beta-amyloid peptides (Aβ) are responsible for neuronal death both in vitro and in vivo. Previously, L17 and F19 residues were identified as playing key roles in the stabilization of the Aβ40 conformation and in the reduction of its neurotoxicity. In this study, the effects of L17A/F19A mutations on the neurotoxicity of Aβ genetic mutant Arctic-type Aβ40(E22G) were tested. The results showed that compared to Aβ40(E22G), Aβ40(L17A/F19A/E22G) reduced the rate of conformation conversion, aggregation, and cytotoxicity, suggesting that L17 and F19 are critical residues responsible for conformational changes which may trigger the neurotoxic cascade of Aβ. Aβ40(L17A/F19A/E22G) also had decreased damage due to reactive oxygen species. The results are consistent with the discordant helix hypothesis, and confirm that residues 17–25 are in the discordant helix region. Compared to Aβ40(L17A/F19A), reduction in aggregation of Aβ40(L17A/F19A/E22G) was less significantly decreased. This observation provides an explanation based on the discordant helix hypothesis that the mutation of E22 to G22 of Aβ40(E22G) alters the propensity of the discordant helix. Arctic-type Aβ40(E22G) aggregates more severely than wild-type Aβ40, with a consequential increase in toxicity.
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Affiliation(s)
- Yi-Ru Chen
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department and Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Hsien-bin Huang
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan, R.O.C
| | - Chi-Jen Lo
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Chih-Ching Wang
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Li-Kang Ho
- Department and Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Hsin-Tzu Liu
- Voiding Dysfunction Therapeutic Center in the Research Department, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, R.O.C
| | - Ming-Shi Shiao
- Department of Life Science, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C
| | - Ta-Hsien Lin
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
| | - Yi-Cheng Chen
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
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Abstract
The ability to improve protein thermostability via protein engineering is of great scientific interest and also has significant practical value. In this report we present PROTS-RF, a robust model based on the Random Forest algorithm capable of predicting thermostability changes induced by not only single-, but also double- or multiple-point mutations. The model is built using 41 features including evolutionary information, secondary structure, solvent accessibility and a set of fragment-based features. It achieves accuracies of 0.799,0.782, 0.787, and areas under receiver operating characteristic (ROC) curves of 0.873, 0.868 and 0.862 for single-, double- and multiple- point mutation datasets, respectively. Contrary to previous suggestions, our results clearly demonstrate that a robust predictive model trained for predicting single point mutation induced thermostability changes can be capable of predicting double and multiple point mutations. It also shows high levels of robustness in the tests using hypothetical reverse mutations. We demonstrate that testing datasets created based on physical principles can be highly useful for testing the robustness of predictive models.
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Affiliation(s)
- Yunqi Li
- Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas, United States of America
| | - Jianwen Fang
- Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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Wittgen HGM, van den Heuvel JJMW, Krieger E, Schaftenaar G, Russel FGM, Koenderink JB. Phenylalanine 368 of multidrug resistance-associated protein 4 (MRP4/ABCC4) plays a crucial role in substrate-specific transport activity. Biochem Pharmacol 2012; 84:366-73. [PMID: 22542979 DOI: 10.1016/j.bcp.2012.04.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/11/2012] [Accepted: 04/13/2012] [Indexed: 11/19/2022]
Abstract
Multidrug resistance-associated protein 4 (MRP4) is a membrane transporter that mediates the cellular efflux of a wide range of anionic drugs and endogenous molecules. MRP4 transport can influence the pharmacokinetics of drugs and their metabolites, therefore more knowledge about the molecular determinants important for its transport function would be of relevance. Here, we substituted amino acids Phe(368), Trp(995), and Arg(998) with conservative or non-conservative residues, and determined the effect on transport of the model substrates estradiol 17-β-d-glucuronide (E(2)17βG), cyclic guanosine monophosphate (cGMP), methotrexate (MTX), and folic acid into membrane vesicles isolated from baculovirus transduced HEK293 cells overexpressing the mutant MRP4 proteins. This revealed that all Arg(998) mutations appeared to be deleterious, whereas the effect of a Phe(368) or Trp(995) replacement was dependent on the amino acid introduced and the substrate studied. Substitution of Phe(368) with Trp (F368W) induced a gain-of-function of E(2)17βG transport and a loss-of-function of MTX transport, which could not be attributed to an altered substrate binding. Moreover, we did not observe any modification in ATP or ADP handling for F368W. These results, in combination with docking of substrates in a homology model of MRP4 in the inward- and outward-facing conformation, suggest that Phe(368) and Trp(995) do not play an important role in the initial binding of substrates. They, however, might interact with the substrates during rearrangement of helixes for substrate translocation, funneling the substrates to the exit site in the outward-facing conformation.
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Affiliation(s)
- Hanneke G M Wittgen
- Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, The Netherlands
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Guo X, Li J, Wang T, Liu Z, Chen X, Li Y, Gu Z, Mao X, Guan W, Li Y. A mutation in intracellular loop 4 affects the drug-efflux activity of the yeast multidrug resistance ABC transporter Pdr5p. PLoS One 2012; 7:e29520. [PMID: 22238618 PMCID: PMC3253106 DOI: 10.1371/journal.pone.0029520] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 11/29/2011] [Indexed: 11/18/2022] Open
Abstract
Multidrug resistance protein Pdr5p is a yeast ATP-binding cassette (ABC) transporter in the plasma membrane. It confers multidrug resistance by active efflux of intracellular drugs. However, the highly polymorphic Pdr5p from clinical strain YJM789 loses its ability to expel azole and cyclohexmide. To investigate the role of amino acid changes in this functional change, PDR5 chimeras were constructed by segmental replacement of homologous BY4741 PDR5 fragments. Functions of PDR5 chimeras were evaluated by fluconazole and cycloheximide resistance assays. Their expression, ATPase activity, and efflux efficiency for other substrates were also analyzed. Using multiple lines of evidence, we show that an alanine-to-methionine mutation at position 1352 located in the predicted short intracellular loop 4 significantly contributes to the observed transport deficiency. The degree of impairment is likely correlated to the size of the mutant residue.
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Affiliation(s)
- Xiaoxian Guo
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Jingkai Li
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Tanjun Wang
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhenhua Liu
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xin Chen
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Yudong Li
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Xuming Mao
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Wenjun Guan
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- * E-mail: (WG); (YQL)
| | - Yongquan Li
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- * E-mail: (WG); (YQL)
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Vithayathil R, Hooy RM, Cocco MJ, Weiss GA. The scope of phage display for membrane proteins. J Mol Biol 2011; 414:499-510. [PMID: 22037583 PMCID: PMC3230673 DOI: 10.1016/j.jmb.2011.10.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 10/09/2011] [Accepted: 10/12/2011] [Indexed: 02/03/2023]
Abstract
Numerous examples of phage display applied to soluble proteins demonstrate the power of the technique for protein engineering, affinity reagent discovery and structure-function studies. Recent reports have expanded phage display to include membrane proteins (MPs). The scope and limitations of MP display remain undefined. Therefore, we report data from the phage display of representative types of membrane-associated proteins including plasma, nuclear, peripheral, single and multipass. The peripheral MP neuromodulin displays robustly with packaging by conventional M13-KO7 helper phage. The monotopic MP Nogo-66 can also display on the phage surface, if packaged by the modified M13-KO7(+) helper phage. The modified phage coat of KO7(+) can better mimic the zwitterionic character of the plasma membrane. Four examples of putatively α-helical, integral MPs failed to express as fusions to an anchoring phage coat protein and therefore did not display on the phage surface. However, the β-barrel MPs ShuA (Shigella heme uptake A) and MOMP (major outer membrane protein), which pass through the membrane 22 and 16 times, respectively, can display surprisingly well on the surfaces of both conventional and KO7(+) phages. The results provide a guide for protein engineering and large-scale mutagenesis enabled by the phage display of MPs.
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Affiliation(s)
- Rosemarie Vithayathil
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Richard M. Hooy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Melanie J. Cocco
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Gregory A. Weiss
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92697, USA
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Abstract
HIV cell entry and infection are driven by binding events to the CD4 and chemokine receptors with associated conformational change of the viral glycoprotein, gp120. Scyllatoxin miniprotein CD4 mimetics and a small molecule inhibitor of CD4 binding, NBD-556, also effectively induce gp120 conformational change. In this study we examine the fluctuation profile of gp120 in context of CD4, a miniprotein mimetic, and NBD-556 with the aim of understanding the effect of ligand binding on gp120 conformational dynamics. Analysis of molecular dynamics trajectories indicate that NBD-556 binding in the Phe 43 cavity enhances the overall mobility of gp120, especially in the outer domain in comparison to CD4 or miniprotein bound complex. Interactions with the more flexible bridging sheet strengthen upon NBD-556 binding and may contribute to gp120 restructuring. The enhanced mobility of D368, E370, and I371 with NBD-556 bound in the Phe 43 cavity suggests that interactions with α3-helix in the outer domain are not optimal, providing further insights into gp120--small molecule interactions that may impact small molecule designs.
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Affiliation(s)
- Indira Shrivastava
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh 3083 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh PA 15213
| | - Judith M. LaLonde
- Chemistry Department, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010
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Chong SH, Lee C, Kang G, Park M, Ham S. Structural and thermodynamic investigations on the aggregation and folding of acylphosphatase by molecular dynamics simulations and solvation free energy analysis. J Am Chem Soc 2011; 133:7075-83. [PMID: 21500781 DOI: 10.1021/ja1116233] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein engineering method to study the mutation effects on muscle acylphosphatase (AcP) has been actively applied to describe kinetics and thermodynamics associated with AcP aggregation as well as folding processes. Despite the extensive mutation experiments, the molecular origin and the structural motifs for aggregation and folding kinetics as well as thermodynamics of AcP have not been rationalized at the atomic resolution. To this end, we have investigated the mutation effects on the structures and thermodynamics for the aggregation and folding of AcP by using the combination of fully atomistic, explicit-water molecular dynamics simulations, and three-dimensional reference interaction site model theory. The results indicate that the A30G mutant with the fastest experimental aggregation rate displays considerably decreased α1-helical contents as well as disrupted hydrophobic core compared to the wild-type AcP. Increased solvation free energy as well as hydrophobicity upon A30G mutation is achieved due to the dehydration of hydrophilic side chains in the disrupted α1-helix region of A30G. In contrast, the Y91Q mutant with the slowest aggregation rate shows a non-native H-bonding network spanning the mutation site to hydrophobic core and α1-helix region, which rigidifies the native state protein conformation with the enhanced α1-helicity. Furthermore, Y91Q exhibits decreased solvation free energy and hydrophobicity compared to wild type due to more exposed and solvated hydrophilic side chains in the α1-region. On the other hand, the experimentally observed slower folding rates in both mutants are accompanied by decreased helicity in α2-helix upon mutation. We here provide the atomic-level structures and thermodynamic quantities of AcP mutants and rationalize the structural origin for the changes that occur upon introduction of those mutations along the AcP aggregation and folding processes.
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Affiliation(s)
- Song-Ho Chong
- Department of Chemistry, Sookmyung Women's University, Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
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Abstract
BACKGROUND Rhodopsin, the prototypic member of G protein-coupled receptors (GPCRs), undergoes isomerization of 11-cis-retinal to all-trans-retinal upon photoactivation. Although the basic mechanism by which rhodopsin is activated is well understood, the roles of whole transmembrane (TM) helix-III during rhodopsin photoactivation in detail are not completely clear. PRINCIPAL FINDINGS We herein use single-cysteine mutagenesis technique to investigate conformational changes in TM helices of rhodopsin upon photoactivation. Specifically, we study changes in accessibility and reactivity of cysteine residues introduced into the TM helix-III of rhodopsin. Twenty-eight single-cysteine mutants of rhodopsin (P107C-R135C) were prepared after substitution of all natural cysteine residues (C140/C167/C185/C222/C264/C316) by alanine. The cysteine mutants were expressed in COS-1 cells and rhodopsin was purified after regeneration with 11-cis-retinal. Cysteine accessibility in these mutants was monitored by reaction with 4, 4'-dithiodipyridine (4-PDS) in the dark and after illumination. Most of the mutants except for T108C, G109C, E113C, I133C, and R135C showed no reaction in the dark. Wide variation in reactivity was observed among cysteines at different positions in the sequence 108-135 after photoactivation. In particular, cysteines at position 115, 119, 121, 129, 131, 132, and 135, facing 11-cis-retinal, reacted with 4-PDS faster than neighboring amino acids. The different reaction rates of mutants with 4-PDS after photoactivation suggest that the amino acids in different positions in helix-III are exposed to aqueous environment to varying degrees. SIGNIFICANCE Accessibility data indicate that an aqueous/hydrophobic boundary in helix-III is near G109 and I133. The lack of reactivity in the dark and the accessibility of cysteine after photoactivation indicate an increase of water/4-PDS accessibility for certain cysteine-mutants at Helix-III during formation of Meta II. We conclude that photoactivation resulted in water-accessible at the chromophore-facing residues of Helix-III.
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Affiliation(s)
- Wen-bin Ou
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Tingfang Yi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jong-Myoung Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - H. Gobind Khorana
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Azurmendi HF, Mitra S, Ayala I, Li L, Finkielstein CV, Capelluto DGS. Backbone (1)H, (15)N, and (13)C resonance assignments and secondary structure of the Tollip CUE domain. Mol Cells 2010; 30:581-5. [PMID: 20957454 DOI: 10.1007/s10059-010-0145-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 08/19/2010] [Accepted: 08/27/2010] [Indexed: 01/21/2023] Open
Abstract
The Toll-interacting protein (Tollip) is a negative regulator of the Toll-like receptor (TLR)-mediated inflammation response. Tollip is a modular protein that contains an Nterminal Tom1-binding domain (TBD), a central conserved domain 2 (C2), and a C-terminal coupling of ubiquitin to endoplasmic reticulum degradation (CUE) domain. Here, we report the sequence-specific backbone (1)H, (15)N, and (13)C assignments of the human Tollip CUE domain. The CUE domain was found to be a stable dimer as determined by size-exclusion chromatography and molecular crosslinking studies. Analysis of the backbone chemical shift data indicated that the CUE domain exhibits three helical elements corresponding to 52% of the protein backbone. Circular dichroism spectrum analysis confirmed the helical nature of this domain. Comparison of the location of these helical regions with those reported for yeast CUE domains suggest differences in length for all helical elements. We expect the structural analysis presented here will be the foundation for future studies on the biological significance of the Tollip CUE domain, its molecular interactions, and the mechanisms that modulate its function during the inflammatory response.
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Affiliation(s)
- Hugo F Azurmendi
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Abstract
Protein structure is generally more conserved than sequence, but for regions that can adopt different structures in different environments, does this hold true? Understanding how structurally disordered regions evolve altered secondary structure element propensities as well as conformational flexibility among paralogs are fundamental questions for our understanding of protein structural evolution. We have investigated the evolutionary dynamics of structural disorder in protein families containing both orthologs and paralogs using phylogenetic tree reconstruction, protein structure disorder prediction, and secondary structure prediction in order to shed light upon these questions. Our results indicate that the extent and location of structurally disordered regions are not universally conserved. As structurally disordered regions often have high conformational flexibility, this is likely to have an effect on how protein structure evolves as spatially altered conformational flexibility can also change the secondary structure propensities for homologous regions in a protein family.
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Ouellet J, Melcher S, Iqbal A, Ding Y, Lilley DMJ. Structure of the three-way helical junction of the hepatitis C virus IRES element. RNA 2010; 16:1597-1609. [PMID: 20581129 PMCID: PMC2905758 DOI: 10.1261/rna.2158410] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 05/04/2010] [Indexed: 05/29/2023]
Abstract
The hepatitis C virus internal ribosome entry site (IRES) element contains a three-way junction that is important in the overall RNA conformation, and for its role in the internal initiation of translation. The junction also illustrates some important conformational principles in the folding of three-way helical junctions. It is formally a 3HS(4) junction, with the possibility of two alternative stacking conformers. However, in principle, the junction can also undergo two steps of branch migration that would form 2HS(1)HS(3) and 2HS(2)HS(2) junctions. Comparative gel electrophoresis and ensemble fluorescence resonance energy transfer (FRET) studies show that the junction is induced to fold by the presence of Mg(2+) ions in low micromolar concentrations, and suggest that the structure adopted is based on coaxial stacking of the two helices that do not terminate in a hairpin loop (i.e., helix IIId). Single-molecule FRET studies confirm this conclusion, and indicate that there is no minor conformer present based on an alternative choice of helical stacking partners. Moreover, analysis of single-molecule FRET data at an 8-msec resolution failed to reveal evidence for structural transitions. It seems probable that this junction adopts a single conformation as a unique and stable fold.
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Affiliation(s)
- Jonathan Ouellet
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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de Noronha SMR, Corrêa SAA, Poletti EF, Lopes DD, da Silva CC, Sforça ML, Shimuta SI, Zanchin NIT, Nakaie CR, da Silva IDCG. Structural analysis of three peptides related to the transmambranic helix VI of AT1 receptor. Neuropeptides 2010; 44:115-8. [PMID: 20006383 DOI: 10.1016/j.npep.2009.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 11/11/2009] [Accepted: 11/12/2009] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Angiotensin II (AII) is the main active product of the renin angiotensin system. Better known effects of AII are via AT1 receptor (AT1R). Expression of AT1R mutants (L265D and L262D) in CHO cells increased cAMP formation when compared to CHO cells expressing the wild type (WT) AT1R. Morphological transformation of CHO cells transfected with mutants correlated with their increased cAMP formation. DNA synthesis was inhibited in these cells too, indicating that cAMP promotes inhibitory effects on transfected CHO cells growth and causes their morphological change from a tumorigenic phenotype to a non-tumorigenic one. OBJECTIVES To assess the importance of leucine 262 and 265 in determining AT1R structure by means of a comparative structural analysis of two mutant peptides and of a wild-type fragment. METHODOLOGY Three peptides had their conformation compared by circular dichroism (CD): L262D(259-272), L265D(259-272) (mutants) and WT(260-277). RESULTS Secondary structures were: beta-turn for WT and L262D and random coil for L265D. CONCLUSIONS Strong correlation was found in the results of biochemical, cellular and structural approaches used to compare WT AT1R to mutant types. Random coil structure of the L265D mutant may be a key point to explain those changes observed in biochemical (binding and signal transduction) and proliferation assays (Correa et al., 2005). beta-Turn formation is an important step during early protein folding and this secondary simple structure is present in L262D and WT, but not in L265D. Therefore, leucine 265 seems to play a crucial role in determining an entirely functional AT1R.
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Affiliation(s)
- Samuel Marcos Ribeiro de Noronha
- Ginecologia Molecular/Ginecologia, UNIFESP-R. Pedro de Toledo, 791 - 4o. Andar, V. Clementino, CEP04039032 Sao Paulo, SP, Brazil.
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Ravindranath MH, Taniguchi M, Chen CW, Ozawa M, Kaneku H, El-Awar N, Cai J, Terasaki PI. HLA-E monoclonal antibodies recognize shared peptide sequences on classical HLA class Ia: relevance to human natural HLA antibodies. Mol Immunol 2010; 47:1121-31. [PMID: 19944464 DOI: 10.1016/j.molimm.2009.10.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/20/2009] [Accepted: 10/25/2009] [Indexed: 01/15/2023]
Abstract
The non-classical HLA-Ib molecule, HLA-E share several peptide sequence similarities with the heavy chains of classical HLA class Ia (-B and -C) molecules. Therefore, the antibodies to HLA-E, that recognize shared sequences, may bind to HLA-Ia alleles. This hypothesis is tested by examining the affinity of HLA-E monoclonal antibodies (HLA-E-MAbs) to HLA-Ia molecules and by inhibiting the antibody binding to both HLA-E and HLA-Ia with the shared peptide sequence(s). Single recombinant HLA molecule-coated beads are used for antibody binding. The antibody binding is evaluated by measuring mean fluorescence index [MFI] with Luminex multiplex flow-cytometric technology. The peptide-inhibition experiments are carried out with synthetic shared peptides, most prevalent to HLA-E and HLA-Ia alleles. The number of HLA-Ia alleles recognized by the HLA-E-MAbs varies with the density of the antigen (quantity of antigen-coated beads) and dilution of MAb. Binding of HLA-E-MAbs to beta2 microglobulin (beta(2)m)-free HLA-Ia antigens confirms the location of the epitopes on the heavy chain (HC) of the antigens. Strikingly, the nature of alleles of HLA-Ia recognized by different HLA-E-MAbs is identical. The binding of HLA-E-MAbs to the HLA-Ia is inhibited dosimetrically by the adjacent peptides, (115)QFAYDGKDY(123) and (137)DTAAQI(142), but not by (126)LNEDLRSWTA(135), another closer shared peptide sequence. The inhibitory peptide sequences in HLA-E are at the alpha2-helix terminal facing beta(2)m. The HLA-Ia alleles recognized by HLA-E-MAb (e.g., MEM-E/02) are similar to those recognized by the natural anti-HLA antibodies found in the sera of healthy non-alloimmunized males. This study postulates that some, if not all, of the natural HLA-Ia antibodies seen in healthy males could be anti-HLA-E antibodies cross-reacting with HLA-Ia alleles.
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Wang X, Hald H, Ernst HA, Egebjerg J, Christensen KV, Gajhede M, Kastrup JS, Mirza O. Over-expression, purification and characterization of an Asc-1 homologue from Gloeobacter violaceus. Protein Expr Purif 2010; 71:179-83. [PMID: 20074644 DOI: 10.1016/j.pep.2010.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/07/2010] [Accepted: 01/08/2010] [Indexed: 11/18/2022]
Abstract
The human alanine-serine-cysteine transporter 1 (Asc-1) belongs to the slc7a family of solute carrier transporters. Asc-1 mediates the uptake of d-serine in an exchanger-type fashion, coupling the process to the release of alanine and cysteine. Among the bacterial Asc-1 homologues, one transporter shows a significantly higher sequence identity (35%) than other bacterial homologues. Therefore, this homologue from Gloeobacter violaceus might represent the best bacterial target for structural studies probing the molecular mechanism of Asc-1. We have over-expressed the G. violaceus transporter by auto-induction, and performed purification and biophysical characterization. In addition, growth studies indicate a preference for alanine as nitrogen source in cells expressing the G. violaceus transporter. It was observed that use of the auto-induction method and subsequent optimization of the length of auto-induction was crucial for obtaining high yields and purity of the transporter. The transporter was purified with yields in the range of 0.2-0.4mg per L culture and eluted in a single peak from a size-exclusion column. The circular dichroism spectrum revealed a folded and apparently all-helical protein.
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Affiliation(s)
- Xiaole Wang
- Biostructural Research, Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark
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McMahon SK, Pretorius CJ, Ungerer JPJ, Salmon NJ, Conwell LS, Pearen MA, Batch JA. Neonatal complete generalized glucocorticoid resistance and growth hormone deficiency caused by a novel homozygous mutation in Helix 12 of the ligand binding domain of the glucocorticoid receptor gene (NR3C1). J Clin Endocrinol Metab 2010; 95:297-302. [PMID: 19933394 DOI: 10.1210/jc.2009-1003] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Glucocorticoid resistance is a rare genetic condition characterized by reduced sensitivity to cortisol signaling and subsequent hyperactivation of the hypothalamic-pituitary-adrenal axis. OBJECTIVE The objective was to confirm the diagnosis of glucocorticoid resistance in the patient, to determine the degree of suppression of cortisol and ACTH levels in response to dexamethasone, and to determine the underlying genetic abnormality and functional consequences of the mutation. PATIENT AND METHODS The patient presented on the first day of life with profound hypoglycemia. Initial cortisol levels were appropriately elevated; however, the patient was found to have persistently elevated levels of both cortisol and ACTH. The baby developed a tanned appearance and severe hypertension and fatigued easily with feeding. Serial oral dexamethasone suppression tests were performed with doses escalating from 0.125 mg to 12 mg dexamethasone given at 2300 h. Sequencing of the glucocorticoid receptor gene was performed along with functional studies of the glucocorticoid receptor. GH secretion was assessed with an arginine glucagon stimulation test. RESULTS Cortisol and ACTH levels did not suppress with doses of up to 12 mg dexamethasone. A 2-bp deletion was found at amino acid position 773 of the glucocorticoid receptor ligand binding domain. A complete lack of dexamethasone binding and in vitro biological effect was demonstrated. GH stimulation testing was consistent with GH deficiency. CONCLUSION The homozygous mutation in the ligand-binding domain of the glucocorticoid receptor gene resulted in a functionally inactive glucocorticoid receptor and apparent complete glucocorticoid resistance with biochemical GH deficiency.
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Affiliation(s)
- Sarah K McMahon
- Department of Endocrinology and Diabetes, Royal Children's Hospital, Brisbane, Herston, Queensland 4029, Australia.
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Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L. Glyphosate resistance by engineering the flavoenzyme glycine oxidase. J Biol Chem 2009; 284:36415-36423. [PMID: 19864430 PMCID: PMC2794757 DOI: 10.1074/jbc.m109.051631] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/12/2009] [Indexed: 11/06/2022] Open
Abstract
Glycine oxidase from Bacillus subtilis is a homotetrameric flavoprotein of great potential biotechnological use because it catalyzes the oxidative deamination of various amines and d-isomer of amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Glyphosate (N-phosphonomethylglycine), a broad spectrum herbicide, is an interesting synthetic amino acid: this compound inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids in plants and certain bacteria. In recent years, transgenic crops resistant to glyphosate were mainly generated by overproducing the plant enzyme or by introducing a 5-enolpyruvylshikimate-3-phosphate synthase insensitive to this herbicide. In this work, we propose that the enzymatic oxidation of glyphosate could be an effective alternative to this important biotechnological process. To reach this goal, we used a rational design approach (together with site saturation mutagenesis) to generate a glycine oxidase variant more active on glyphosate than on the physiological substrate glycine. The glycine oxidase containing three point mutations (G51S/A54R/H244A) reaches an up to a 210-fold increase in catalytic efficiency and a 15,000-fold increase in the specificity constant (the k(cat)/K(m) ratio between glyphosate and glycine) as compared with wild-type glycine oxidase. The inspection of its three-dimensional structure shows that the alpha2-alpha3 loop (comprising residues 50-60 and containing two of the mutated residues) assumes a novel conformation and that the newly introduced residue Arg(54) could be the key residue in stabilizing glyphosate binding and destabilizing glycine positioning in the binding site, thus increasing efficiency on the herbicide.
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Affiliation(s)
- Mattia Pedotti
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Tommaso Moschetti
- Department of Biochemical Sciences, "Sapienza," University of Rome, 00185 Rome, Italy
| | - Carmelinda Savino
- Consiglio Nazionale delle Richerche Institute of Molecular Biology and Pathology, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences, "Sapienza," University of Rome, 00185 Rome, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy.
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Galaleldeen A, Strange RW, Whitson LJ, Antonyuk SV, Narayana N, Taylor AB, Schuermann JP, Holloway SP, Hasnain SS, Hart PJ. Structural and biophysical properties of metal-free pathogenic SOD1 mutants A4V and G93A. Arch Biochem Biophys 2009; 492:40-7. [PMID: 19800308 PMCID: PMC2787720 DOI: 10.1016/j.abb.2009.09.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 09/25/2009] [Accepted: 09/27/2009] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease characterized by the destruction of motor neurons in the spinal cord and brain. A subset of ALS cases are linked to dominant mutations in copper-zinc superoxide dismutase (SOD1). The pathogenic SOD1 variants A4V and G93A have been the foci of multiple studies aimed at understanding the molecular basis for SOD1-linked ALS. The A4V variant is responsible for the majority of familial ALS cases in North America, causing rapidly progressing paralysis once symptoms begin and the G93A SOD1 variant is overexpressed in often studied murine models of the disease. Here we report the three-dimensional structures of metal-free A4V and of metal-bound and metal-free G93A SOD1. In the metal-free structures, the metal-binding loop elements are observed to be severely disordered, suggesting that these variants may share mechanisms of aggregation proposed previously for other pathogenic SOD1 proteins.
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Affiliation(s)
- Ahmad Galaleldeen
- Department of Biochemistry and the X-ray Crystallography Core Laboratory, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
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Punta M, Love J, Handelman S, Hunt JF, Shapiro L, Hendrickson WA, Rost B. Structural genomics target selection for the New York consortium on membrane protein structure. ACTA ACUST UNITED AC 2009; 10:255-68. [PMID: 19859826 PMCID: PMC2780672 DOI: 10.1007/s10969-009-9071-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 09/30/2009] [Indexed: 01/02/2023]
Abstract
The New York Consortium on Membrane Protein Structure (NYCOMPS), a part of the Protein Structure Initiative (PSI) in the USA, has as its mission to establish a high-throughput pipeline for determination of novel integral membrane protein structures. Here we describe our current target selection protocol, which applies structural genomics approaches informed by the collective experience of our team of investigators. We first extract all annotated proteins from our reagent genomes, i.e. the 96 fully sequenced prokaryotic genomes from which we clone DNA. We filter this initial pool of sequences and obtain a list of valid targets. NYCOMPS defines valid targets as those that, among other features, have at least two predicted transmembrane helices, no predicted long disordered regions and, except for community nominated targets, no significant sequence similarity in the predicted transmembrane region to any known protein structure. Proteins that feed our experimental pipeline are selected by defining a protein seed and searching the set of all valid targets for proteins that are likely to have a transmembrane region structurally similar to that of the seed. We require sequence similarity aligning at least half of the predicted transmembrane region of seed and target. Seeds are selected according to their feasibility and/or biological interest, and they include both centrally selected targets and community nominated targets. As of December 2008, over 6,000 targets have been selected and are currently being processed by the experimental pipeline. We discuss how our target list may impact structural coverage of the membrane protein space.
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Affiliation(s)
- Marco Punta
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.
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Braker JD, Hodel KJ, Mullins DR, Friesen JA. Identification of hydrophobic amino acids required for lipid activation of C. elegans CTP:phosphocholine cytidylyltransferase. Arch Biochem Biophys 2009; 492:10-6. [PMID: 19836342 DOI: 10.1016/j.abb.2009.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 10/09/2009] [Accepted: 10/10/2009] [Indexed: 11/18/2022]
Abstract
CTP:phosphocholine cytidylyltransferase (CCT), critical for phosphatidylcholine biosynthesis, is activated by translocation to the membrane surface. The lipid activation region of Caenorhabditis elegans CCT is between residues 246 and 266 of the 347 amino acid polypeptide, a region proposed to form an amphipathic alpha helix. When leucine 246, tryptophan 249, isoleucine 256, isoleucine 257, or phenylalanine 260, on the hydrophobic face of the helix, were changed individually to serine low activity was observed in the absence of lipid vesicles, similar to wild-type CCT, while lipid stimulated activity was reduced compared to wild-type CCT. Mutational analysis of phenylalanine 260 implicated this residue as a contributor to auto-inhibition of CCT while mutation of L246, W249, I256, and I257 simultaneously to serine resulted in significantly higher activity in the absence of lipid vesicles and an enzyme that was not lipid activated. These results support a concerted mechanism of lipid activation that requires multiple residues on the hydrophobic face of the putative amphipathic alpha helix.
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Affiliation(s)
- Jay D Braker
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA
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Kalmatsky B, Bhagan S, Tang Q, Bargiello TA, Dowd T. Structural studies of the N-terminus of Connexin 32 using 1H NMR spectroscopy. Arch Biochem Biophys 2009; 490:9-16. [PMID: 19638273 PMCID: PMC4510928 DOI: 10.1016/j.abb.2009.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Revised: 07/03/2009] [Accepted: 07/22/2009] [Indexed: 10/20/2022]
Abstract
The amino terminus of gap junction proteins, connexins, plays a fundamental role in voltage gating and ion permeation. We have previously shown with (1)H NMR that the structure of the N-terminus of a representative connexin molecule contains a flexible turn around glycine 12 [P.E. Purnick, D.C. Benjamin, V.K. Verselis, T.A. Bargiello, T.L. Dowd, Arch. Biochem. Biophys. 381 (2000) 181-190] allowing the N-terminus to reside at the cytoplasmic entry of the channel forming a voltage-sensor. Previous functional studies or neuropathies have shown that the mutation G12Y and G12S form non-functional channels while functional channels are formed from G12P. Using 2D (1)H NMR we show that similar to G12, the structure of the G12P mutant contains a more flexible turn around residue 12, whereas the G12S and G12Y mutants contain tighter, helical turns in this region. These results suggest an unconstrained turn is required around residue 12 to position the N-terminus within the pore allowing the formation of the cytoplasmic channel vestibule, which appears to be critical for proper channel function.
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Affiliation(s)
- B.D. Kalmatsky
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York, 11210
| | - S. Bhagan
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York, 11210
| | - Q. Tang
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461
| | - T. A. Bargiello
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461
| | - T.L. Dowd
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York, 11210
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Pires R, Hartlieb B, Signor L, Schoehn G, Lata S, Roessle M, Moriscot C, Popov S, Hinz A, Jamin M, Boyer V, Sadoul R, Forest E, Svergun DI, Göttlinger HG, Weissenhorn W. A crescent-shaped ALIX dimer targets ESCRT-III CHMP4 filaments. Structure 2009; 17:843-56. [PMID: 19523902 DOI: 10.1016/j.str.2009.04.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/27/2009] [Accepted: 04/15/2009] [Indexed: 12/20/2022]
Abstract
ALIX recruits ESCRT-III CHMP4 and is involved in membrane remodeling during endosomal receptor sorting, budding of some enveloped viruses, and cytokinesis. We show that ALIX dimerizes via the middle domain (ALIX(-V)) in solution. Structural modeling based on small angle X-ray scattering (SAXS) data reveals an elongated crescent-shaped conformation for dimeric ALIX lacking the proline-rich domain (ALIX(BRO1-V)). Mutations at the dimerization interface prevent dimerization and induce an open elongated monomeric conformation of ALIX(-V) as determined by SAXS modeling. ALIX dimerizes in vivo and dimeric ALIX colocalizes with CHMP4B upon coexpression. We show further that ALIX dimerization affects HIV-1 budding. C-terminally truncated activated CHMP4B retaining the ALIX binding site forms linear, circular, and helical filaments in vitro, which can be bridged by ALIX. Our data suggest that dimeric ALIX represents the active form that interacts with ESCRT-III CHMP4 polymers and functions as a scaffolding protein during membrane remodeling processes.
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Affiliation(s)
- Ricardo Pires
- Unit of Virus Host Cell Interactions (UVHCI) UMI 3265, Université Joseph Fourier-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, Cedex 9, France
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Dimisianos G, Traeger-Synodinos J, Vrettou C, Papassotiriou I, Kanavakis E. A Rare 33 bp In‐Frame Deletion (α63–74 or α64–74 or α65–75) in the α1‐Globin Gene Causing α+‐Thalassemia: A Second Observation. Hemoglobin 2009; 28:137-43. [PMID: 15182056 DOI: 10.1081/hem-120035914] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The most frequent defects resulting in alpha-thalassemia (thal) include large deletions that remove one or both of the duplicated alpha-globin genes on chromosome 16. Less commonly, alpha-thal mutations involve single nucleotide substitutions or micro-deletions, leading either directly to decreased alpha-globin chain synthesis by the affected allele, or indirectly through production of hyperunstable variant alpha-globin chains. Here we describe the characterization of a 33 bp in-frame deletion within the alpha1-globin gene, in a woman with hematological findings consistent with an alpha-thal trait. The amino acids predicted to be missing as a result of the 33 bp deletion are at the end of the E helix and the EF corner of the alpha-globin protein chain, and are not normally involved in the heme contact, although it is presumed that alpha-globin chain folding and hemoglobin (Hb) formation will be disrupted. The observation of inclusion and Heinz bodies indicates the synthesis of some abnormal Hb (or globin chains). An identical mutation has been previously observed in a single case, a Canadian individual of Greek descent, indicating that it is a rare mutation, and probably of the same origin. Possible mechanisms underlying the mutation at the DNA level are discussed.
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Affiliation(s)
- Gerasimos Dimisianos
- Medical Genetics, Athens University, Aghia Sophia Children's Hospital, Athens, Greece
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