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Schweitzer-Stenner R. Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides. Int J Mol Sci 2022; 23:ijms23105643. [PMID: 35628453 PMCID: PMC9147007 DOI: 10.3390/ijms23105643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
The Flory isolated pair hypothesis (IPH) is one of the corner stones of the random coil model, which is generally invoked to describe the conformational dynamics of unfolded and intrinsically disordered proteins (IDPs). It stipulates, that individual residues sample the entire sterically allowed space of the Ramachandran plot without exhibiting any correlations with the conformational dynamics of its neighbors. However, multiple lines of computational, bioinformatic and experimental evidence suggest that nearest neighbors have a significant influence on the conformational sampling of amino acid residues. This implies that the conformational entropy of unfolded polypeptides and proteins is much less than one would expect based on the Ramachandran plots of individual residues. A further implication is that the Gibbs energies of residues in unfolded proteins or polypeptides are not additive. This review provides an overview of what is currently known and what has yet to be explored regarding nearest neighbor interactions in unfolded proteins.
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Carreón YJP, Gómez-López ML, Díaz-Hernández O, Vazquez-Vergara P, Moctezuma RE, Saniger JM, González-Gutiérrez J. Patterns in Dried Droplets to Detect Unfolded BSA. Sensors (Basel) 2022; 22:1156. [PMID: 35161907 DOI: 10.3390/s22031156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/12/2022]
Abstract
The morphological analysis of patterns in dried droplets has allowed the generation of efficient techniques for the detection of molecules of medical interest. However, the effectiveness of this method to reveal the coexistence of macromolecules of the same species, but different conformational states, is still unknown. To address this problem, we present an experimental study on pattern formation in dried droplets of bovine serum albumin (BSA), in folded and unfolded conformational states, in saline solution (NaCl). Folded proteins produce a well-defined coffee ring and crystal patterns all over the dry droplet. Depending on the NaCl concentration, the crystals can be small, large, elongated, entangled, or dense. Optical microscopy reveals that the relative concentration of unfolded proteins determines the morphological characteristics of deposits. At a low relative concentration of unfolded proteins (above 2%), small amorphous aggregates emerge in the deposits, while at high concentrations (above 16%), the “eye-like pattern”, a large aggregate surrounded by a uniform coating, is produced. The radial intensity profile, the mean pixel intensity, and the entropy make it possible to characterize the patterns in dried droplets. We prove that it is possible to achieve 100% accuracy in identifying 4% of unfolded BSA contained in a protein solution.
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Santiago J, Santos MAS, Fardilha M, Silva JV. Stress response pathways in the male germ cells and gametes. Mol Hum Reprod 2021; 26:1-13. [PMID: 31814009 DOI: 10.1093/molehr/gaz063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/31/2019] [Indexed: 12/20/2022] Open
Abstract
The unfolded protein response (UPR) is a conserved and essential cellular pathway involved in protein quality control that is activated in response to several cellular stressors such as diseases states, ageing, infection and toxins. The cytosol, endoplasmic reticulum (ER) and mitochondria are continuously exposed to new proteins and in situations of aberrant protein folding; one of three lines of defence may be activated: (i) heat-shock response, (ii) mitochondrial UPR and (iii) ER UPR. These pathways lead to different signal transduction mechanisms that activate or upregulate transcription factors that, in turn, regulate genes that increase the cell's ability to correct the conformation of poorly folded proteins or, ultimately, lead to apoptosis. Despite the recent progress in understanding such biological processes, few studies have focused on the implications of the UPR in male infertility, highlighting the need for a first approach concerning the presence of these components in the male reproductive system. In testis, there is a high rate of protein synthesis, and the UPR mechanisms are well described. However, the presence of these mechanisms in spermatozoa, apparently transcriptionally inactive cells, is contentious, and it is unclear how sperm cells deal with stress. Here, we review current concepts and mechanisms of the UPR and highlight the relevance of these stress response pathways in male fertility, especially the presence and functional activation of those components in male germinal cells and spermatozoa.
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Affiliation(s)
- J Santiago
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal
| | - M A S Santos
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal
| | - M Fardilha
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal
| | - J V Silva
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193, Aveiro, Portugal.,Reproductive Genetics and Embryo-fetal Development Group, Institute for Innovation and Health Research (I3S), University of Porto, 4200-135, Porto, Portugal.,Department of Microscopy, Laboratory of Cell Biology, and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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Menon R, Bonney EA, Condon J, Mesiano S, Taylor RN. Novel concepts on pregnancy clocks and alarms: redundancy and synergy in human parturition. Hum Reprod Update 2016; 22:535-60. [PMID: 27363410 DOI: 10.1093/humupd/dmw022] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/16/2016] [Indexed: 12/19/2022] Open
Abstract
The signals and mechanisms that synchronize the timing of human parturition remain a mystery and a better understanding of these processes is essential to avert adverse pregnancy outcomes. Although our insights into human labor initiation have been informed by studies in animal models, the timing of parturition relative to fetal maturation varies among viviparous species, indicative of phylogenetically different clocks and alarms; but what is clear is that important common pathways must converge to control the birth process. For example, in all species, parturition involves the transition of the myometrium from a relaxed to a highly excitable state, where the muscle rhythmically and forcefully contracts, softening the cervical extracellular matrix to allow distensibility and dilatation and thus a shearing of the fetal membranes to facilitate their rupture. We review a number of theories promulgated to explain how a variety of different timing mechanisms, including fetal membrane cell senescence, circadian endocrine clocks, and inflammatory and mechanical factors, are coordinated as initiators and effectors of parturition. Many of these factors have been independently described with a focus on specific tissue compartments.In this review, we put forth the core hypothesis that fetal membrane (amnion and chorion) senescence is the initiator of a coordinated, redundant signal cascade leading to parturition. Whether modified by oxidative stress or other factors, this process constitutes a counting device, i.e. a clock, that measures maturation of the fetal organ systems and the production of hormones and other soluble mediators (including alarmins) and that promotes inflammation and orchestrates an immune cascade to propagate signals across different uterine compartments. This mechanism in turn sensitizes decidual responsiveness and eventually promotes functional progesterone withdrawal in the myometrium, leading to increased myometrial cell contraction and the triggering of parturition. Linkage of these processes allows convergence and integration of the gestational clocks and alarms, prompting a timely and safe birth. In summary, we provide a comprehensive synthesis of the mediators that contribute to the timing of human labor. Integrating these concepts will provide a better understanding of human parturition and ultimately improve pregnancy outcomes.
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Affiliation(s)
- Ramkumar Menon
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine and Perinatal Research, The University of Texas Medical Branch at Galveston, 301 University Blvd., MRB, Room 11.138, Galveston, TX 77555-1062, USA
| | - Elizabeth A Bonney
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Vermont College of Medicine, 792 College Parkway, Fanny Allen Campus, Suite 101, Colchester, Burlington, VT 05446, USA
| | - Jennifer Condon
- Department of Obstetrics and Gynecology, Wayne State University, Perinatal Research Branch, NICHD, Detroit, MI 48201, USA
| | - Sam Mesiano
- Department of Reproductive Biology and Obstetrics and Gynecology, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Robert N Taylor
- Department of Obstetrics and Gynecology, Medical Center Boulevard, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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Yang X, Srivastava R, Howell SH, Bassham DC. Activation of autophagy by unfolded proteins during endoplasmic reticulum stress. Plant J 2016; 85:83-95. [PMID: 26616142 DOI: 10.1111/tpj.13091] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 11/18/2015] [Accepted: 11/20/2015] [Indexed: 05/20/2023]
Abstract
Endoplasmic reticulum stress is defined as the accumulation of unfolded proteins in the endoplasmic reticulum, and is caused by conditions such as heat or agents that cause endoplasmic reticulum stress, including tunicamycin and dithiothreitol. Autophagy, a major pathway for degradation of macromolecules in the vacuole, is activated by these stress agents in a manner dependent on inositol-requiring enzyme 1b (IRE1b), and delivers endoplasmic reticulum fragments to the vacuole for degradation. In this study, we examined the mechanism for activation of autophagy during endoplasmic reticulum stress in Arabidopsis thaliana. The chemical chaperones sodium 4-phenylbutyrate and tauroursodeoxycholic acid were found to reduce tunicamycin- or dithiothreitol-induced autophagy, but not autophagy caused by unrelated stresses. Similarly, over-expression of BINDING IMMUNOGLOBULIN PROTEIN (BIP), encoding a heat shock protein 70 (HSP70) molecular chaperone, reduced autophagy. Autophagy activated by heat stress was also found to be partially dependent on IRE1b and to be inhibited by sodium 4-phenylbutyrate, suggesting that heat-induced autophagy is due to accumulation of unfolded proteins in the endoplasmic reticulum. Expression in Arabidopsis of the misfolded protein mimics zeolin or a mutated form of carboxypeptidase Y (CPY*) also induced autophagy in an IRE1b-dependent manner. Moreover, zeolin and CPY* partially co-localized with the autophagic body marker GFP-ATG8e, indicating delivery to the vacuole by autophagy. We conclude that accumulation of unfolded proteins in the endoplasmic reticulum is a trigger for autophagy under conditions that cause endoplasmic reticulum stress.
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Affiliation(s)
- Xiaochen Yang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Interdepartmental Plant Biology Program, Iowa State University, Ames, IA, 50011, USA
| | - Renu Srivastava
- Plant Sciences Institute, Iowa State University, Ames, IA, 50011, USA
| | - Stephen H Howell
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Interdepartmental Plant Biology Program, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institute, Iowa State University, Ames, IA, 50011, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Interdepartmental Plant Biology Program, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institute, Iowa State University, Ames, IA, 50011, USA
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Djinovic-Carugo K, Carugo O. Missing strings of residues in protein crystal structures. Intrinsically Disord Proteins 2015; 3:e1095697. [PMID: 28232893 DOI: 10.1080/21690707.2015.1095697] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 10/22/2022]
Abstract
A large fraction of the protein crystal structures deposited in the Protein Data Bank are incomplete, since the position of one or more residues is not reported, despite these residues are part of the material that was analyzed. This may bias the use of the protein crystal structures by molecular biologists. Here we observe that in the large majority of the protein crystal structures strings of residues are missing. Polar residues incline to occur in missing strings together with glycine, while apolar and aromatic residues tend to avoid them. Particularly flexible residues, as shown by their extremely high B-factors, by their exposure to the solvent and by their secondary structures, flank the missing strings. These data should be a helpful guideline for crystallographers that encounter regions of flat and uninterpretable electron density as well as end-users of crystal structures.
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Affiliation(s)
- Kristina Djinovic-Carugo
- Department of Structural and Computational Biology; Max F. Perutz Laboratories, Vienna University, Vienna Biocenter (VBC); Vienna, Austria; Department of Biochemistry; Faculty of Chemistry and Chemical Technology, University of Ljubljana; Ljubljana, Slovenia
| | - Oliviero Carugo
- Department of Structural and Computational Biology; Max F. Perutz Laboratories, Vienna University, Vienna Biocenter (VBC); Vienna, Austria; Department of Chemistry; Pavia University; Pavia, Italy
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Dicks N, Gutierrez K, Michalak M, Bordignon V, Agellon LB. Endoplasmic reticulum stress, genome damage, and cancer. Front Oncol 2015; 5:11. [PMID: 25692096 PMCID: PMC4315039 DOI: 10.3389/fonc.2015.00011] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/12/2015] [Indexed: 01/30/2023] Open
Abstract
Endoplasmic reticulum (ER) stress has been linked to many diseases, including cancer. A large body of work has focused on the activation of the ER stress response in cancer cells to facilitate their survival and tumor growth; however, there are some studies suggesting that the ER stress response can also mitigate cancer progression. Despite these contradictions, it is clear that the ER stress response is closely associated with cancer biology. The ER stress response classically encompasses activation of three separate pathways, which are collectively categorized the unfolded protein response (UPR). The UPR has been extensively studied in various cancers and appears to confer a selective advantage to tumor cells to facilitate their enhanced growth and resistance to anti-cancer agents. It has also been shown that ER stress induces chromatin changes, which can also facilitate cell survival. Chromatin remodeling has been linked with many cancers through repression of tumor suppressor and apoptosis genes. Interplay between the classic UPR and genome damage repair mechanisms may have important implications in the transformation process of normal cells into cancer cells.
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Affiliation(s)
- Naomi Dicks
- Department of Animal Science, McGill University , Montréal, QC , Canada
| | - Karina Gutierrez
- Department of Animal Science, McGill University , Montréal, QC , Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta , Edmonton, AB , Canada
| | - Vilceu Bordignon
- Department of Animal Science, McGill University , Montréal, QC , Canada
| | - Luis B Agellon
- School of Dietetics and Human Nutrition, McGill University , Montréal, QC , Canada
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8
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Jaeken L, Vasilievich Matveev V. Coherent Behavior and the Bound State of Water and K(+) Imply Another Model of Bioenergetics: Negative Entropy Instead of High-energy Bonds. Open Biochem J 2012; 6:139-59. [PMID: 23264833 PMCID: PMC3527877 DOI: 10.2174/1874091x01206010139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 09/06/2012] [Accepted: 09/12/2012] [Indexed: 11/22/2022] Open
Abstract
Observations of coherent cellular behavior cannot be integrated into widely accepted membrane (pump) theory (MT) and its steady state energetics because of the thermal noise of assumed ordinary cell water and freely soluble cytoplasmic K(+). However, Ling disproved MT and proposed an alternative based on coherence, showing that rest (R) and action (A) are two different phases of protoplasm with different energy levels. The R-state is a coherent metastable low-entropy state as water and K(+) are bound to unfolded proteins. The A-state is the higher-entropy state because water and K(+) are free. The R-to-A phase transition is regarded as a mechanism to release energy for biological work, replacing the classical concept of high-energy bonds. Subsequent inactivation during the endergonic A-to-R phase transition needs an input of metabolic energy to restore the low entropy R-state. Matveev's native aggregation hypothesis allows to integrate the energetic details of globular proteins into this view.
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Affiliation(s)
- Laurent Jaeken
- Laboratory of Biochemistry, Karel de Grote University College, Department of Applied Engineering, Salesianenlaan 30, B-2660, Antwerp, Belgium
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9
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Abstract
Recent findings from genetic studies suggest that defective mitochondrial quality control may play an important role in the development of Parkinson's disease (PD). Such defects may result in the impairment of neuronal mitochondria, which leads to both synaptic dysfunction and cell death and results in neurodegeneration. Here, we review state-of-the-art knowledge of how pathways affecting mitochondrial quality control might contribute to PD, with a particular emphasis on the molecular mechanisms employed by PTEN-induced putative kinase 1 (PINK1), HtrA2 and Parkin to regulate mitochondrial quality control.
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Affiliation(s)
- Inês Pimenta de Castro
- Cell Death Regulation Laboratory, MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN UK
- IPATIMUP and Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - L. Miguel Martins
- Cell Death Regulation Laboratory, MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN UK
| | - Samantha Hui Yong Loh
- Cell Death Regulation Laboratory, MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN UK
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Bagai I, Ragsdale SW, Zuiderweg ERP. Pseudo-4D triple resonance experiments to resolve HN overlap in the backbone assignment of unfolded proteins. J Biomol NMR 2011; 49:69-74. [PMID: 21190062 PMCID: PMC3091507 DOI: 10.1007/s10858-010-9465-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/30/2010] [Indexed: 05/30/2023]
Abstract
The solution NMR resonance assignment of the protein backbone is most commonly carried out using triple resonance experiments that involve (15)N and (1)HN resonances. The assignment becomes problematic when there is resonance overlap of (15)N-(1)HN cross peaks. For such residues, one cannot unambiguously link the "left" side of the NH root to the "right" side, and the residues associated with such overlapping HN resonances remain often unassigned. Here we present a solution to this problem: a hybrid (4d,3d) reduced-dimensionality HN(CO)CA(CON)CA sequence. In this experiment, the Ca(i) resonance is modulated with the frequency of the Ca(i-1) resonance, which helps in resolving the ambiguity involved in connecting the Ca(i) and Ca(i-1) resonances for overlapping NH roots. The experiment has limited sensitivity, and is only suited for small or unfolded proteins. In a companion experiment, (4d,3d) reduced-dimensionality HNCO(N)CA, the Ca(i) resonance is modulated with the frequency of the CO(i-1) resonance, hence resolving the ambiguity existent in pairing up the Ca(i) and CO(i-1) resonances for overlapping NH roots.
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Affiliation(s)
- Ireena Bagai
- Department of Biological Chemistry, University of Michigan Medical School, MSRB III, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5605, USA
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, MSRB III, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5605, USA
| | - Erik R. P. Zuiderweg
- Department of Biological Chemistry, University of Michigan Medical School, 4220D MSRB III, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5605, USA
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Motáčková V, Nováček J, Zawadzka-Kazimierczuk A, Kazimierczuk K, Žídek L, Šanderová H, Krásný L, Koźmiński W, Sklenář V. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J Biomol NMR 2010; 48:169-77. [PMID: 20890634 PMCID: PMC2966349 DOI: 10.1007/s10858-010-9447-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 09/01/2010] [Indexed: 05/11/2023]
Abstract
A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.
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Affiliation(s)
- Veronika Motáčková
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jiří Nováček
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | | | - Lukáš Žídek
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hana Šanderová
- Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Libor Krásný
- Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
| | - Vladimír Sklenář
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Haynes CM, Yang Y, Blais SP, Neubert TA, Ron D. The matrix peptide exporter HAF-1 signals a mitochondrial UPR by activating the transcription factor ZC376.7 in C. elegans. Mol Cell 2010; 37:529-40. [PMID: 20188671 PMCID: PMC2846537 DOI: 10.1016/j.molcel.2010.01.015] [Citation(s) in RCA: 380] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 06/15/2009] [Accepted: 11/17/2009] [Indexed: 01/02/2023]
Abstract
Genetic analyses previously implicated the matrix-localized protease ClpP in signaling the stress of protein misfolding in the mitochondrial matrix to activate nuclear-encoded mitochondrial chaperone genes in C. elegans (UPR(mt)). Here, we report that haf-1, a gene encoding a mitochondria-localized ATP-binding cassette protein, is required for signaling within the UPR(mt) and for coping with misfolded protein stress. Peptide efflux from isolated mitochondria was ATP dependent and required HAF-1 and the protease ClpP. Defective UPR(mt) signaling in the haf-1-deleted worms was associated with failure of the bZIP protein, ZC376.7, to localize to nuclei in worms with perturbed mitochondrial protein folding, whereas zc376.7(RNAi) strongly inhibited the UPR(mt). These observations suggest a simple model whereby perturbation of the protein-folding environment in the mitochondrial matrix promotes ClpP-mediated generation of peptides whose haf-1-dependent export from the matrix contributes to UPR(mt) signaling across the mitochondrial inner membrane.
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Affiliation(s)
- Cole M. Haynes
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Yun Yang
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Steven P. Blais
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Thomas A. Neubert
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016
| | - David Ron
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Department of Cell Biology, New York University School of Medicine, New York, New York 10016
- Department of Medicine, New York University School of Medicine, New York, New York 10016
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Wang Y, Trewhella J, Goldenberg DP. Small-angle X-ray scattering of reduced ribonuclease A: effects of solution conditions and comparisons with a computational model of unfolded proteins. J Mol Biol 2008; 377:1576-92. [PMID: 18329044 PMCID: PMC2651769 DOI: 10.1016/j.jmb.2008.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 02/04/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
Abstract
The disulfide-reduced form of bovine ribonuclease A, with the Cys thiols irreversibly blocked, was characterized by small-angle x-ray scattering. To help resolve the conflicting results and interpretations from previous studies of this model unfolded protein, we measured scattering profiles using a range of solution conditions and compared them with the profiles predicted by a computational model for a random-coil polypeptide. Analysis of the simulated and experimental profiles reveals that scattering intensities at intermediate angles, corresponding to interatomic distances in the range of 5-20 A, are particularly sensitive to changes in solvation and can be used to assess the internal scaling behavior of the polypeptide chain, expressed as a mass fractal dimension, D(m). This region of the scattering curve is also much less sensitive to experimental artifacts than is the very small angle regime (the Guinier region) that has been more typically used to characterize unfolded proteins. The experimental small-angle x-ray scattering profiles closely matched those predicted by the computational model assuming relatively small solvation energies. The scaling behavior of the polypeptide approaches that of a well-solvated polymer under conditions where it has a large net charge and at high urea concentrations. At lower urea concentrations and neutral pH, the behavior of the chain approaches that expected for theta-conditions, where the effects of slightly unfavorable interactions with solvent balance those of excluded volume, leading to scaling behavior comparable to that of an idealized random walk chain. Though detectable, the shift toward more compact conformations at lower urea concentrations does not correspond to a transition to a globule state and is associated with little or no reduction in conformational entropy. This type of collapse, therefore, is unlikely to greatly reduce the conformational search for the native state.
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Affiliation(s)
- Yuanyuan Wang
- Department of Chemistry, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112-0840, USA
| | - Jill Trewhella
- Department of Chemistry, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112-0840, USA
- School of Molecular and Microbial Biosciences, The University of Sydney, NSW 2006 Australia
| | - David P. Goldenberg
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112-0840, USA
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Page R, Peti W, Wilson IA, Stevens RC, Wüthrich K. NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc Natl Acad Sci U S A 2005; 102:1901-5. [PMID: 15677718 PMCID: PMC548552 DOI: 10.1073/pnas.0408490102] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the Joint Center for Structural Genomics, one-dimensional (1D) 1H NMR spectroscopy is routinely used to characterize the folded state of protein targets and, thus, serves to guide subsequent crystallization efforts and to identify proteins for NMR structure determination. Here, we describe 1D 1H NMR screening of a group of 79 mouse homologue proteins, which correlates the NMR data with the outcome of subsequent crystallization experiments and crystallographic structure determination. Based on the 1D 1H NMR spectra, the proteins are classified into four groups, "A" to "D." A-type proteins are candidates for structure determination by NMR or crystallography; "B"-type are earmarked for crystallography; "C" indicates folded globular proteins with broadened line shapes; and "D" are nonglobular, "unfolded" polypeptides. The results obtained from coarse- and fine-screen crystallization trials imply that only A- and B-type proteins should be used for extensive crystallization trials in the future, with C and D proteins subjected only to coarse-screen crystallization trials. Of the presently studied 79 soluble protein targets, 63% yielded A- or B-quality 1D 1H NMR spectra. Although similar yields of crystallization hits were obtained for all four groups, A to D, crystals from A- and B-type proteins diffracted on average to significantly higher resolution than crystals produced from C- or D-type proteins. Furthermore, the output of refined crystal structures from this test set of proteins was 4-fold higher for A- and B-type than for C- and D-type proteins.
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Affiliation(s)
- Rebecca Page
- Department of Molecular Biology and Joint Center for Structural Genomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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