1
|
Gupta MN, Uversky VN. Reexamining the diverse functions of arginine in biochemistry. Biochem Biophys Res Commun 2024; 705:149731. [PMID: 38432110 DOI: 10.1016/j.bbrc.2024.149731] [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: 12/24/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Arginine in a free-state and as part of peptides and proteins shows distinct tendency to form clusters. In free-form, it has been found useful in cryoprotection, as a drug excipient for both solid and liquid formulations, as an aggregation suppressor, and an eluent in protein chromatography. In many cases, the mechanisms by which arginine acts in all these applications is either debatable or at least continues to attract interest. It is quite possible that arginine clusters may be involved in many such applications. Furthermore, it is possible that such clusters are likely to behave as intrinsically disordered polypeptides. These considerations may help in understanding the roles of arginine in diverse applications and may even lead to better strategies for using arginine in different situations.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya Str., 7, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| |
Collapse
|
2
|
Song R, Hu M, Qin X, Qiu L, Wang P, Zhang X, Liu R, Wang X. The Roles of Lipid Metabolism in the Pathogenesis of Chronic Diseases in the Elderly. Nutrients 2023; 15:3433. [PMID: 37571370 PMCID: PMC10420821 DOI: 10.3390/nu15153433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Lipid metabolism plays crucial roles in cellular processes such as hormone synthesis, energy production, and fat storage. Older adults are at risk of the dysregulation of lipid metabolism, which is associated with progressive declines in the physiological function of various organs. With advancing age, digestion and absorption commonly change, thereby resulting in decreased nutrient uptake. However, in the elderly population, the accumulation of excess fat becomes more pronounced due to a decline in the body's capacity to utilize lipids effectively. This is characterized by enhanced adipocyte synthesis and reduced breakdown, along with diminished peripheral tissue utilization capacity. Excessive lipid accumulation in the body, which manifests as hyperlipidemia and accumulated visceral fat, is linked to several chronic lipid-related diseases, including cardiovascular disease, type 2 diabetes, obesity, and nonalcoholic fatty liver disease. This review provides a summary of the altered lipid metabolism during aging, including lipid digestion, absorption, anabolism, and catabolism, as well as their associations with age-related chronic diseases, which aids in developing nutritional interventions for older adults to prevent or alleviate age-related chronic diseases.
Collapse
Affiliation(s)
- Rui Song
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (R.S.); (M.H.); (X.Q.); (L.Q.)
| | - Mengxiao Hu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (R.S.); (M.H.); (X.Q.); (L.Q.)
| | - Xiyu Qin
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (R.S.); (M.H.); (X.Q.); (L.Q.)
| | - Lili Qiu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (R.S.); (M.H.); (X.Q.); (L.Q.)
| | - Pengjie Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; (P.W.); (X.Z.); (R.L.)
| | - Xiaoxu Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; (P.W.); (X.Z.); (R.L.)
| | - Rong Liu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; (P.W.); (X.Z.); (R.L.)
| | - Xiaoyu Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (R.S.); (M.H.); (X.Q.); (L.Q.)
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; (P.W.); (X.Z.); (R.L.)
| |
Collapse
|
3
|
Zhang Y, Fan N, Wen W, Liu S, Mo X, An Y, Zhou P. Genome-wide identification and analysis of LEA_2 gene family in alfalfa ( Medicago sativa L.) under aluminum stress. FRONTIERS IN PLANT SCIENCE 2022; 13:976160. [PMID: 36518511 PMCID: PMC9742422 DOI: 10.3389/fpls.2022.976160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Late embryonic development abundant proteins (LEAs) are a large family of proteins commonly existing in plants. LEA_2 is the largest subfamily in the LEA, it plays an important role in plant resistance to abiotic stress. In order to explore the characteristics of LEA_2 gene family members in alfalfa (Medicago sativa L.), 155 members of LEA_2 (MsLEA_2) family were identified from alfalfa genome. Bioinformatics analysis was conducted from the aspects of phylogenetic relationship, chromosome distribution, chromosome colinearity, physical and chemical properties, motif composition, exon-intron structure, cis-element and so on. Expression profiles of MsLEA_2 gene were obtained based on Real-time fluorescent quantitative PCR (qRT-PCR) analysis and previous RNA-seq data under aluminum (Al) stress. Bioinformatics results were shown that the MsLEA_2 genes are distributed on all 32 chromosomes. Among them, 85 genes were present in the gene clusters, accounting for 54.83%, and chromosome Chr7.3 carries the largest number of MsLEA_2 (19 LEA_2 genes on Chr7.3). Chr7.3 has a unique structure of MsLEA_2 distribution, which reveals a possible special role of Chr7.3 in ensuring the function of MsLEA_2. Transcriptional structure analysis revealed that the number of exons in each gene varies from 1 to 3, and introns varies from 0 to 2. Cis-element analysis identified that the promoter region of MsLEA_2 is rich in ABRE, MBS, LTR, and MeJARE, indicating MsLEA_2 has stress resistance potential under abiotic stress. RNA-seq data and qRT-PCR analyses showed that most of the MsLEA_2 members were up-regulated when alfalfa exposed to Al stress. This study revealed that phylogenetic relationship and possible function of LEA_ 2 gene in alfalfa, which were helpful for the functional analysis of LEA_ 2 proteins in the future and provided a new theoretical basis for improving Al tolerance of alfalfa.
Collapse
Affiliation(s)
- Yujing Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Nana Fan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wuwu Wen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Siyan Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Mo
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, China
| | - Peng Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
4
|
Gustchina A, Li M, Andrianova AG, Kudzhaev AM, Lountos GT, Sekula B, Cherry S, Tropea JE, Smirnov IV, Wlodawer A, Rotanova TV. Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases. Int J Mol Sci 2022; 23:11425. [PMID: 36232729 PMCID: PMC9569914 DOI: 10.3390/ijms231911425] [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: 08/19/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
ATP-dependent Lon proteases are key participants in the quality control system that supports the homeostasis of the cellular proteome. Based on their unique structural and biochemical properties, Lon proteases have been assigned in the MEROPS database to three subfamilies (A, B, and C). All Lons are single-chain, multidomain proteins containing an ATPase and protease domains, with different additional elements present in each subfamily. LonA and LonC proteases are soluble cytoplasmic enzymes, whereas LonBs are membrane-bound. Based on an analysis of the available sequences of Lon proteases, we identified a number of enzymes currently assigned to the LonB subfamily that, although presumably membrane-bound, include structural features more similar to their counterparts in the LonA subfamily. This observation was confirmed by the crystal structure of the proteolytic domain of the enzyme previously assigned as Bacillus subtilis LonB, combined with the modeled structure of its ATPase domain. Several structural features present in both domains differ from their counterparts in either LonA or LonB subfamilies. We thus postulate that this enzyme is the founding member of a newly identified LonBA subfamily, so far found only in the gene sequences of firmicutes.
Collapse
Affiliation(s)
- Alla Gustchina
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna G Andrianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Arsen M Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - George T Lountos
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bartosz Sekula
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Lodz, Poland
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Joseph E Tropea
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| |
Collapse
|
5
|
Kudzhaev AM, Andrianova AG, Gustchina AE, Smirnov IV, Rotanova TV. ATP-Dependent Lon Proteases in the Cellular Protein Quality Control System. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Huynh AT, Nguyen TTN, Villegas CA, Montemorso S, Strauss B, Pearson RA, Graham JG, Oribello J, Suresh R, Lustig B, Wang N. Prediction and confirmation of a switch-like region within the N-terminal domain of hSIRT1. Biochem Biophys Rep 2022; 30:101275. [PMID: 35592613 PMCID: PMC9112024 DOI: 10.1016/j.bbrep.2022.101275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022] Open
Abstract
Many proteins display conformational changes resulting from allosteric regulation. Often only a few residues are crucial in conveying these structural and functional allosteric changes. These regions that undergo a significant change in structure upon receiving an input signal, such as molecular recognition, are defined as switch-like regions. Identifying these key residues within switch-like regions can help elucidate the mechanism of allosteric regulation and provide guidance for synthetic regulation. In this study, we combine a novel computational workflow with biochemical methods to identify a switch-like region in the N-terminal domain of human SIRT1 (hSIRT1), a lysine deacetylase that plays important roles in regulating cellular pathways. Based on primary sequence, computational methods predicted a region between residues 186-193 in hSIRT1 to exhibit switch-like behavior. Mutations were then introduced in this region and the resulting mutants were tested for allosteric reactions to resveratrol, a known hSIRT1 allosteric regulator. After fine-tuning the mutations based on comparison of known secondary structures, we were able to pinpoint M193 as the residue essential for allosteric regulation, likely by communicating the allosteric signal. Mutation of this residue maintained enzyme activity but abolished allosteric regulation by resveratrol. Our findings suggest a method to predict switch-like regions in allosterically regulated enzymes based on the primary sequence. If further validated, this could be an efficient way to identify key residues in enzymes for therapeutic drug targeting and other applications.
Collapse
Affiliation(s)
- Angelina T. Huynh
- Department of Chemistry, San José State University, San José, California, 95192, USA
| | - Thi-Tina N. Nguyen
- Department of Biological Sciences, San José State University, San José, California, 95192, USA
| | - Carina A. Villegas
- Department of Biological Sciences, San José State University, San José, California, 95192, USA
| | - Saira Montemorso
- Department of Chemistry, San José State University, San José, California, 95192, USA
| | - Benjamin Strauss
- Department of Computer Science, San José State University, San José, California, 95192, USA
| | - Richard A. Pearson
- Department of Chemistry, San José State University, San José, California, 95192, USA
| | - Jason G. Graham
- Department of Biomedical, Chemical, and Materials Engineering, San José State University, San José, California, 95192, USA
| | - Jonathan Oribello
- Department of Chemistry, San José State University, San José, California, 95192, USA
| | - Rohit Suresh
- Department of Chemistry, San José State University, San José, California, 95192, USA
| | - Brooke Lustig
- Department of Chemistry, San José State University, San José, California, 95192, USA
| | - Ningkun Wang
- Department of Chemistry, San José State University, San José, California, 95192, USA
| |
Collapse
|
7
|
Athar HUR, Zulfiqar F, Moosa A, Ashraf M, Zafar ZU, Zhang L, Ahmed N, Kalaji HM, Nafees M, Hossain MA, Islam MS, El Sabagh A, Siddique KHM. Salt stress proteins in plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:999058. [PMID: 36589054 PMCID: PMC9800898 DOI: 10.3389/fpls.2022.999058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.
Collapse
Affiliation(s)
- Habib-ur-Rehman Athar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
| | - Anam Moosa
- Department of Plant Pathology, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Zafar Ullah Zafar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Lixin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nadeem Ahmed
- College of Life Sciences, Northwest A&F University, Yangling, China
- Department of Botany, Mohy-ud-Din Islamic University, Nerian Sharif, Pakistan
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, Warsaw, Poland
| | - Muhammad Nafees
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Sohidul Islam
- Department of Agronomy, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Ayman El Sabagh
- Faculty of Agriculture, Department of Field Crops, Siirt University, Siirt, Türkiye
- Agronomy Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Petrth WA, Australia
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
| |
Collapse
|
8
|
Kursula P. Small-angle X-ray scattering for the proteomics community: current overview and future potential. Expert Rev Proteomics 2021; 18:415-422. [PMID: 34210208 DOI: 10.1080/14789450.2021.1951242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Proteins are biological nanoparticles. For structural proteomics and hybrid structural biology, complementary methods are required that allow both high throughput and accurate automated data analysis. Small-angle X-ray scattering (SAXS) is a method for observing the size and shape of particles, such as proteins and complexes, in solution. SAXS data can be used to model both the structure, oligomeric state, conformational changes, and flexibility of biomolecular samples.Areas covered: The key principles of SAXS, its sample requirements, and its current and future applications for structural proteomics are briefly reviewed. Recent technical developments in SAXS experiments are discussed, and future potential of the method in structural proteomics is evaluated.Expert opinion: SAXS is a method suitable for several aspects of integrative structural proteomics, with current technical developments allowing for higher throughput and time-resolved studies, as well as the analysis of complex samples, such as membrane proteins. Increasing automation and streamlined data analysis are expected to equip SAXS for structure-based screening workflows. Originally, structural genomics had a heavy focus on folded, crystallizable proteins and complexes - SAXS is a method allowing an expansion of this focus to flexible and disordered systems.
Collapse
Affiliation(s)
- Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| |
Collapse
|
9
|
Murvai N, Kalmar L, Szabo B, Schad E, Micsonai A, Kardos J, Buday L, Han KH, Tompa P, Tantos A. Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14. Int J Mol Sci 2021; 22:6190. [PMID: 34201246 PMCID: PMC8230022 DOI: 10.3390/ijms22126190] [Citation(s) in RCA: 7] [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: 04/25/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/04/2022] Open
Abstract
Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana's Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14.
Collapse
Grants
- G.0029.12 Research Foundation Flanders
- 2010-88343 Korea Research Council of Fundamental Science and Technology
- NTM2231712 National Research Council of Science and Technology
- K124670 National Research, Development and Innovation Office, Hungary
- K131702 National Research, Development and Innovation Office, Hungary
- K125340 National Research, Development and Innovation Office, Hungary
- K120391 National Research, Development and Innovation Office, Hungary
- KH125597 National Research, Development and Innovation Office, Hungary
- PD135510 National Research, Development and Innovation Office, Hungary
- Bolyai János Scholarship Hungarian Academy of Sciences
- 20171582 SOLEIL Synchrotron, France
- 20180805 SOLEIL Synchrotron, France
- 20181890 SOLEIL Synchrotron, France
- Lendület Grant Hungarian Academy of Sciences
Collapse
Affiliation(s)
- Nikoletta Murvai
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Lajos Kalmar
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Beata Szabo
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - Eva Schad
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - László Buday
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - Kyou-Hoon Han
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Gene Editing Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Peter Tompa
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Agnes Tantos
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| |
Collapse
|
10
|
CONAN: A Tool to Decode Dynamical Information from Molecular Interaction Maps. Biophys J 2019; 114:1267-1273. [PMID: 29590584 PMCID: PMC5883949 DOI: 10.1016/j.bpj.2018.01.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/19/2017] [Accepted: 01/22/2018] [Indexed: 02/07/2023] Open
Abstract
The analysis of contacts is a powerful tool to understand biomolecular function in a series of contexts, from the investigation of dynamical behavior at equilibrium to the study of nonequilibrium dynamics in which the system moves between multiple states. We thus propose a tool called CONtact ANalysis (CONAN) that, from molecular dynamics (MD) trajectories, analyzes interresidue contacts, creates videos of time-resolved contact maps, and performs correlation, principal component, and cluster analysis, revealing how specific contacts relate to functionally relevant states sampled by MD. We present how CONAN can identify features describing the dynamics of ubiquitin both at equilibrium and during mechanical unfolding. Additionally, we show the analysis of MD trajectories of an α-synuclein mutant peptide that undergoes an α-β conformational transition that can be easily monitored using CONAN, which identifies the multiple states that the peptide explores along its conformational dynamics. The high versatility and ease of use of the software make CONAN a tool that can significantly facilitate the understanding of the complex dynamical behavior of proteins or other biomolecules. CONAN and its documentation are freely available for download on GitHub.
Collapse
|
11
|
Kumar R, Feltrup TM, Kukreja RV, Patel KB, Cai S, Singh BR. Evolutionary Features in the Structure and Function of Bacterial Toxins. Toxins (Basel) 2019; 11:toxins11010015. [PMID: 30609803 PMCID: PMC6356308 DOI: 10.3390/toxins11010015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 12/21/2022] Open
Abstract
Toxins can function both as a harmful and therapeutic molecule, depending on their concentrations. The diversity in their function allows us to ask some very pertinent questions related to their origin and roles: (a) What makes them such effective molecules? (b) Are there evolutionary features encoded within the structures of the toxins for their function? (c) Is structural hierarchy in the toxins important for maintaining their structure and function? (d) Do protein dynamics play a role in the function of toxins? and (e) Do the evolutionary connections to these unique features and functions provide the fundamental points in driving evolution? In light of the growing evidence in structural biology, it would be appropriate to suggest that protein dynamics and flexibility play a much bigger role in the function of the toxin than the structure itself. Discovery of IDPs (intrinsically disorder proteins), multifunctionality, and the concept of native aggregation are shaking the paradigm of the requirement of a fixed three-dimensional structure for the protein’s function. Growing evidence supporting the above concepts allow us to redesign the structure-function aspects of the protein molecules. An evolutionary model is necessary and needs to be developed to study these important aspects. The criteria for a well-defined model would be: (a) diversity in structure and function, (b) unique functionality, and (c) must belong to a family to define the evolutionary relationships. All these characteristics are largely fulfilled by bacterial toxins. Bacterial toxins are diverse and widely distributed in all three forms of life (Bacteria, Archaea and Eukaryotes). Some of the unique characteristics include structural folding, sequence and functional combination of domains, targeting a cellular process to execute their function, and most importantly their flexibility and dynamics. In this work, we summarize certain unique aspects of bacterial toxins, including role of structure in defining toxin function, uniqueness in their enzymatic function, and interaction with their substrates and other proteins. Finally, we have discussed the evolutionary aspects of toxins in detail, which will help us rethink the current evolutionary theories. A careful study, and appropriate interpretations, will provide answers to several questions related to the structure-function relationship of proteins, in general. Additionally, this will also allow us to refine the current evolution theories.
Collapse
Affiliation(s)
- Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA.
| | - Thomas M Feltrup
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA.
| | - Roshan V Kukreja
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA.
| | - Kruti B Patel
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA.
| | - Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts, Dartmouth, MA 02747, USA.
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA.
| |
Collapse
|
12
|
Sinz A. Cross‐Linking/Mass Spectrometry for Studying Protein Structures and Protein–Protein Interactions: Where Are We Now and Where Should We Go from Here? Angew Chem Int Ed Engl 2018; 57:6390-6396. [DOI: 10.1002/anie.201709559] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/06/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of PharmacyMartin Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle (Saale) Germany
| |
Collapse
|
13
|
Sinz A. Vernetzung/Massenspektrometrie zur Untersuchung von Proteinstrukturen und Protein‐Protein‐Wechselwirkungen: Wo stehen wir und welchen Weg wollen wir einschlagen? Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrea Sinz
- Abteilung für Pharmazeutische Chemie & BioanalytikInstitut für PharmazieMartin-Luther-Universität Halle-Wittenberg Wolfgang-Langenbeck-Straße 4 06120 Halle (Saale) Deutschland
| |
Collapse
|
14
|
Al-Naqshabandi MA, Weis DD. Quantifying Protection in Disordered Proteins Using Millisecond Hydrogen Exchange-Mass Spectrometry and Peptic Reference Peptides. Biochemistry 2017; 56:4064-4072. [DOI: 10.1021/acs.biochem.6b01312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - David D. Weis
- Department
of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, United States
| |
Collapse
|
15
|
The neglected functions of intrinsically disordered proteins and the origin of life. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 126:31-46. [DOI: 10.1016/j.pbiomolbio.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/11/2017] [Indexed: 10/20/2022]
|
16
|
Schor M, Mey ASJS, MacPhee CE. Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins. Biophys Rev 2016; 8:429-439. [PMID: 28003858 PMCID: PMC5135723 DOI: 10.1007/s12551-016-0234-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/14/2016] [Indexed: 01/02/2023] Open
Abstract
Intrinsically disordered proteins, proteins that do not have a well-defined three-dimensional structure, make up a significant proportion of our proteome and are particularly prevalent in signaling and regulation. Although their importance has been realized for two decades, there is a lack of high-resolution experimental data. Molecular dynamics simulations have been crucial in reaching our current understanding of the dynamical structural ensemble sampled by intrinsically disordered proteins. In this review, we discuss enhanced sampling simulation methods that are particularly suitable to characterize the structural ensemble, along with examples of applications and limitations. The dynamics within the ensemble can be rigorously analyzed using Markov state models. We discuss recent developments that make Markov state modeling a viable approach for studying intrinsically disordered proteins. Finally, we briefly discuss challenges and future directions when applying molecular dynamics simulations to study intrinsically disordered proteins.
Collapse
Affiliation(s)
- Marieke Schor
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | | | - Cait E. MacPhee
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
17
|
Pancsa R, Tompa P. Essential functions linked with structural disorder in organisms of minimal genome. Biol Direct 2016; 11:45. [PMID: 27608806 PMCID: PMC5016991 DOI: 10.1186/s13062-016-0149-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/03/2016] [Indexed: 12/13/2022] Open
Abstract
Abstract Intrinsically disordered regions (IDRs) of proteins fulfill important regulatory roles in most organisms. However, the proteins of certain endosymbiont and intracellular pathogenic bacteria with extremely reduced genomes contain disproportionately small amounts of IDRs, consisting almost entirely of folded domains. As their genomes co-evolving with their hosts have been reduced in unrelated lineages, the proteomes of these bacteria represent independently evolved minimal protein sets. We systematically analyzed structural disorder in a representative set of such minimal organisms to see which types of functionally relevant longer IDRs are invariably retained in them. We found that a few characteristic functions are consistently linked with conformational disorder: ribosomal proteins, key components of the protein production machinery, a central coordinator of DNA metabolism and certain housekeeping chaperones seem to strictly rely on structural disorder even in genome-reduced organisms. We propose that these functions correspond to the most essential and probably also the most ancient ones fulfilled by structural disorder in cellular organisms. Reviewers This article was reviewed by Michael Gromiha, Zoltan Gaspari and Sandor Pongor. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0149-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rita Pancsa
- Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Vrije Universiteit Brussel (VUB), 1050 Pleinlaan 2, Brussels, Belgium
| | - Peter Tompa
- Structural Biology Research Center (SBRC), Flanders Institute for Biotechnology (VIB), Vrije Universiteit Brussel (VUB), 1050 Pleinlaan 2, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Magyar Tudósok körútja 2., Budapest, Hungary.
| |
Collapse
|
18
|
De Geyter J, Tsirigotaki A, Orfanoudaki G, Zorzini V, Economou A, Karamanou S. Protein folding in the cell envelope of Escherichia coli. Nat Microbiol 2016; 1:16107. [PMID: 27573113 DOI: 10.1038/nmicrobiol.2016.107] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]
Abstract
While the entire proteome is synthesized on cytoplasmic ribosomes, almost half associates with, localizes in or crosses the bacterial cell envelope. In Escherichia coli a variety of mechanisms are important for taking these polypeptides into or across the plasma membrane, maintaining them in soluble form, trafficking them to their correct cell envelope locations and then folding them into the right structures. The fidelity of these processes must be maintained under various environmental conditions including during stress; if this fails, proteases are called in to degrade mislocalized or aggregated proteins. Various soluble, diffusible chaperones (acting as holdases, foldases or pilotins) and folding catalysts are also utilized to restore proteostasis. These responses can be general, dealing with multiple polypeptides, with functional overlaps and operating within redundant networks. Other chaperones are specialized factors, dealing only with a few exported proteins. Several complex machineries have evolved to deal with binding to, integration in and crossing of the outer membrane. This complex protein network is responsible for fundamental cellular processes such as cell wall biogenesis; cell division; the export, uptake and degradation of molecules; and resistance against exogenous toxic factors. The underlying processes, contributing to our fundamental understanding of proteostasis, are a treasure trove for the development of novel antibiotics, biopharmaceuticals and vaccines.
Collapse
Affiliation(s)
- Jozefien De Geyter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Alexandra Tsirigotaki
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Valentina Zorzini
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Spyridoula Karamanou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| |
Collapse
|
19
|
Kerfeld CA, Melnicki MR. Assembly, function and evolution of cyanobacterial carboxysomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:66-75. [PMID: 27060669 DOI: 10.1016/j.pbi.2016.03.009] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 05/19/2023]
Abstract
All cyanobacteria contain carboxysomes, RuBisCO-encapsulating bacterial microcompartments that function as prokaryotic organelles. The two carboxysome types, alpha and beta, differ fundamentally in components, assembly, and species distribution. Alpha carboxysomes share a highly-conserved gene organization, with evidence of horizontal gene transfer from chemoautotrophic proteobacteria to the picocyanobacteria, and seem to co-assemble shells concomitantly with aggregation of cargo enzymes. In contrast, beta carboxysomes assemble an enzymatic core first, with an encapsulation peptide playing a critical role in formation of the surrounding shell. Based on similarities in assembly, and phylogenetic analysis of the pentameric shell protein conserved across all bacterial microcompartments, beta carboxysomes appear to be more closely related to the microcompartments of heterotrophic bacteria (metabolosomes) than to alpha carboxysomes, which appear deeply divergent. Beta carboxysomes can be found in the basal cyanobacterial clades that diverged before the ancestor of the chloroplast and have recently been shown to be able to encapsulate functional RuBisCO enzymes resurrected from ancestrally-reconstructed sequences, consistent with an ancient origin. Alpha and beta carboxysomes are not only distinct units of evolution, but are now emerging as genetic/metabolic modules for synthetic biology; heterologous expression and redesign of both the shell and the enzymatic core have recently been achieved.
Collapse
Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Matthew R Melnicki
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
20
|
Ithuralde RE, Turjanski AG. Phosphorylation Regulates the Bound Structure of an Intrinsically Disordered Protein: The p53-TAZ2 Case. PLoS One 2016; 11:e0144284. [PMID: 26742101 PMCID: PMC4712144 DOI: 10.1371/journal.pone.0144284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/15/2015] [Indexed: 12/20/2022] Open
Abstract
Disordered regions and Intrinsically Disordered Proteins (IDPs) are involved in critical cellular processes and may acquire a stable three-dimensional structure only upon binding to their partners. IDPs may follow a folding-after-binding process, known as induced folding, or a folding-before-binding process, known as conformational selection. The transcription factor p53 is involved in the regulation of cellular events that arise upon stress or DNA damage. The p53 domain structure is composed of an N-terminal transactivation domain (p53TAD), a DNA Binding Domain and a tetramerization domain. The activity of TAD is tightly regulated by interactions with cofactors, inhibitors and phosphorylation. To initiate transcription, p53TAD binds to the TAZ2 domain of CBP, a co-transcription factor, and undergoes a folding and binding process, as revealed by the recent NMR structure of the complex. The activity of p53 is regulated by phosphorylation at multiple sites on the TAD domain and recent studies have shown that modifications at three residues affect the binding towards TAZ2. However, we still do not know how these phosphorylations affect the structure of the bound state and, therefore, how they regulate the p53 function. In this work, we have used computational simulations to understand how phosphorylation affects the structure of the p53TAD:TAZ2 complex and regulates the recognition mechanism. Phosphorylation has been proposed to enhance binding by direct interaction with the folded protein or by changing the unbound conformation of IDPs, for example by pre-folding the protein favoring the recognition mechanism. Here, we show an interesting turn in the p53 case: phosphorylation mainly affects the bound structure of p53TAD, highlighting the complexity of IDP protein-protein interactions. Our results are in agreement with previous experimental studies, allowing a clear picture of how p53 is regulated by phosphorylation and giving new insights into how post-translational modifications can regulate the function of IDPs.
Collapse
Affiliation(s)
- Raúl Esteban Ithuralde
- Departamento de Química Inorgánica, Analítica y Química Física y Departamento de Química Biológica-Facultad de Ciencias Exacas y Naturales-Universidad de Buenos Aires, ciudad de Buenos Aires, Argentina
- INQUIMAE-Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires/Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, ciudad de Buenos Aires, Argentina
| | - Adrián Gustavo Turjanski
- Departamento de Química Inorgánica, Analítica y Química Física y Departamento de Química Biológica-Facultad de Ciencias Exacas y Naturales-Universidad de Buenos Aires, ciudad de Buenos Aires, Argentina
- INQUIMAE-Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires/Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, ciudad de Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
21
|
Ambadipudi S, Zweckstetter M. Targeting intrinsically disordered proteins in rational drug discovery. Expert Opin Drug Discov 2015; 11:65-77. [DOI: 10.1517/17460441.2016.1107041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Susmitha Ambadipudi
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, 37073 Göttingen, Germany
| |
Collapse
|
22
|
Oshokoya OO, JiJi RD. “Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”. Anal Chim Acta 2015; 892:59-68. [DOI: 10.1016/j.aca.2015.08.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/11/2015] [Indexed: 01/25/2023]
|
23
|
Walsh G. Protein Structure and Engineering. Proteins 2015. [DOI: 10.1002/9781119117599.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
24
|
Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, Shively J, Cannon GC, Kerfeld CA. Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component. Life (Basel) 2015; 5:1141-71. [PMID: 25826651 PMCID: PMC4499774 DOI: 10.3390/life5021141] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in three model organisms and show that CsoS2 is vital for α-carboxysome biogenesis. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle (M)-, and C-terminal region. Repetitive motifs can be identified in the N- and M-regions. Multiple lines of evidence suggest CsoS2 is highly flexible, possibly an intrinsically disordered protein. Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome. Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.
Collapse
Affiliation(s)
- Fei Cai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Zhicheng Dou
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Susan L Bernstein
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Ryan Leverenz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Eric B Williams
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Sabine Heinhorst
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Jessup Shively
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Gordon C Cannon
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
25
|
D'Urzo A, Konijnenberg A, Rossetti G, Habchi J, Li J, Carloni P, Sobott F, Longhi S, Grandori R. Molecular basis for structural heterogeneity of an intrinsically disordered protein bound to a partner by combined ESI-IM-MS and modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:472-481. [PMID: 25510932 DOI: 10.1007/s13361-014-1048-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/04/2014] [Accepted: 11/08/2014] [Indexed: 06/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered N(TAIL) domain and the phosphoprotein X domain (P(XD)) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire N(TAIL) domain bound to P(XD) at atomic resolution.
Collapse
Affiliation(s)
- Annalisa D'Urzo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Hackl EV. Effect of Temperature on the Conformation of Natively Unfolded Protein 4E-BP1 in Aqueous and Mixed Solutions Containing Trifluoroethanol and Hexafluoroisopropanol. Protein J 2014; 34:18-28. [DOI: 10.1007/s10930-014-9595-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
27
|
Thermally-induced structural changes in an armadillo repeat protein suggest a novel thermosensor mechanism in a molecular chaperone. FEBS Lett 2014; 589:123-30. [PMID: 25436418 DOI: 10.1016/j.febslet.2014.11.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/18/2014] [Accepted: 11/19/2014] [Indexed: 01/12/2023]
Abstract
Molecular chaperones are commonly identified by their ability to suppress heat-induced protein aggregation. The muscle-specific molecular chaperone UNC-45B is known to be involved in myosin folding and is trafficked to the sarcomeres A-band during thermal stress. Here, we identify temperature-dependent structural changes in the UCS chaperone domain of UNC-45B that occur within a physiologically relevant heat-shock range. We show that distinct changes to the armadillo repeat protein topology result in exposure of hydrophobic patches, and increased flexibility of the molecule. These rearrangements suggest the existence of a novel thermosensor within the chaperone domain of UNC-45B. We propose that these changes may function to suppress aggregation under stress by allowing binding to a wide variety of aggregation prone loops on its client.
Collapse
|
28
|
Rapid proteasomal degradation of posttranscriptional regulators of the TIS11/tristetraprolin family is induced by an intrinsically unstructured region independently of ubiquitination. Mol Cell Biol 2014; 34:4315-28. [PMID: 25246635 DOI: 10.1128/mcb.00643-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The TIS11/tristetraprolin (TTP) CCCH tandem zinc finger proteins are major effectors in the destabilization of mRNAs bearing AU-rich elements (ARE) in their 3' untranslated regions. In this report, we demonstrate that the Drosophila melanogaster dTIS11 protein is short-lived due to its rapid ubiquitin-independent degradation by the proteasome. Our data indicate that this mechanism is tightly associated with the intrinsically unstructured, disordered N- and C-terminal domains of the protein. Furthermore, we show that TTP, the mammalian TIS11/TTP protein prototype, shares the same three-dimensional characteristics and is degraded by the same proteolytic pathway as dTIS11, thereby indicating that this mechanism has been conserved across evolution. Finally, we observed a phosphorylation-dependent inhibition of dTIS11 and TTP degradation by the proteasome in vitro, raising the possibility that such modifications directly affect proteasomal recognition for these proteins. As a group, RNA-binding proteins (RNA-BPs) have been described as enriched in intrinsically disordered regions, thus raising the possibility that the mechanism that we uncovered for TIS11/TTP turnover is widespread among other RNA-BPs.
Collapse
|
29
|
Decreased lipid absorption due to reduced pancreatic lipase activity in aging male mice. Biogerontology 2014; 15:463-73. [PMID: 25033985 DOI: 10.1007/s10522-014-9512-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
Abstract
Malnutrition due to aging is partly caused by decreased absorption of nutrients by the gastrointestinal tract. However, the underlying mechanism is unclear and changes in lipid absorption with aging are poorly understood. In this study, changes in lipid absorption with aging were examined in mice aged 3 and 25 months. After overnight fasting, blood samples were collected from snipped tails and then soybean oil was administered orally. Three hours later, mice were sacrificed by decapitation and the liver, pancreas, small intestine and blood were collected. The increase in serum triacylglycerol after soybean oil administration was significantly lower in the older mice, indicating a decrease in lipid absorption with aging. Measurement of mRNA levels for triacylglycerol absorption-related genes showed that mRNA for pancreatic lipase tended to decrease in 25-month-old mice. There was no significant difference in the protein level of pancreatic lipase, but the enzyme activity showed a significant decrease in the older mice. To examine this mechanism, expression levels of mRNA for protein turnover-related genes in the pancreas were measured. The level of a proteasomal mRNA showed a significant decrease in 25-month-old mice. This suggests that the ability to degrade unfolded protein decreases in the aging pancreas, and that this leads to reduction of pancreatic lipase activity and a decrease in lipid absorption.
Collapse
|
30
|
Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 326] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| |
Collapse
|
31
|
Communie G, Ruigrok RWH, Jensen MR, Blackledge M. Intrinsically disordered proteins implicated in paramyxoviral replication machinery. Curr Opin Virol 2014; 5:72-81. [DOI: 10.1016/j.coviro.2014.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/01/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
|
32
|
Tomko RJ, Hochstrasser M. The intrinsically disordered Sem1 protein functions as a molecular tether during proteasome lid biogenesis. Mol Cell 2014; 53:433-43. [PMID: 24412063 DOI: 10.1016/j.molcel.2013.12.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/19/2013] [Accepted: 12/05/2013] [Indexed: 11/27/2022]
Abstract
The intrinsically disordered yeast protein Sem1 (DSS1 in mammals) participates in multiple protein complexes, including the proteasome, but its role(s) within these complexes is uncertain. We report that Sem1 enforces the ordered incorporation of subunits Rpn3 and Rpn7 into the assembling proteasome lid. Sem1 uses conserved acidic segments separated by a flexible linker to grasp Rpn3 and Rpn7. The same segments are used for protein binding in other complexes, but in the proteasome lid they are uniquely deployed for recognizing separate polypeptides. We engineered TEV protease-cleavage sites into Sem1 to show that the tethering function of Sem1 is important for the biogenesis and integrity of the Rpn3-Sem1-Rpn7 ternary complex but becomes dispensable once the ternary complex incorporates into larger lid precursors. Thus, although Sem1 is a stoichiometric component of the mature proteasome, it has a distinct, chaperone-like function specific to early stages of proteasome assembly.
Collapse
Affiliation(s)
- Robert J Tomko
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.
| |
Collapse
|
33
|
Huang YJ, Acton TB, Montelione GT. DisMeta: a meta server for construct design and optimization. Methods Mol Biol 2014; 1091:3-16. [PMID: 24203321 DOI: 10.1007/978-1-62703-691-7_1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered or unstructured regions in proteins are both common and biologically important, particularly in regulation, signaling, and modulating intermolecular recognition processes. From a practical point of view, however, such disordered regions often can pose significant challenges for crystallization. Disordered regions are also detrimental to NMR spectral quality, complicating the analysis of resonance assignments and three-dimensional protein structures by NMR methods. The DisMeta Server has been used by Northeastern Structural Genomics (NESG) consortium as a primary tool for construct design and optimization in preparing samples for both NMR and crystallization studies. It is a meta-server that generates a consensus analysis of eight different sequence-based disorder predictors to identify regions that are likely to be disordered. DisMeta also identifies predicted secretion signal peptides, transmembrane segments, and low-complexity regions. Identification of disordered regions, by either experimental or computational methods, is an important step in the NESG structure production pipeline, allowing the rational design of protein constructs that have improved expression and solubility, improved crystallization, and better quality NMR spectra.
Collapse
Affiliation(s)
- Yuanpeng Janet Huang
- Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ, USA
| | | | | |
Collapse
|
34
|
Creamer TP. Transient disorder: Calcineurin as an example. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e26412. [PMID: 28516023 PMCID: PMC5424781 DOI: 10.4161/idp.26412] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 01/11/2023]
Abstract
How intrinsically disordered proteins and regions evade degradation by cellular machinery evolved to recognize unfolded and misfolded chains remains a vexing question. One potential means by which this can occur is the disorder is transient in nature. That is, the disorder exists just long enough for it to be bound by a partner biomolecule and fold. A review of 30 y of studies of calmodulin’s activation of calcineurin suggests that the regulatory domain of this vital phosphatase is a transiently disordered region. During activation, the regulatory domain progresses from a folded state, to disordered, followed by folding upon being bound by calmodulin. The transient disordered state of this domain is part of a critical intermediate state that facilitates the rapid binding of calmodulin. Building upon “fly-casting” as a means of facilitating partner binding, the mechanism by which calcineurin undergoes activation and subsequent deactivation could be considered “catch and release.”
Collapse
Affiliation(s)
- Trevor P Creamer
- Center for Structural Biology; Department of Molecular and Cellular Biochemistry; University of Kentucky; Lexington, KY USA
| |
Collapse
|
35
|
Skjevik AA, Mileni M, Baumann A, Halskau O, Teigen K, Stevens RC, Martinez A. The N-terminal sequence of tyrosine hydroxylase is a conformationally versatile motif that binds 14-3-3 proteins and membranes. J Mol Biol 2013; 426:150-68. [PMID: 24055376 DOI: 10.1016/j.jmb.2013.09.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 01/17/2023]
Abstract
Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the synthesis of catecholamine neurotransmitters, and a reduction in TH activity is associated with several neurological diseases. Human TH is regulated, among other mechanisms, by Ser19-phosphorylation-dependent interaction with 14-3-3 proteins. The N-terminal sequence (residues 1-43), which corresponds to an extension to the TH regulatory domain, also interacts with negatively charged membranes. By using X-ray crystallography together with molecular dynamics simulations and structural bioinformatics analysis, we have probed the conformations of the Ser19-phosphorylated N-terminal peptide [THp-(1-43)] bound to 14-3-3γ, free in solution and bound to a phospholipid bilayer, and of the unphosphorylated peptide TH-(1-43) both free and bilayer bound. As seen in the crystal structure of THp-(1-43) complexed with 14-3-3γ, the region surrounding pSer19 adopts an extended conformation in the bound state, whereas THp-(1-43) adopts a bent conformation when free in solution, with higher content of secondary structure and higher number of internal hydrogen bonds. TH-(1-43) in solution presents the highest mobility and least defined structure of all forms studied, and it shows an energetically more favorable interaction with membranes relative to THp-(1-43). Cationic residues, notably Arg15 and Arg16, which are the recognition sites of the kinases phosphorylating at Ser19, are also contributing to the interaction with the membrane. Our results reveal the structural flexibility of this region of TH, in accordance with the functional versatility and conformational adaptation to different partners. Furthermore, this structural information has potential relevance for the development of therapeutics for neurodegenerative disorders, through modulation of TH-partner interactions.
Collapse
Affiliation(s)
| | - Mauro Mileni
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Oyvind Halskau
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5020 Bergen, Norway
| | - Knut Teigen
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Raymond C Stevens
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.
| |
Collapse
|
36
|
Gray TA, Murray E, Nowicki MW, Remnant L, Scherl A, Muller P, Vojtesek B, Hupp TR. Development of a fluorescent monoclonal antibody-based assay to measure the allosteric effects of synthetic peptides on self-oligomerization of AGR2 protein. Protein Sci 2013; 22:1266-78. [PMID: 23780840 DOI: 10.1002/pro.2299] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 11/12/2022]
Abstract
Many regulatory proteins are homo-oligomeric and designing assays that measure self-assembly will provide novel approaches to study protein allostery and screen for novel small molecule modulators of protein interactions. We present an assay to begin to define the biochemical determinants that regulate dimerization of the cancer-associated oncoprotein AGR2. A two site-sandwich microtiter assay ((2S) MTA) was designed using a DyLight800-labeled monoclonal antibody that binds to an epitope in AGR2 to screen for synthetic self-peptides that might regulate dimer stability. Peptides derived from the intrinsically disordered N-terminal region of AGR2 increase in trans oligomer stability as defined using the (2S) MTA assay. A DSS-crosslinking assay that traps the AGR2 dimer through K95-K95 adducts confirmed that Δ45-AGR2 was a more stable dimer using denaturing gel electrophoresis. A titration of wt-AGR2, Δ45-AGR2 (more stable dimer), and monomeric AGR2(E60A) revealed that Δ45-AGR2 was more active in binding to Reptin than either wt-AGR2 or the AGR2(E60A) mutant. Our data have defined a functional role for the AGR2 dimer in the binding to its most well characterized interacting protein, Reptin. The ability to regulate AGR2 oligomerization in trans opens the possibility for developing small molecules that regulate its' biochemical activity as potential cancer therapeutics. The data also highlight the utility of this oligomerization assay to screen chemical libraries for ligands that could regulate AGR2 dimer stability and its' oncogenic potential.
Collapse
Affiliation(s)
- Terry A Gray
- Institute of Genetics and Molecular Medicine, Cell Signaling Unit, University of Edinburgh, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Braselmann E, Chaney JL, Clark PL. Folding the proteome. Trends Biochem Sci 2013; 38:337-44. [PMID: 23764454 DOI: 10.1016/j.tibs.2013.05.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 02/07/2023]
Abstract
Protein folding is an essential prerequisite for protein function and hence cell function. Kinetic and thermodynamic studies of small proteins that refold reversibly were essential for developing our current understanding of the fundamentals of protein folding mechanisms. However, we still lack sufficient understanding to accurately predict protein structures from sequences, or the effects of disease-causing mutations. To date, model proteins selected for folding studies represent only a small fraction of the complexity of the proteome and are unlikely to exhibit the breadth of folding mechanisms used in vivo. We are in urgent need of new methods - both theoretical and experimental - that can quantify the folding behavior of a truly broad set of proteins under in vivo conditions. Such a shift in focus will provide a more comprehensive framework from which to understand the connections between protein folding, the molecular basis of disease, and cell function and evolution.
Collapse
Affiliation(s)
- Esther Braselmann
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | | | | |
Collapse
|
38
|
Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (January/February/March, 2013). INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25496. [PMID: 28516015 PMCID: PMC5424799 DOI: 10.4161/idp.25496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 01/13/2023]
Abstract
The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for “intrinsically disordered protein OR natively unfolded protein” returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a “Digested Disorder” project, which will encompass a series of reader’s digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest covers papers published during the period of January, February and March of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
Collapse
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicince; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| |
Collapse
|
39
|
|
40
|
|