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Shan C, Zhang L, Chen L, Li S, Zhang Y, Ye L, Lin Y, Kuang W, Shi X, Ma J, Adnan M, Sun X, Cui R. Interaction of negative regulator OsWD40-193 with OseEF1A1 inhibits Oryza sativa resistance to Hirschmanniella mucronata infection. Int J Biol Macromol 2023; 248:125841. [PMID: 37479204 DOI: 10.1016/j.ijbiomac.2023.125841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Rice is a crucial food crop worldwide, but it is highly susceptible to Hirschmanniella mucronata, a migratory parasitic nematode. No rice variety has been identified that could resist H. mucronata infection. Therefore, it is very important to study the interaction between rice and H. mucronata to breed resistant rice varieties. Here, we demonstrated that protein OsWD40-193 interacted with the extension factor OseEF1A1 and both were negative regulators inhibiting rice resistance to H. mucronata infection. Overexpression of either OsWD40-193 or OseEF1A1 led to enhance susceptibility to H. mucronata, whereas the absence of OsWD40-193 or OseEF1A1 led to resistance. Further transcriptomic analysis showed that OseEF1A1 deletion altered the expression of genes association with salicylic acid, jasmonic acid and abolic acid signaling pathways and increased the accumulation of secondary metabolites to enhance resistance in rice. Our study showed that H. mucronata infection affected the expression of negative regulators in rice and inhibited rice resistance, which was conducive to the infection of nematode. Together, our data showed that H. mucronata affected the expression of negative regulators to facilitate its infection and provided potential target genes to engineering resistance germplasm via gene editing of the negative regulators.
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Affiliation(s)
- Chonglei Shan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Lianhu Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
| | - Lanlan Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Songyan Li
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Yifan Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Lifang Ye
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Yachun Lin
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xugen Shi
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Jian Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Muhammad Adnan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Xiaotang Sun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
| | - Ruqiang Cui
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
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Thakkar R, Upreti D, Ishiguro S, Tamura M, Comer J. Computational design of a cyclic peptide that inhibits the CTLA4 immune checkpoint. RSC Med Chem 2023; 14:658-670. [PMID: 37122540 PMCID: PMC10131585 DOI: 10.1039/d2md00409g] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Proteins involved in immune checkpoint pathways, such as CTLA4, PD1, and PD-L1, have become important targets for cancer immunotherapy; however, development of small molecule drugs targeting these pathways has proven difficult due to the nature of their protein-protein interfaces. Here, using a hierarchy of computational techniques, we design a cyclic peptide that binds CTLA4 and follow this with experimental verification of binding and biological activity, using bio-layer interferometry, cell culture, and a mouse tumor model. Beginning from a template excised from the X-ray structure of the CTLA4:B7-2 complex, we generate several peptide sequences using flexible docking and modeling steps. These peptides are cyclized head-to-tail to improve structural and proteolytic stability and screened using molecular dynamics simulation and MM-GBSA calculation. The standard binding free energies for shortlisted peptides are then calculated in explicit-solvent simulation using a rigorous multistep technique. The most promising peptide, cyc(EIDTVLTPTGWVAKRYS), yields the standard free energy -6.6 ± 3.5 kcal mol-1, which corresponds to a dissociation constant of ∼15 μmol L-1. The binding affinity of this peptide for CTLA4 is measured experimentally (31 ± 4 μmol L-1) using bio-layer interferometry. Treatment with this peptide inhibited tumor growth in a co-culture of Lewis lung carcinoma (LLC) cells and antigen primed T cells, as well as in mice with an orthotropic Lewis lung carcinoma allograft model.
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Affiliation(s)
- Ravindra Thakkar
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Deepa Upreti
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Susumu Ishiguro
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Masaaki Tamura
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
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Vance TDR, Yip P, Jiménez E, Li S, Gawol D, Byrnes J, Usón I, Ziyyat A, Lee JE. SPACA6 ectodomain structure reveals a conserved superfamily of gamete fusion-associated proteins. Commun Biol 2022; 5:984. [PMID: 36115925 PMCID: PMC9482655 DOI: 10.1038/s42003-022-03883-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
SPACA6 is a sperm-expressed surface protein that is critical for gamete fusion during mammalian sexual reproduction. Despite this fundamental role, little is known about how SPACA6 specifically functions. We elucidated the crystal structure of the SPACA6 ectodomain at 2.2-Å resolution, revealing a two-domain protein containing a four-helix bundle and Ig-like β-sandwich connected via a quasi-flexible linker. This structure is reminiscent of IZUMO1, another gamete fusion-associated protein, making SPACA6 and IZUMO1 founding members of a superfamily of fertilization-associated proteins, herein dubbed the IST superfamily. The IST superfamily is defined structurally by its distorted four-helix bundle and a pair of disulfide-bonded CXXC motifs. A structure-based search of the AlphaFold human proteome identified more protein members to this superfamily; remarkably, many of these proteins are linked to gamete fusion. The SPACA6 structure and its connection to other IST-superfamily members provide a missing link in our knowledge of mammalian gamete fusion.
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Affiliation(s)
- Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Patrick Yip
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Elisabet Jiménez
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028, Barcelona, Spain
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Diana Gawol
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Isabel Usón
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Ahmed Ziyyat
- Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014, Paris, France
- Service d'Histologie, d'Embryologie, Biologie de la Reproduction, AP-HP, Hôpital Cochin, F-75014, Paris, France
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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Fan Z, Zhai Y, Wang Y, Zhang L, Song M, Flaishman MA, Ma H. Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L. FRONTIERS IN PLANT SCIENCE 2022; 13:948084. [PMID: 35909733 PMCID: PMC9334019 DOI: 10.3389/fpls.2022.948084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
WD40 proteins serve as crucial regulators in a broad spectrum of plant developmental and physiological processes, including anthocyanin biosynthesis. However, in fig (Ficus carica L.), neither the WD40 family nor any member involved in anthocyanin biosynthesis has been elucidated. In the present study, 204 WD40 genes were identified from the fig genome and phylogenetically classified into 5 clusters and 12 subfamilies. Bioinformatics analysis prediction localized 109, 69, and 26 FcWD40 proteins to the cytoplasm, nucleus and other cellular compartments, respectively. RNA-seq data mining revealed 127 FcWD40s expressed at FPKM > 10 in fig fruit. Most of these genes demonstrated higher expression in the early stages of fruit development. FcWD40-97 was recruited according to three criteria: high expression in fig fruit, predicted nuclear localization, and closest clustering with TTG1s identified in other plants. FcWD40-97, encoding 339 amino acids including 5 WD-repeat motifs, showed 88.01 and 87.94% amino acid sequence similarity to apple and peach TTG1, respectively. The gene is located on fig chromosome 4, and is composed of 1 intron and 2 exons. Promoter analysis revealed multiple light-responsive elements, one salicylic acid-responsive element, three methyl jasmonate-responsive elements, and one MYB-binding site involved in flavonoid biosynthesis gene regulation. FcWD40-97 was in the FPKM > 100 expression level group in fig fruit, and higher expression was consistently found in the peel compared to the flesh at the same development stages. Expression level did not change significantly under light deprivation, whereas in leaves and roots, its expression was relatively low. Transient expression verified FcWD40-97's localization to the nucleus. Yeast two-hybrid (Y2H) and biomolecular fluorescence complementation (BiFC) assays revealed that FcWD40-97 interacts with FcMYB114, FcMYB123, and FcbHLH42 proteins in vitro and in vivo, showing that FcWD40-97 functions as a member of the MYB-bHLH-WD40 (MBW) complex in anthocyanin-biosynthesis regulation in fig. We therefore renamed FcWD40-97 as FcTTG1. Our results provide the first systematic analysis of the FcWD40 family and identification of FcTTG1 in fig pigmentation.
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Affiliation(s)
- Zhiyi Fan
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yanlei Zhai
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yuan Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Long Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Miaoyu Song
- College of Horticulture, China Agricultural University, Beijing, China
| | - Moshe A. Flaishman
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
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Genome Wide Identification and Characterization of Apple WD40 Proteins and Expression Analysis in Response to ABA, Drought, and Low Temperature. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Basic WD40 proteins, which are characterized by a conserved WD40 domain, comprise a superfamily of regulatory proteins in plants and play important roles in plant growth and development. However, WD40 genes have been rarely studied in apple (Malus × domestica Borkh.). In this study, 346 WD40 genes classified in 12 subfamilies, were identified in the apple genome. Evolutionary analysis of WD40 proteins in apple and Arabidopsis revealed that the genes were classifiable into 14 groups, and the exon/intron structure of each group showed a similar structure. Analysis of collinearity showed that the large-scale amplification of WD40 genes in apple was largely attributable to recent whole-genome replication events. Nineteen candidate stress-related genes, selected by GO annotation and comparison with Arabidopsis homologs, showed different expression profiles in six organs at different developmental stages in response to exogenous abscisic acid (ABA), drought, and low temperature. Eight genes (MdWD40-17, 24, 70, 74, 219, 256, 283, and 307) showed a distinct response to one or more treatments (ABA, drought, and low temperature) as indicated by quantitative real-time PCR analysis. Taken together, these data provide rich resources for further study of MdWD40 genes and their potential roles in stress responses in apple.
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Genome-Wide Identification and Characterization of Polygalacturonase Gene Family in Maize ( Zea mays L.). Int J Mol Sci 2021; 22:ijms221910722. [PMID: 34639068 PMCID: PMC8509529 DOI: 10.3390/ijms221910722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
Polygalacturonase (PG, EC 3.2.1.15) is a crucial enzyme for pectin degradation and is involved in various developmental processes such as fruit ripening, pollen development, cell expansion, and organ abscission. However, information on the PG gene family in the maize (Zea mays L.) genome and the specific members involved in maize anther development are still lacking. In this study, we identified 55 PG family genes from the maize genome and further characterized their evolutionary relationship and expression patterns. Phylogenetic analysis revealed that ZmPGs are grouped into six Clades, and gene structures of the same Clade are highly conserved, suggesting their functional conservation. The ZmPGs are randomly distributed across maize chromosomes, and collinearity analysis showed that many ZmPGs might be derived from tandem duplications and segmental duplications, and these genes are under purifying selection. Furthermore, gene expression analysis provided insights into possible functional divergence among ZmPGs. Based on the RNA-seq data analysis, we found that many ZmPGs are expressed in various tissues while 18 ZmPGs are highly expressed in maize anther, and their detailed expression profiles in different anther developmental stages were further investigated by using RT-qPCR analysis. These results provide valuable information for further functional characterization and application of the ZmPGs in maize.
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Yang X, Wang J, Xia X, Zhang Z, He J, Nong B, Luo T, Feng R, Wu Y, Pan Y, Xiong F, Zeng Y, Chen C, Guo H, Xu Z, Li D, Deng G. OsTTG1, a WD40 repeat gene, regulates anthocyanin biosynthesis in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:198-214. [PMID: 33884679 DOI: 10.1111/tpj.15285] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Anthocyanins play an important role in the growth of plants, and are beneficial to human health. In plants, the MYB-bHLH-WD40 (MBW) complex activates the genes for anthocyanin biosynthesis. However, in rice, the WD40 regulators remain to be conclusively identified. Here, a crucial anthocyanin biosynthesis gene was fine mapped to a 43.4-kb genomic region on chromosome 2, and a WD40 gene OsTTG1 (Oryza sativa TRANSPARENT TESTA GLABRA1) was identified as ideal candidate gene. Subsequently, a homozygous mutant (osttg1) generated by CRISPR/Cas9 showed significantly decreased anthocyanin accumulation in various rice organs. OsTTG1 was highly expressed in various rice tissues after germination, and it was affected by light and temperature. OsTTG1 protein was localized to the nucleus, and can physically interact with Kala4, OsC1, OsDFR and Rc. Furthermore, a total of 59 hub transcription factor genes might affect rice anthocyanin biosynthesis, and LOC_Os01g28680 and LOC_Os02g32430 could have functional redundancy with OsTTG1. Phylogenetic analysis indicated that directional selection has driven the evolutionary divergence of the indica and japonica OsTTG1 alleles. Our results suggest that OsTTG1 is a vital regulator of anthocyanin biosynthesis, and an important gene resource for the genetic engineering of anthocyanin biosynthesis in rice and other plants.
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Affiliation(s)
- Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Junrui Wang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, 530007, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jie He
- Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Tongping Luo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Rui Feng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yanyan Wu
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yu Zeng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Can Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Hui Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhijian Xu
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Guofu Deng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
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Ma S, Dong Z, Cui Q, Liu JY, Zhang JT. eIF3i regulation of protein synthesis, cell proliferation, cell cycle progression, and tumorigenesis. Cancer Lett 2020; 500:11-20. [PMID: 33301799 DOI: 10.1016/j.canlet.2020.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/22/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023]
Abstract
eIF3i, a 36-kDa protein, is a putative subunit of the eIF3 complex important for translation initiation of mRNAs. It is a WD40 domain-containing protein with seven WD40 repeats that forms a β-propeller structure with an important function in pre-initiation complex formation and mRNA translation initiation. In addition to participating in the eIF3 complex formation for global translational control, eIF3i may bind to specific mRNAs and regulate their translation individually. Furthermore, eIF3i has been shown to bind to TGF-β type II receptor and participate in TGF-β signaling. It may also participate in and regulate other signaling pathways including Wnt/β-catenin pathway via translational regulation of COX-2 synthesis. These multiple canonical and noncanonical functions of eIF3i in translational control and in regulating signal transduction pathways may be responsible for its role in cell differentiation, cell cycle regulation, proliferation, and tumorigenesis. In this review, we will critically evaluate recent progresses and assess future prospects in studying eIF3i.
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Affiliation(s)
- Shijie Ma
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China.
| | - Zizheng Dong
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA
| | - Qingbin Cui
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA.
| | - Jian-Ting Zhang
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA.
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Vance TDR, Ye Q, Conroy B, Davies PL. Essential role of calcium in extending RTX adhesins to their target. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100036. [PMID: 32984811 PMCID: PMC7493085 DOI: 10.1016/j.yjsbx.2020.100036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/12/2020] [Accepted: 09/02/2020] [Indexed: 11/25/2022]
Abstract
Elongated beta-sandwich repeats are a major part of bacterial RTX adhesins. The repeats are arranged in tandem to extend away from the bacterial surface. Calcium ions are coordinated in the linkers between repeats to stiffen the protein. Rigidification of the tandem repeats further helps extension of the adhesin. The repeats differ greatly between species, but all have Ca2+ in their linkers.
RTX adhesins are long, multi-domain proteins present on the outer membrane of many Gram-negative bacteria. From this vantage point, adhesins use their distal ligand-binding domains for surface attachment leading to biofilm formation. To expand the reach of the ligand-binding domains, RTX adhesins maintain a central extender region of multiple tandem repeats, which makes up most of the proteins’ large molecular weight. Alignments of the 10-15-kDa extender domains show low sequence identity between adhesins. Here we have produced and structurally characterized protein constructs of four tandem repeats (tetra-tandemers) from two different RTX adhesins. In comparing the tetra-tandemers to each other and already solved structures from Marinomonas primoryensis and Salmonella enterica, the extender domains fold as diverse beta-sandwich structures with widely differing calcium contents. However, all the tetra-tandemers have at least one calcium ion coordinated in the linker region between beta-sandwich domains whose role appears to be the rigidification of the extender region to help the adhesin extend its reach.
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Affiliation(s)
- Tyler D R Vance
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
| | - Qilu Ye
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
| | - Brigid Conroy
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
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Liu YC, Ma W, Niu JF, Li B, Zhou W, Liu S, Yan YP, Ma J, Wang ZZ. Systematic analysis of SmWD40s, and responding of SmWD40-170 to drought stress by regulation of ABA- and H 2O 2-induced stomal movement in Salvia miltiorrhiza bunge. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 153:131-140. [PMID: 32502715 DOI: 10.1016/j.plaphy.2020.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/28/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
WD40 proteins play crucial roles in response to abiotic stress. By screening the genome sequences of Salvia miltiorrhiza Bunge, 225 SmWD40 genes were identified and divided into 9 subfamilies (I-IX). Physiological, biochemical, gene structure, conserved protein motif and GO annotation analyses were performed on SmWD40 family members. The SmWD40-170 was found in 110 SmWD40 genes that contain drought response elements, SmWD40-170 was one of these genes whose response in terms of expression under drought was significant. The expression of SmWD40-170 was also up-regulated by ABA and H2O2. Through observed the stomatal phenotype of SmWD40-170 transgenic lines, the stomatal closure was abolished under dehydration, ABA and H2O2 treatment in SmWD40-170 knockdown lines. Abscisic acid (ABA), as the key phytohormone, elevates reactive oxygen species (ROS) levels under drought stress. The ABA-ROS interaction mediated the generation of H2O2 and the activation of anion channel in guard cells. The osmolality alteration of guard cells further accelerated the stomatal closure. As a second messenger, nitric oxide (NO) regulated ABA signaling, the NO stimulated protein kinase activity inhibited the K+ influx which result in stomatal closure. These NO-relevant events were essential for ABA-induced stomatal closure. The reduction of NO production was also observed in the guard cells of SmWD40-170 knockdown lines. The abolished of stomatal closure attributed to the SmWD40-170 deficiency induced the reduction of NO content. In general, the SmWD40-170 is a critical drought response gene in SmWD40 gene family and regulates ABA- and H2O2-induced stomatal movement by affecting the synthesis of NO.
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Affiliation(s)
- Yuan-Chu Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Wen Ma
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Jun-Feng Niu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Bin Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Wen Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Shuai Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Ya-Ping Yan
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Ji Ma
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Zhe-Zhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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11
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McNeill SM, Giles NM, Preston D, Jones PP, Crowley JD, Giles GI. Quadruply Stranded Metallo-Supramolecular Helicate [Pd 2(hextrz) 4] 4+ Acts as a Molecular Mimic of Cytolytic Peptides. Chem Res Toxicol 2020; 33:1822-1834. [PMID: 32347099 DOI: 10.1021/acs.chemrestox.0c00061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Pd2(hextrz)4]4+ is a quadruply stranded helicate, a novel bioinorganic complex designed to mimic the structure and function of proteins due to its high stability and supramolecular size. We have previously reported that [Pd2(hextrz)4]4+ exhibited cytotoxicity toward a range of cell lines, with IC50 values ranging from 3 to 10 μM. Here we demonstrate that [Pd2(hextrz)4]4+ kills cells by forming pores within the cell membrane, a mechanism of cell death analogous to the naturally occurring cytolytic peptides. [Pd2(hextrz)4]4+ induced cell death is characterized by an initial influx of Ca2+, followed by nuclear condensation and mitochondrial swelling. This is accompanied by progressive cell membrane damage that results in the formation of large blebs at the cell surface. This allows the efflux of molecules from the cell leading to loss of cell viability. These data suggest that it may be possible to design metallo-supramolecular complexes to mimic the cytotoxic action of pore forming proteins and peptides and so provide a new class of drug to treat cancer, autoimmune disorders, and microbial infection.
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Affiliation(s)
- Samantha M McNeill
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Niroshini M Giles
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Dan Preston
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Peter P Jones
- Department of Physiology and HeartOtago, University of Otago, Dunedin, New Zealand
| | - James D Crowley
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Gregory I Giles
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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12
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Miotto M, Di Rienzo L, Corsi P, Ruocco G, Raimondo D, Milanetti E. Simulated Epidemics in 3D Protein Structures to Detect Functional Properties. J Chem Inf Model 2020; 60:1884-1891. [PMID: 32011881 DOI: 10.1021/acs.jcim.9b01027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The outcome of an epidemic is closely related to the network of interactions between individuals. Likewise, protein functions depend on the 3D arrangement of their residues and the underlying energetic interaction network. Borrowing ideas from the theoretical framework that has been developed to address the spreading of real diseases, we study for the first time the diffusion of a fictitious epidemic inside the protein nonbonded interaction network, aiming to study network features and properties. Our approach allows us to probe the overall stability and the capability of propagating information in complex 3D structures, proving to be very efficient in addressing different problems, from the assessment of thermal stability to the identification of functional sites.
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Affiliation(s)
- Mattia Miotto
- Department of Physics, Sapienza University, Rome 00185, Italy.,Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome 00161, Italy
| | | | - Pietro Corsi
- Department of Science, Roma Tre University, Rome 00154, Italy
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University, Rome 00185, Italy.,Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome 00161, Italy
| | - Domenico Raimondo
- Department of Molecular Medicine, Sapienza University, Rome 00161, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Rome 00185, Italy.,Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome 00161, Italy
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Mannige RV. An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h). PeerJ 2017; 5:e3327. [PMID: 28533975 PMCID: PMC5436576 DOI: 10.7717/peerj.3327] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/18/2017] [Indexed: 12/19/2022] Open
Abstract
The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ = − 100° left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.
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Affiliation(s)
- Ranjan V Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Multiscale Institute, Redwood City, CA, United States
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14
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Hsiao YC, Hsu YF, Chen YC, Chang YL, Wang CS. A WD40 protein, AtGHS40, negatively modulates abscisic acid degrading and signaling genes during seedling growth under high glucose conditions. JOURNAL OF PLANT RESEARCH 2016; 129:1127-1140. [PMID: 27443795 DOI: 10.1007/s10265-016-0849-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/18/2016] [Indexed: 06/06/2023]
Abstract
The Arabidopsis thaliana T-DNA insertion mutant glucose hypersensitive (ghs) 40-1 exhibited hypersensitivity to glucose (Glc) and abscisic acid (ABA). The ghs40-1 mutant displayed severely impaired cotyledon greening and expansion and showed enhanced reduction in hypocotyl elongation of dark-grown seedlings when grown in Glc concentrations higher than 3 %. The Glc-hypersensitivity of ghs40-1 was correlated with the hyposensitive phenotype of 35S::AtGHS40 seedlings. The phenotypes of ghs40-1 were recovered by complementation with 35S::AtGHS40. The AtGHS40 (At5g11240) gene encodes a WD40 protein localized primarily in the nucleus and nucleolus using transient expression of AtGHS40-mRFP in onion cells and of AtGHS40-EGFP and EGFP-AtGHS40 in Arabidopsis protoplasts. The ABA biosynthesis inhibitor fluridone extensively rescued Glc-mediated growth arrest. Quantitative real time-PCR analysis showed that AtGHS40 was involved in the control of Glc-responsive genes. AtGHS40 acts downstream of HXK1 and is activated by ABI4 while ABI4 expression is negatively modulated by AtGHS40 in the Glc signaling network. However, AtGHS40 may not affect ABI1 and SnRK2.6 gene expression. Given that AtGHS40 inhibited ABA degrading and signaling gene expression levels under high Glc conditions, a new circuit of fine-tuning modulation by which ABA and ABA signaling gene expression are modulated in balance, occurred in plants. Thus, AtGHS40 may play a role in ABA-mediated Glc signaling during early seedling development. The biochemical function of AtGHS40 is also discussed.
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Affiliation(s)
- Yu-Chun Hsiao
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
- NCHU-UCD Plant and Food Biotechnology Center, NCHU, Taichung, 40227, Taiwan
- Agricultural Biotechnology Center, NCHU, Taichung, 40227, Taiwan
| | - Yi-Feng Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
- NCHU-UCD Plant and Food Biotechnology Center, NCHU, Taichung, 40227, Taiwan
- Agricultural Biotechnology Center, NCHU, Taichung, 40227, Taiwan
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yun-Chu Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
- NCHU-UCD Plant and Food Biotechnology Center, NCHU, Taichung, 40227, Taiwan
- Agricultural Biotechnology Center, NCHU, Taichung, 40227, Taiwan
| | - Yi-Lin Chang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Co-Shine Wang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan.
- NCHU-UCD Plant and Food Biotechnology Center, NCHU, Taichung, 40227, Taiwan.
- Agricultural Biotechnology Center, NCHU, Taichung, 40227, Taiwan.
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15
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Mannige RV, Kundu J, Whitelam S. The Ramachandran Number: An Order Parameter for Protein Geometry. PLoS One 2016; 11:e0160023. [PMID: 27490241 PMCID: PMC4973960 DOI: 10.1371/journal.pone.0160023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 07/12/2016] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called ϕ and ψ. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional plot drawn in the space of the angles ϕ and ψ, called a Ramachandran plot. By contrast, a recently-discovered nanomaterial made from peptoids, structural isomers of peptides, displays a secondary-structure motif corresponding to two regions on the Ramachandran plot [Mannige et al., Nature 526, 415 (2015)]. In order to describe such ‘higher-order’ secondary structure in a compact way we introduce here a means of describing regions on the Ramachandran plot in terms of a single Ramachandran number, R, which is a structurally meaningful combination of ϕ and ψ. We show that the potential applications of R are numerous: it can be used to describe the geometric content of protein structures, and can be used to draw diagrams that reveal, at a glance, the frequency of occurrence of regular secondary structures and disordered regions in large protein datasets. We propose that R might be used as an order parameter for protein geometry for a wide range of applications.
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Affiliation(s)
- Ranjan V. Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States of America
- * E-mail: (RVM); (SW)
| | - Joyjit Kundu
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States of America
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States of America
- * E-mail: (RVM); (SW)
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16
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Li W, Wang B, Wang M, Chen M, Yin JM, Kaleri GM, Zhang RJ, Zuo TN, You X, Yang Q. Cloning and characterization of a potato StAN11 gene involved in anthocyanin biosynthesis regulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:364-72. [PMID: 24304603 DOI: 10.1111/jipb.12136] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 11/25/2013] [Indexed: 05/16/2023]
Abstract
Anthocyanins are a class of products of plant secondary metabolism and are responsible for tubers color in potato. The biosynthesis of anthocyanins is a complex biological process, in which multiple genes are involved including structural genes and regulatory genes. In this study, StAN11, a WD40-repeat gene, was cloned from potato cultivar Chieftain (Solanum tuberosum L.). StAN11 (HQ599506) contained no intron and its open reading frame (ORF) was 1,029 bp long, encoding a putative protein of 342 amino acids. In order to verify its role in anthocyanin biosynthesis, StAN11 was inserted behind the CaMV-35S promoter of pCMBIA1304 and the recombination vector was introduced into the potato cultivar Désirée plants by Agrobacterium-mediated transformation. The color of transgenic tuber skin was significantly deepened, compared to the wild-type control, which was highly consistent with the accumulation of anthocyanin and expression of StAN11 in transgenic lines tuber skin. Further analysis on the expression of Flavonone-3-hydroxylase (F3H), Dihydroflavonol reductase (DFR), Anthocyanidin synthase (ANS), and Flavonoid 3-O-glucosyl transferase (3GT) in transgenic plants revealed that only DFR was upregulated. This result suggested that StAN11 regulated anthocyanin biosynthesis in potato by controlling DFR expression and accumulation of anthocyanin could be increased through overexpression of StAN11 in the tubers with the genetic background of anthocyanin biosynthesis.
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Affiliation(s)
- Wang Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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17
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Mannige RV. Origination of the Protein Fold Repertoire from Oily Pluripotent Peptides. Proteomes 2014; 2:154-168. [PMID: 28250375 PMCID: PMC5302733 DOI: 10.3390/proteomes2020154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/27/2014] [Accepted: 03/20/2014] [Indexed: 11/16/2022] Open
Abstract
While the repertoire of protein folds that exists today underlies most of life’s capabilities, our mechanistic picture of protein fold origination is incomplete. This paper discusses a hypothetical mechanism for the emergence of the protein fold repertoire from highly dynamic and collapsed peptides, exemplified by peptides with high oil content or hydrophobicity. These peptides are called pluripotent to emphasize their capacity to evolve into numerous folds transiently available to them. As evidence, the paper will discuss previous simulation work on the superior fold evolvability of oily peptides, trace (“fossil”) evidence within proteomes seen today, and a general relationship between protein dynamism and evolvability. Aside from implications on the origination of protein folds, the hypothesis implies that the vanishing utility of a random peptide in protein origination may be relatively exaggerated, as some random peptides with a certain composition (e.g., oily) may fare better than others. In later sections, the hypothesis is discussed in the context of existing discussions regarding the spontaneous origination of biomolecules.
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Affiliation(s)
- Ranjan V Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720,USA.
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18
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Mannige RV. Dynamic New World: Refining Our View of Protein Structure, Function and Evolution. Proteomes 2014; 2:128-153. [PMID: 28250374 PMCID: PMC5302727 DOI: 10.3390/proteomes2010128] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/12/2014] [Accepted: 02/20/2014] [Indexed: 01/06/2023] Open
Abstract
Proteins are crucial to the functioning of all lifeforms. Traditional understanding posits that a single protein occupies a single structure ("fold"), which performs a single function. This view is radically challenged with the recognition that high structural dynamism-the capacity to be extra "floppy"-is more prevalent in functional proteins than previously assumed. As reviewed here, this dynamic take on proteins affects our understanding of protein "structure", function, and evolution, and even gives us a glimpse into protein origination. Specifically, this review will discuss historical developments concerning protein structure, and important new relationships between dynamism and aspects of protein sequence, structure, binding modes, binding promiscuity, evolvability, and origination. Along the way, suggestions will be provided for how key parts of textbook definitions-that so far have excluded membership to intrinsically disordered proteins (IDPs)-could be modified to accommodate our more dynamic understanding of proteins.
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Affiliation(s)
- Ranjan V Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road,Berkeley, CA 94720, USA.
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19
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Abstract
In the present article, we provide a brief overview of the main approaches to analysing the sequence-structure relationship of proteins and outline a novel method of structure prediction. The proposed method involves finding a set of rules that describes a correlation between the distribution of residues in a sequence and the essential structural characteristics of a protein structure. The residue distribution rules specify the 'favourable' residues that are required in certain positions of a polypeptide chain in order for it to assume a particular protein fold, and the 'unfavourable' residues incompatible with the given fold. Identification of amino acid distribution rules derives from examination of inter-residue contacts. We describe residue distribution rules for a large group of β-sandwich-like proteins characterized by a specific arrangement of strands in their two β-sheets. It was shown that this method has very high accuracy (approximately 85%). The advantage of the residue rule approach is that it makes possible prediction of protein folding even in polypeptide chains that have very low global sequence similarities, as low as 18%. Another potential benefit is that a better understanding of which residues play essential roles in a given protein fold may facilitate rational protein engineering design.
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20
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Guilloux A, Caudron B, Jestin JL. A method to predict edge strands in beta-sheets from protein sequences. Comput Struct Biotechnol J 2013; 7:e201305001. [PMID: 24688737 PMCID: PMC3962219 DOI: 10.5936/csbj.201305001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/27/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022] Open
Abstract
There is a need for rules allowing three-dimensional structure information to be derived from protein sequences. In this work, consideration of an elementary protein folding step allows protein sub-sequences which optimize folding to be derived for any given protein sequence. Classical mechanics applied to this system and the energy conservation law during the elementary folding step yields an equation whose solutions are taken over the field of rational numbers. This formalism is applied to beta-sheets containing two edge strands and at least two central strands. The number of protein sub-sequences optimized for folding per amino acid in beta-strands is shown in particular to predict edge strands from protein sequences. Topological information on beta-strands and loops connecting them is derived for protein sequences with a prediction accuracy of 75%. The statistical significance of the finding is given. Applications in protein structure prediction are envisioned such as for the quality assessment of protein structure models.
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Affiliation(s)
- Antonin Guilloux
- Analyse algébrique, Institut de Mathématiques de Jussieu, Université Pierre et Marie Curie, Paris VI, France
| | - Bernard Caudron
- Centre d'Informatique pour la Biologie, Institut Pasteur, Paris, France
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21
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Affiliation(s)
- Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa 31905, Israel;
| | - Leonid Pereyaslavets
- Department of Structural Biology, Stanford University, Stanford, California 94305; ,
| | | | - Michael Levitt
- Department of Structural Biology, Stanford University, Stanford, California 94305; ,
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22
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Krajewski Z, Tkacz E. Feature Selection of Protein Structural Classification Using SVM Classifier. Biocybern Biomed Eng 2013. [DOI: 10.1016/s0208-5216(13)70055-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Albornos L, Martín I, Iglesias R, Jiménez T, Labrador E, Dopico B. ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae. BMC PLANT BIOLOGY 2012; 12:207. [PMID: 23134664 PMCID: PMC3499167 DOI: 10.1186/1471-2229-12-207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 10/12/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. RESULTS ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. CONCLUSIONS We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40 amino acid tandem repeat proteins and also from known cell wall proteins with repeat sequences. Several putative roles in plant physiology can be inferred from the characteristics found.
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Affiliation(s)
- Lucía Albornos
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Ignacio Martín
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Rebeca Iglesias
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Teresa Jiménez
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Emilia Labrador
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Berta Dopico
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
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AKSIANOV EVGENIY, ALEXEEVSKI ANDREI. SHEEP: A TOOL FOR DESCRIPTION OF β-SHEETS IN PROTEIN 3D STRUCTURES. J Bioinform Comput Biol 2012; 10:1241003. [DOI: 10.1142/s021972001241003x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The description of a protein fold is a hard problem due to significant variability of main structural units, β-sheets and α-helixes, and their mutual arrangements. An adequate description of the structural units is an important step in objective protein structure classification, which to date is based on expert judgment in a number of cases. Explicit determination and description of structural units is more complicated for β-sheets than for α-helixes due to β-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify β-sheets detected by commonly used DSSP and Stride algorithms and represent the result as a “β-sheet map,” a table describing certain β-sheet features. In our approach, β-sheets (rather than β-strands) are considered as holistic objects. Both hydrogen bonds and geometrical restrains are explored for the determination of β-sheets. The algorithm is implemented in SheeP program. It was tested for prediction architectures of domains from 93 well-defined all-β and α/β SCOP protein domain families, and showed 93% of correct results. The Web-service http://mouse.belozersky.msu.ru/sheep allows to detect β-sheets in a given protein structure, visualize β-sheet maps, as well as input three-dimensional structures with highlighted β-sheets and their structural features.
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Affiliation(s)
- EVGENIY AKSIANOV
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia
| | - ANDREI ALEXEEVSKI
- Department of Bioengineering and Bioinformatics & Belozersky Institute of Physico-Chemical, Biology, Moscow State University, Leninskie Gory 1-37 & 1-40, Moscow 119991, Russia
- Scientific Research Institute for System Studies (NIISI RAN), Moscow, Russia
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25
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Ouyang Y, Huang X, Lu Z, Yao J. Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice. BMC Genomics 2012; 13:100. [PMID: 22429805 PMCID: PMC3329404 DOI: 10.1186/1471-2164-13-100] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 03/20/2012] [Indexed: 02/04/2023] Open
Abstract
Background WD40 proteins represent a large family in eukaryotes, which have been involved in a broad spectrum of crucial functions. Systematic characterization and co-expression analysis of OsWD40 genes enable us to understand the networks of the WD40 proteins and their biological processes and gene functions in rice. Results In this study, we identify and analyze 200 potential OsWD40 genes in rice, describing their gene structures, genome localizations, and evolutionary relationship of each member. Expression profiles covering the whole life cycle in rice has revealed that transcripts of OsWD40 were accumulated differentially during vegetative and reproductive development and preferentially up or down-regulated in different tissues. Under phytohormone treatments, 25 OsWD40 genes were differentially expressed with treatments of one or more of the phytohormone NAA, KT, or GA3 in rice seedlings. We also used a combined analysis of expression correlation and Gene Ontology annotation to infer the biological role of the OsWD40 genes in rice. The results suggested that OsWD40 genes may perform their diverse functions by complex network, thus were predictive for understanding their biological pathways. The analysis also revealed that OsWD40 genes might interact with each other to take part in metabolic pathways, suggesting a more complex feedback network. Conclusions All of these analyses suggest that the functions of OsWD40 genes are diversified, which provide useful references for selecting candidate genes for further functional studies.
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Affiliation(s)
- Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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26
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Murphy BM, Zhang N, Payne RW, Davis JM, Abdul-Fattah AM, Matsuura JE, Herman AC, Manning MC. Structure, stability, and mobility of a lyophilized IgG1 monoclonal antibody as determined using second-derivative infrared spectroscopy. J Pharm Sci 2011; 101:81-91. [PMID: 21918984 DOI: 10.1002/jps.22753] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 06/13/2011] [Accepted: 08/18/2011] [Indexed: 12/11/2022]
Abstract
There are many aspects of stabilization of lyophilized proteins. Of these various factors, retention of native structure, having sufficient amount of stabilizer to embed the protein within an amorphous matrix, and dampening β-relaxations have been shown to be critical in optimizing protein stability during storage. In this study, an IgG1 was lyophilized with varying amounts of sucrose. In some formulations, a small amount of sorbitol was added as a plasticizer. The structure of the protein in dried state was monitored using infrared (IR) spectroscopy. The IR spectra indicated increasing retention of the native structure, which correlated with stability as indicated by size-exclusion chromatography as well as micro-flow imaging. Maximal stability was achieved with a 2:1 mass ratio of sucrose to protein, which is more than that would be expected based on earlier studies. Analysis of both high and low frequency bands associated with intramolecular β-sheet structure provides additional information on the structure of antibodies in the solid state. Finally, there is a correlation between the bandwidth of the β-sheet bands and the enthalpy of relaxation, suggesting that amide I bands can provide some indication of the degree of coupling to the sugar matrix, as well as structural heterogeneity of the protein.
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27
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Andreeva A, Murzin AG. Structural classification of proteins and structural genomics: new insights into protein folding and evolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1190-7. [PMID: 20944210 PMCID: PMC2954204 DOI: 10.1107/s1744309110007177] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/24/2010] [Indexed: 11/10/2022]
Abstract
During the past decade, the Protein Structure Initiative (PSI) centres have become major contributors of new families, superfamilies and folds to the Structural Classification of Proteins (SCOP) database. The PSI results have increased the diversity of protein structural space and accelerated our understanding of it. This review article surveys a selection of protein structures determined by the Joint Center for Structural Genomics (JCSG). It presents previously undescribed β-sheet architectures such as the double barrel and spiral β-roll and discusses new examples of unusual topologies and peculiar structural features observed in proteins characterized by the JCSG and other Structural Genomics centres.
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Affiliation(s)
- Antonina Andreeva
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England
| | - Alexey G. Murzin
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England
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28
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Stott KM, Yusof AM, Perham RN, Jones DD. A surface loop directs conformational switching of a lipoyl domain between a folded and a novel misfolded structure. Structure 2010; 17:1117-27. [PMID: 19679089 DOI: 10.1016/j.str.2009.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 06/30/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
A prominent surface loop links the first two beta strands of the lipoyl domain (E2plip) from the pyruvate dehydrogenase multienzyme complex of Escherichia coli. We show here that shortening this loop by two residues generates a protein that populates two structurally distinct stable conformers: an active, native-like monomer (HM) and a functionally compromised misfolded dimer (LM). Conversion of LM to HM was observed after exposure to temperatures above 50 degrees C. Removal of two additional residues from the loop caused the protein to adopt exclusively the misfolded conformation. Detailed NMR structural studies of the misfolded dimer reveal that the N-terminal half of the domain was unfolded and dynamic, whereas the C-terminal halves of two monomers had associated to form a structure with two-fold symmetry and a topology mimicking that of the folded monomer. The surface loop is therefore a hitherto unsuspected determinant in the folding process that leads to a functional protein.
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29
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Protein Structure Hierarchy. INTERDISCIPLINARY APPLIED MATHEMATICS 2010. [PMCID: PMC7139416 DOI: 10.1007/978-1-4419-6351-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complexity of protein structures requires a description of their structural components. This chapter describes the elements of protein secondary structure — regular local structural patterns — such as helices, sheets, turns, and loops. Helices and sheets tend to fall into specific regions in the {ϕ, ψ} space of the Ramachandran plot (see Figures 28 and 29). The corresponding width and shape of each region reflects the spread of that motif as found in proteins.
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30
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Rathore RS. Study on β-sheet packing, stabilized by aromatic interactions in a tri-peptide crystal. Z KRIST-CRYST MATER 2009. [DOI: 10.1524/zkri.219.9.567.44043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The role of unconventional aromatic interactions in the β-sheet packing, inside the crystal, has been highlighted. Crystal structure of terminally blocked tri-peptide, Z-L-Ala-L-Ala-L-Leu-pNA has been determined. There are four different conformers of tri-peptide inside the unit-cell, in space group P1. All the four independent molecules are described by semi-extended backbone conformations which form an anti-parallel β-sheet. The inter β-sheet packing is predominantly stabilized by C—H…π and π…π interactions. In π…π interactions, the center-to-center distance between aromatic rings varies from 3.8 Å to 4.6 Å while the closest distance of approach ranges from 3.4 Å to 3.8 Å. The associations of aromatic-aromatic rings are described by either face-to-face or inclined arrangements.
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31
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Verma A, Wenzel W. A free-energy approach for all-atom protein simulation. Biophys J 2009; 96:3483-94. [PMID: 19413955 DOI: 10.1016/j.bpj.2008.12.3921] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 11/24/2008] [Accepted: 12/01/2008] [Indexed: 11/29/2022] Open
Abstract
All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 A to the native conformation and an average Z-score of -3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded beta-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger beta beta alpha motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 A to their respective experimental conformations.
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Affiliation(s)
- Abhinav Verma
- Institute of Scientific Computing, Forschungszentrum Karlsruhe, Karlsruhe, Germany
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32
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Mounce BC, Kurt N, Ellison PA, Cavagnero S. Nonrandom distribution of intramolecular contacts in native single-domain proteins. Proteins 2009; 75:404-12. [DOI: 10.1002/prot.22258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Nandi N. Chiral discrimination in the confined environment of biological nanospace: reactions and interactions involving amino acids and peptides. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350902999682] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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SRWD: a novel WD40 protein subfamily regulated by salt stress in rice (OryzasativaL.). Gene 2008; 424:71-9. [PMID: 18755256 DOI: 10.1016/j.gene.2008.07.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 07/12/2008] [Accepted: 07/15/2008] [Indexed: 02/04/2023]
Abstract
By analysis with microarray data, we found that a gene encoding a novel protein containing five WD40 repeats, was regulated by salt stress in rice and named as SRWD1 (Salt responsive WD40 protein 1). By database searching, additional four SRWD1-like genes (SRWD2-SRWD5) were found in rice genome, and these five SRWD genes formed a novel WD40 subfamily. Phylogenetic analysis showed that plant SRWD proteins divided into four groups. The significant functional divergences during SRWD evolution were found. The tissue-specific and salt responsive expression profiling for SRWD genes was investigated based on microarray data. It was found that all five SRWD genes in rice were regulated by salt stress. Further, we found that SRWD1 was regulated with different patterns by salt stress in two rice cultivars responding differently to salt stress. Our study correlates WD40 proteins with salt stress in plants and provides fundamental information for the further investigation of plant SRWD proteins.
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35
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Kowadlo G, Hall NE, Burgess AW. De novo design of beta-helical polypeptides. Growth Factors 2007; 25:168-90. [PMID: 18049953 DOI: 10.1080/08977190701679772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Many proteins, including several growth factor receptors such as the IGF-1R and EGFR family, contain variants of the beta-helix fold. Inspection of the irregular protein beta-helices suggested that different families of regular beta-helical polypeptides can be designed using a series of hinged vectors and the constraints imposed by the geometry of a peptide backbone. We have conceived beta-helices with five and six beta-strands per turn and designed, in detail, a series of regular beta-helices with rhomboidal or triangular cross-sections. Each beta-helix was modeled by threading C(alpha) atoms to follow the vectorial beta-helix and then creating the H-bonded polypeptide backbone and appropriate side-chain orientations. The conformational stability of these regular beta-helices was assessed using molecular dynamics simulations. Several potential repeat amino acid sequences were identified for different geometries of beta-helix. Regular beta-helices offer new possibilities for the study of protein folding, the production of nanofibers, catalysts, inhibitors of growth factor receptors and drug carriers.
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Affiliation(s)
- Gideon Kowadlo
- Ludwig Institute for Cancer Research, Tumor Biology Branch, Melbourne, Australia
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36
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Han W, Wu YD. Molecular dynamics studies of hexamers of amyloid-beta peptide (16-35) and its mutants: influence of charge states on amyloid formation. Proteins 2007; 66:575-87. [PMID: 17115426 DOI: 10.1002/prot.21232] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To study the early stage of amyloid-beta peptide (Abeta) aggregation, hexamers of the wild-type (WT) Abeta(16-35) and its mutants with amyloid-like conformations have been studied by molecular dynamics simulations in explicit water for a total time of 1.7 micros. We found that the amyloid-like structures in the WT oligomers are destabilized by the solvation of ionic D23/K28 residues, which are buried in the fibrils. This means that the desolvation of D23/K28 residues may contribute to the kinetic barrier of aggregation in the early stage. In the E22Q/D23N, D23N/K28Q, and E22Q/D23N/K28Q mutants, hydration becomes much less significant because the mutated residues have neutral amide side-chains. These amide side-chains can form linear cross-strand hydrogen bond chains, or "polar zippers", if dehydrated. These "polar zippers" increase the stability of the amyloid-like conformation, reducing the barrier for the early-stage oligomerization. This is in accord with experimental observations that both the D23/K28 lactamization and the E22Q/D23N mutation promote aggregation. We also found that the E22Q/D23N mutant prefers an amyloid-like conformation that differs from the one found for WT Abeta. This suggests that different amyloid structures may be formed under different conditions.
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Affiliation(s)
- Wei Han
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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37
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Choi IG, Kim SH. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci U S A 2006; 103:14056-61. [PMID: 16959887 PMCID: PMC1560931 DOI: 10.1073/pnas.0606239103] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, the evolution of genes may have been constrained or selected to those genetic changes that results in structurally stable proteins occupying one of the four "allowed" regions of the protein structure space, "structural selection," an important component of natural selection in gene evolution. Our studies on tracing the "common structural ancestor" for each protein sequence family of known structure suggest that: (i) recently emerged proteins belong mostly to three classes; (ii) the proteins that emerged earlier evolved to gain a new class; and (iii) the proteins that emerged earliest evolved to become the present-day proteins in the four major classes, with the fourth-class proteins becoming the most dominant population. Furthermore, our studies also show that not all present-day proteins evolved from one single set of proteins in the last common ancestral organism, but new common ancestral proteins were "born" at different evolutionary times, not traceable to one or two ancestral proteins: "the multiple birth model" for the evolution of protein sequence families.
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Affiliation(s)
- In-Geol Choi
- *Physical Biosciences Division, Lawrence Berkeley National Laboratory, and
| | - Sung-Hou Kim
- *Physical Biosciences Division, Lawrence Berkeley National Laboratory, and
- Department of Chemistry, University of California, Berkeley, CA 94720
- To whom correspondence should be addressed. E-mail:
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38
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Duan HY, Li FG, Wu XD, Ma DM, Wang M, Hou YX. The cloning and sequencing of a cDNA encoding a WD repeat protein in cotton (Gossypium hirsutum L.). ACTA ACUST UNITED AC 2006; 17:49-55. [PMID: 16753817 DOI: 10.1080/10425170500476418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this research, one 1156 bp cDNA containing full open reading frame and encoding a novel 24-kDa protein with four tandem WD repeat motifs was cloned from cotton, therefore was named GhWDR and the GenBank accession number is AY870657. By search of GhWDR cDNA and amino acid sequences in the database, we found that GhWDR and OSJNBa0003G23.2 from Oryza sativa show 90% sequence identity and 84% identity to WD-repeat protein from Arabidopsis thaliana, and also has high sequence identity to other WD repeat proteins, most of which are similar to Pop3 from fission yeast (accession number T39922) and Lst8p from Saccharomyces cerevisiae (accession number NP014392). Therefore, we proposed that GhWDR could act in some cellular processes as pop3 or LST8 does. In addition, the expression of GhWDR in various tissues was studied by RT-PCR, and it is expressed in all of the studied tissues, but the level of expression is low in the leaves when compared to that of other tissues.
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Affiliation(s)
- Hong Y Duan
- College of Biological Sciences, China Agriculture University, Beijing 100094, P. R. China
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39
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Fokas AS, Papatheodorou TS, Kister AE, Gelfand IM. A geometric construction determines all permissible strand arrangements of sandwich proteins. Proc Natl Acad Sci U S A 2005; 102:15851-3. [PMID: 16249331 PMCID: PMC1276083 DOI: 10.1073/pnas.0507335102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For a large class of proteins called sandwich-like proteins (SPs), the secondary structures consist of two beta-sheets packed face-to-face, with each beta-sheet consisting typically of three to five beta-strands. An important step in the prediction of the three-dimensional structure of a SP is the prediction of its supersecondary structure, namely the prediction of the arrangement of the beta-strands in the two beta-sheets. Recently, significant progress in this direction was made, where it was shown that 91% of observed SPs form what we here call "canonical motifs." Here, we show that all canonical motifs can be constructed in a simple manner that is based on thermodynamic considerations and uses certain geometric structures. The number of these structures is much smaller than the number of possible strand arrangements. For instance, whereas for SPs consisting of six strands there exist a priori 900 possible strand arrangements, there exist only five geometric structures. Furthermore, the few motifs that are noncanonial can be constructed from canonical motifs by a simple procedure.
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Affiliation(s)
- A S Fokas
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom.
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40
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Anne J, Mechler BM. Valois, a component of the nuage and pole plasm, is involved in assembly of these structures, and binds to Tudor and the methyltransferase Capsuléen. Development 2005; 132:2167-77. [PMID: 15800004 DOI: 10.1242/dev.01809] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Using the Capsuleen (Csul) methyltransferase as bait in the yeast two-hybrid system, we have identified a novel Drosophila protein containing multiple WD repeats and encoded by the valois (vsl) gene, which acts in pole plasm function. Vls is homologous to human MEP50, which forms a complex with the PRMT5 methyltransferase--the human homologue of Csul. We found that Vls localizes to the nuage in the nurse cells and to the pole plasm in the oocyte. Moreover vls is required for the synthesis and/or stability of Oskar and the localization of Tudor (Tud) in both the nuage and at the posterior pole of the oocyte. Furthermore, we show that Vls and a fragment of Tud interact directly in binding assay. As the PMRT5/MEP50 complex is involved in ribonucleoprotein complex assembly, we hypothesize that the Vls complex may play a similar function in assembling the nuage in nurse cells and the polar granules in the oocyte.
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Affiliation(s)
- Joël Anne
- Department of Developmental Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
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41
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Sandberg A, Leckner J, Karlsson BG. Apo-azurin folds via an intermediate that resembles the molten-globule. Protein Sci 2005; 13:2628-38. [PMID: 15388858 PMCID: PMC2286560 DOI: 10.1110/ps.04848204] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The folding of Pseudomonas aeruginosa apo-azurin was investigated with the intent of identifying putative intermediates. Two apo-mutants were constructed by replacing the main metal-binding ligand C112 with a serine (C112S) and an alanine (C112A). The guanidinium-induced unfolding free energies (DeltaG(U-N)(H2O)) of the C112S and C112A mutants were measured to 36.8 +/- 1 kJ mole(-1) and 26.1 +/- 1 kJ mole(-1), respectively, and the m-value of the transition to 23.5 +/- 0.7 kJ mole(-1) M(-1). The difference in folding free energy (DeltaDeltaG(U-N)(H2O)) is largely attributed to the intramolecular hydrogen bonding properties of the serine Ogamma in the C112S mutant, which is lacking in the C112A structure. Furthermore, only the unfolding rates differ between the two mutants, thus pointing to the energy of the native state as the source of the observed Delta DeltaG(U-N)(H2O). This also indicates that the formation of the hydrogen bonds present in C112S but absent in C112A is a late event in the folding of the apo-protein, thus suggesting that formation of the metal-binding site occurs after the rate-limiting formation of the transition state. In both mutants we also noted a burst-phase intermediate. Because this intermediate was capable of binding 1-anilinonaphtalene-8-sulfonate (ANS), as were an acid-induced species at pH 2.6, we ascribe it molten globule-like status. However, despite the presence of an intermediate, the folding of apo-azurin C112S is well approximated by a two-state kinetic mechanism.
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Affiliation(s)
- Anders Sandberg
- Department of Chemistry, Göteborg University, Göteborg, Sweden
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42
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Soto P, Cladera J, Mark AE, Daura X. Stability of SIV gp32 Fusion‐Peptide Single‐Layer Protofibrils as Monitored by Molecular‐Dynamics Simulations. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Patricia Soto
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Josep Cladera
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Alan E. Mark
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Xavier Daura
- Catalan Institution for Research and Advanced Studies (ICREA), Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, Fax: (+34) 93‐581‐2011
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43
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Chaput JC, Szostak JW. Evolutionary optimization of a nonbiological ATP binding protein for improved folding stability. ACTA ACUST UNITED AC 2005; 11:865-74. [PMID: 15217619 DOI: 10.1016/j.chembiol.2004.04.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 04/15/2004] [Accepted: 04/21/2004] [Indexed: 11/20/2022]
Abstract
Structural comparison of in vitro evolved proteins with biological proteins will help determine the extent to which biological proteins sample the structural diversity available in protein sequence space. We have previously isolated a family of nonbiological ATP binding proteins from an unconstrained random sequence library. One of these proteins was further optimized for high-affinity binding to ATP, but biophysical characterization proved impossible due to poor solubility. To determine if such nonbiological proteins can be optimized for improved folding stability, we performed multiple rounds of mRNA-display selection under increasingly denaturing conditions. Starting from a pool of protein variants, we evolved a population of proteins capable of binding ATP in 3 M guanidine hydrochloride. One protein was chosen for further characterization. Circular dichroism, tryptophan fluorescence, and (1)H-(15)N correlation NMR studies show that this protein has a unique folded structure.
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Affiliation(s)
- John C Chaput
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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44
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Soto P, Cladera J, Mark AE, Daura X. Stability of SIV gp32 Fusion‐Peptide Single‐Layer Protofibrils as Monitored by Molecular‐Dynamics Simulations. Angew Chem Int Ed Engl 2005; 44:1065-1067. [PMID: 15630707 DOI: 10.1002/anie.200461935] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Patricia Soto
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Josep Cladera
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Alan E Mark
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Xavier Daura
- Catalan Institution for Research and Advanced Studies (ICREA), Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, Fax: (+34) 93-581-2011
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45
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Kim N, Shiffeldrim N, Gan HH, Schlick T. Candidates for novel RNA topologies. J Mol Biol 2004; 341:1129-44. [PMID: 15321711 DOI: 10.1016/j.jmb.2004.06.054] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Revised: 06/10/2004] [Accepted: 06/21/2004] [Indexed: 10/26/2022]
Abstract
Because the functional repertiore of RNA molecules, like proteins, is closely linked to the diversity of their shapes, uncovering RNA's structural repertoire is vital for identifying novel RNAs, especially in genomic sequences. To help expand the limited number of known RNA families, we use graphical representation and clustering analysis of RNA secondary structures to predict novel RNA topologies and their abundance as a function of size. Representing the essential topological properties of RNA secondary structures as graphs enables enumeration, generation, and prediction of novel RNA motifs. We apply a probabilistic graph-growing method to construct the RNA structure space encompassing the topologies of existing and hypothetical RNAs and cluster all RNA topologies into two groups using topological descriptors and a standard clustering algorithm. Significantly, we find that nearly all existing RNAs fall into one group, which we refer to as "RNA-like"; we consider the other group "non-RNA-like". Our method predicts many candidates for novel RNA secondary topologies, some of which are remarkably similar to existing structures; interestingly, the centroid of the RNA-like group is the tmRNA fold, a pseudoknot having both tRNA-like and mRNA-like functions. Additionally, our approach allows estimation of the relative abundance of pseudoknot and other (e.g. tree) motifs using the "edge-cut" property of RNA graphs. This analysis suggests that pseudoknots dominate the RNA structure universe, representing more than 90% when the sequence length exceeds 120 nt; the predicted trend for <100 nt agrees with data for existing RNAs. Together with our predictions for novel "RNA-like" topologies, our analysis can help direct the design of functional RNAs and identification of novel RNA folds in genomes through an efficient topology-directed search, which grows much more slowly in complexity with RNA size compared to the traditional sequence-based search.
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Affiliation(s)
- Namhee Kim
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
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46
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Hong SY, Lee EY, Yang JO, Kim TY, Kim EH, Cheong MY, Kim SH, Cheong CJ. Conformational transitions and glycation of serum albumin in patients with minimal-change glomerulopathy. Korean J Intern Med 2004; 19:141-8. [PMID: 15481604 PMCID: PMC4531563 DOI: 10.3904/kjim.2004.19.3.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND There has been a lack of study on the structural changes of serum albumin in patients with minimal change disease (MCD). To determine whether glycation and/or conformational transitions of albumin are involved in the pathogenesis of albuminuria, nine patients with MCD were enrolled in a prospective follow-up study for comparison of these parameters in serum albumin during the remission and relapse of nephrotic syndrome. METHODS Circular dichroism measurements were made with purified albumin. Ellipticities at each wavelength were transformed to mean residue ellipticity. Monosaccharide composition was analyzed by high-pH anion-exchange chromatography with pulsed amperometric detection. RESULTS There was no difference in the proportions of alpha-helix, beta-conformation, and beta-turn of albumin between the sera of control patients and those with nephrotic syndrome. However, the proportion of the random configuration was slightly higher in the plasma albumin of patients in relapse than in those in remission. The proportion of the random configuration was lower in the albumin of the serum than in the urine of patients with nephrotic syndrome, but there was no difference in the proportions of alpha-helix, beta-conformation, and beta-tum of albumin between their plasma and urine. CONCLUSION Our results suggest that conformational changes in albumin are involved in albuminuria in patients with MCD.
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Affiliation(s)
| | | | - Jong Oh Yang
- Correspondence to: Jong Oh Yang, M.D., Department of Internal Medicine, Soonchunhyang University Chonan Hospital, 23-20 Bongmyung-dong, Chonan, Chungnam, 330-721, Korea, Tel: 82-41-570-2120, Fax: 82-41-574-5762, E-mail:
| | - Tae Yeong Kim
- Proteome Analysis Team, Korea Basic Science Institute, Daejon, Korea
| | - Eun Hee Kim
- Magnetic Resonance Team, Korea Basic Science Institute, Daejon, Korea
| | - Mi Young Cheong
- Proteome Analysis Team, Korea Basic Science Institute, Daejon, Korea
| | - Soo Hyun Kim
- Proteome Analysis Team, Korea Basic Science Institute, Daejon, Korea
| | - Chae Joon Cheong
- Magnetic Resonance Team, Korea Basic Science Institute, Daejon, Korea
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47
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Chakrabarti S, Sowdhamini R. Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships. FEBS Lett 2004; 569:31-6. [PMID: 15225604 DOI: 10.1016/j.febslet.2004.05.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Accepted: 05/13/2004] [Indexed: 11/21/2022]
Abstract
Structurally conserved regions or structural templates have been identified and examined for features such as amino acid content, solvent accessibility, secondary structures, non-polar interaction, residue packing and extent of structural deviations in 179 aligned members of superfamilies involving 1208 pairs of protein domains. An analysis of these structural features shows that the retention of secondary structural conservation and similar hydrogen bonding pattern within the templates is 2.5 and 1.8 times higher, respectively, than full-length alignments suggesting that they form the minimum structural requirement of a superfamily. The identification and availability of structural templates find value in different areas of protein structure prediction and modelling such as in sensitive sequence searches, accurate sequence alignment and three-dimensional modelling on the basis of distant relationships.
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Affiliation(s)
- Saikat Chakrabarti
- National Centre for Biological Sciences, UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India
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48
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Bromley EV, Taylor MC, Wilkinson SR, Kelly JM. The amino terminal domain of a novel WD repeat protein from Trypanosoma cruzi contains a non-canonical mitochondrial targeting signal. Int J Parasitol 2004; 34:63-71. [PMID: 14711591 DOI: 10.1016/j.ijpara.2003.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
WD (tryptophan/aspartic acid) repeat proteins perform a wide variety of functions in eukaryotic cells. They are characterised by the presence of a number of conserved repeat motifs that contribute to the beta-propeller structures which are the common feature of this large group of proteins. We report here the properties of the first characterised member of this family in the American trypanosome, Trypanosoma cruzi (TcBPP1). In the CL Brener clone the protein is 482 amino acids long and is predicted to contain four WD repeat motifs, flanked by amino and carboxyl terminal extensions. TcBPP1 is a single copy gene present on a 1.0/1.6 Mb pair of homologous chromosomes in a locus that is syntenic with the corresponding regions of Trypanosoma brucei and Leishmania major chromosomes. Consistent with the proposed hybrid nature of the CL Brener clone, the proteins encoded by the two different alleles share only 97% identity at the amino acid level. To determine subcellular location, we examined transfected parasites for the distribution of green fluorescent protein (GFP) fused with different regions of TcBPP1. These studies demonstrated that a 115 amino acid peptide derived from the amino terminal domain of TcBPP1 is able to target GFP to the mitochondrion. Interestingly this region lacks a typical amino terminal presequence suggesting that mitochondrial import is mediated by an alternative targeting signal.
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Affiliation(s)
- Elizabeth V Bromley
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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49
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Deyholos MK, Cavaness GF, Hall B, King E, Punwani J, Van Norman J, Sieburth LE. VARICOSE, a WD-domain protein, is required for leaf blade development. Development 2004; 130:6577-88. [PMID: 14660546 DOI: 10.1242/dev.00909] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To gain insight into the processes controlling leaf development, we characterized an Arabidopsis mutant, varicose (vcs), with leaf and shoot apical meristem defects. The vcs phenotype is temperature dependent; low temperature growth largely suppressed defects, whereas high growth temperatures resulted in severe leaf and meristem defects. VCS encodes a putative WD-domain containing protein, suggesting a function involving protein-protein interactions. Temperature shift experiments indicated that VCS is required throughout leaf development, but normal secondary vein patterning required low temperature early in leaf development. The low-temperature vcs phenotype is enhanced in axr1-3 vcs double mutants and in vcs mutants grown in the presence of polar auxin transport inhibitors, however, vcs has apparently normal auxin responses. Taken together, these observations suggest a role for VCS in leaf blade formation.
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Affiliation(s)
- Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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50
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van Nocker S, Ludwig P. The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function. BMC Genomics 2003; 4:50. [PMID: 14672542 PMCID: PMC317288 DOI: 10.1186/1471-2164-4-50] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Accepted: 12/12/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The WD motif (also known as the Trp-Asp or WD40 motif) is found in a multitude of eukaryotic proteins involved in a variety of cellular processes. Where studied, repeated WD motifs act as a site for protein-protein interaction, and proteins containing WD repeats (WDRs) are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. In the model plant Arabidopsis thaliana, members of this superfamily are increasingly being recognized as key regulators of plant-specific developmental events. RESULTS We analyzed the predicted complement of WDR proteins from Arabidopsis, and compared this to those from budding yeast, fruit fly and human to illustrate both conservation and divergence in structure and function. This analysis identified 237 potential Arabidopsis proteins containing four or more recognizable copies of the motif. These were classified into 143 distinct families, 49 of which contained more than one Arabidopsis member. Approximately 113 of these families or individual proteins showed clear homology with WDR proteins from the other eukaryotes analyzed. Where conservation was found, it often extended across all of these organisms, suggesting that many of these proteins are linked to basic cellular mechanisms. The functional characterization of conserved WDR proteins in Arabidopsis reveals that these proteins help adapt basic mechanisms for plant-specific processes. CONCLUSIONS Our results show that most Arabidopsis WDR proteins are strongly conserved across eukaryotes, including those that have been found to play key roles in plant-specific processes, with diversity in function conferred at least in part by divergence in upstream signaling pathways, downstream regulatory targets and /or structure outside of the WDR regions.
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Affiliation(s)
- Steven van Nocker
- Cell and Molecular Biology Program and Department of Horticulture, 390 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI, 48824, USA
| | - Philip Ludwig
- Cell and Molecular Biology Program and MSU-DOE Plant Research Laboratory, 2240 Biomedical Physical Sciences Building, Michigan State University, East Lansing, MI, 48824, USA
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