scholarly journals Effect of circular permutations on transient partial unfolding in proteins

2016 ◽  
Vol 25 (8) ◽  
pp. 1483-1491 ◽  
Author(s):  
Chen Chen ◽  
Jung-Hun Yun ◽  
Jae-Hoon Kim ◽  
Chiwook Park
Keyword(s):  
Circular Permutations ◽  
Partial Unfolding

scholarly journals E3 Ubiquitin Ligase SPL2 Is a Lanthanide-Binding Protein

2021 ◽  
Vol 22 (11) ◽  
pp. 5712
Author(s):  
Michał Tracz ◽  
Ireneusz Górniak ◽  
Andrzej Szczepaniak ◽  
Wojciech Białek
Keyword(s):  
Ubiquitin Ligase ◽  
Conformational Changes ◽  
Protein Interactions ◽  
E3 Ubiquitin Ligase ◽  
Lanthanide Ions ◽  
E3 Ligases ◽  
Fluorescence Measurements ◽  
Partial Unfolding

The SPL2 protein is an E3 ubiquitin ligase of unknown function. It is one of only three types of E3 ligases found in the outer membrane of plant chloroplasts. In this study, we show that the cytosolic fragment of SPL2 binds lanthanide ions, as evidenced by fluorescence measurements and circular dichroism spectroscopy. We also report that SPL2 undergoes conformational changes upon binding of both Ca2+ and La3+, as evidenced by its partial unfolding. However, these structural rearrangements do not interfere with SPL2 enzymatic activity, as the protein retains its ability to auto-ubiquitinate in vitro. The possible applications of lanthanide-based probes to identify protein interactions in vivo are also discussed. Taken together, the results of this study reveal that the SPL2 protein contains a lanthanide-binding site, showing for the first time that at least some E3 ubiquitin ligases are also capable of binding lanthanide ions.

scholarly journals Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 656
Author(s):  
Vincent Van Deuren ◽  
Yin-Shan Yang ◽  
Karine de Guillen ◽  
Cécile Dubois ◽  
Catherine Anne Royer ◽  
...  
Keyword(s):  
High Pressure ◽  
Staphylococcal Nuclease ◽  
Comparative Assessment ◽  
Side Chain ◽  
Folding Pathway ◽  
Hydrophobic Core ◽  
Folding Pathways ◽  
Partial Unfolding ◽  
Protein Folding Pathways ◽  
Similar Description

Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CH groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CH, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CH when compared to amide groups.

Partial Unfolding of a Monoclonal Antibody: Role of a Single Domain in Driving Protein Aggregation

Biochemistry ◽  
2014 ◽  
Vol 53 (20) ◽  
pp. 3367-3377 ◽  
Author(s):  
Shyam B. Mehta ◽  
Jared S. Bee ◽  
Theodore W. Randolph ◽  
John F. Carpenter
Keyword(s):  
Monoclonal Antibody ◽  
Protein Aggregation ◽  
Single Domain ◽  
Partial Unfolding

scholarly journals Sorting Circular Permutations by Reversal

2003 ◽  
pp. 319-328 ◽  
Author(s):  
Andrew Solomon ◽  
Paul Sutcliffe ◽  
Raymond Lister
Keyword(s):  
Circular Permutations

scholarly journals Mitochondrial ClpX activates an essential biosynthetic enzyme through partial unfolding

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Julia R Kardon ◽  
Jamie A Moroco ◽  
John R Engen ◽  
Tania A Baker
Keyword(s):  
Active Site ◽  
Autonomous System ◽  
Aminolevulinic Acid ◽  
Structural Features ◽  
Biosynthetic Enzyme ◽  
Cofactor Binding ◽  
Partial Unfolding ◽  
Chaperone Interactions ◽  
Aaa Protein ◽  
Insight Into

Mitochondria control the activity, quality, and lifetime of their proteins with an autonomous system of chaperones, but the signals that direct substrate-chaperone interactions and outcomes are poorly understood. We previously discovered that the mitochondrial AAA+ protein unfoldase ClpX (mtClpX) activates the initiating enzyme for heme biosynthesis, 5-aminolevulinic acid synthase (ALAS), by promoting cofactor incorporation. Here, we ask how mtClpX accomplishes this activation. Using S. cerevisiae proteins, we identified sequence and structural features within ALAS that position mtClpX and provide it with a grip for acting on ALAS. Observation of ALAS undergoing remodeling by mtClpX revealed that unfolding is limited to a region extending from the mtClpX-binding site to the active site. Unfolding along this path is required for mtClpX to gate cofactor binding to ALAS. This targeted unfolding contrasts with the global unfolding canonically executed by ClpX homologs and provides insight into how substrate-chaperone interactions direct the outcome of remodeling.

LIGHT-STIMULATED LEAF GROWTH ON INTACT AND EXCISED BEAN PLANTS (PHASEOLUS VULGARIS L.). II. EFFECT OF LIGHT DURATION AND TIMING OF APPLICATION

1999 ◽  
Vol 47 (3) ◽  
pp. 147-152
Author(s):  
Shimon Lavee ◽  
Elizabeth Van Volkenburgh ◽  
Robert E. Cleland
Keyword(s):  
Phaseolus Vulgaris ◽  
White Light ◽  
Leaf Growth ◽  
Relative Rate ◽  
Red Light ◽  
Leaf Expansion ◽  
Leaf Elongation ◽  
Leaf Unfolding ◽  
Light Duration ◽  
Partial Unfolding

The dependence of bean (Phaseolus vulgaris L. cv. Contender) leaf unfolding and expansion on light has been explored in intact and excised plants by varying the duration and timing of exposure to white light. Plants were grown for 10 days in dim red light (RL), and then some were excised. Both the intact and the excised plants were then exposed to varying white light (WL) treatments. In continuous WL, leaf unfolding began after 8 h, and was maximal after 36 h. For plants exposed to short WL treatments, as little as 2 h WL elicited partial unfolding when leaves were returned to RL and measured after 60 h. The relative rate of leaf elongation was most rapid during the first 2 h of WL and it rapidly decreased during the following 6–8 h. An 8 h exposure to WL followed by 52 h RL produced only a slightly lower leaf expansion than continuous WL for 32 h. Leaf elongation after 24 h constant WL irradiance was no longer light-dependent. The response of leaves on excised plants to WL was progressively less if treatment was delayed for 24 h after excision. In contrast, leaves on intact plants did not lose their ability to respond to light even after 48 h in the dark. The ability of leaves on intact or excised plants to elongate in RL decayed rapidly after day 10. These results indicate that light-stimulated leaf expansion in beans is mediated by some factors whose transport to the leaves is influenced by the presence of roots.

Patterns in colored circular permutations

2019 ◽  
Vol 12 (1) ◽  
pp. 157-169
Author(s):  
Daniel Gray ◽  
Charles Lanning ◽  
Hua Wang
Keyword(s):  
Circular Permutations

Abstract 434: A Novel 5-Step Model for the Mechanism of ABCA1-Mediated Nascent HDL Biogenesis

2012 ◽  
Vol 32 (suppl_1) ◽  
Author(s):  
Shuhui Wang ◽  
Gregory Brubaker ◽  
Kailash Gulshan ◽  
Jonathan D Smith
Keyword(s):  
Plasma Membrane ◽  
Membrane Lipids ◽  
Sodium Taurocholate ◽  
Hek293 Cells ◽  
Membrane Remodeling ◽  
Fluorescent Indicators ◽  
Step Model ◽  
Partial Unfolding ◽  
Cell Membrane Protein ◽  
Partially Unfolded

Objective— Lipid-poor apoA-I acts as an acceptor for cell cholesterol and phospholipids via the cell membrane protein ABCA1, generating nascent HDL. However, the mechanism of this process is not understood at the molecular level. Methods and Results— We propose a novel five-step model of nascent HDL biogenesis: ABCA1 remodeling of the plasma membrane lipids exposing phosphatidylserine and apoA-I binding to ABCA1 are the first two independent steps; third, ABCA1 facilitates apoA-I partial unfolding; forth, partially unfolded apoA-I inserts into the modified plasma membrane resulting in apoA-I lipidation; and fifth, nascent HDL is released from the cell. We created fluorescent apoA-I indicators that can monitor apoA-I unfolding and lipidation states. In cell free assays of reconstituted HDL (rHDL) generation from apoAI and DMPC liposomes, the fluorescent indicators demonstrated apoA-I unfolding and lipidation concurrent with rHDL formation. Next, HEK293 cells were stably transfected with different ABCA1 vectors encoding wild type (WT) and W590S and C1477R Tangier disease mutation isoforms. WT ABCA1 mediated cholesterol efflux to apoA-I (requires all steps) and sodium taurocholate (NaTC, requires only the membrane remodeling step,). Although neither mutant could efflux cholesterol efficiently to apoA-I, they were blocked at different steps. The W590S mutant bound apoAI but could not efflux cholesterol to NaTC, thus it was blocked at the membrane remodeling step. However, the C1477R mutant could not bind apoAI but could efflux cholesterol to NaTC, thus its activity was blocked at the apoAI binding step. When the lipidation indicator apoA-I was incubated with stably transfected HEK cells, we observed cell associated lipidated apoA-I in cells expressing WT ABCA1, but mostly unlipidated apoA-I was associated with the cells expressing W590S ABCA1. Conclusion— Our results support a novel five-step model for nascent HDL biogenesis: 1, 2) ABCA1 remodeling of the plasma membrane and apoA-I binding to ABCA1, which facilitate 3) apoA-I partial unfolding and 4) and lipidation by the remodeled membrane, followed by 5) the release of nascent HDL.

Leishmania major biotin protein ligase forms a unique cross-handshake dimer

2021 ◽  
Vol 77 (4) ◽  
pp. 510-521
Author(s):  
Manoj Kumar Rajak ◽  
Sonika Bhatnagar ◽  
Shubhant Pandey ◽  
Sunil Kumar ◽  
Shalini Verma ◽  
...  
Keyword(s):  
Leishmania Major ◽  
Size Exclusion ◽  
Covalent Attachment ◽  
Mitochondrial Enzymes ◽  
Dependent Manner ◽  
Post Translational Modification ◽  
Terminal Domain ◽  
Exclusion Chromatography ◽  
Partial Unfolding ◽  
Biotin Protein Ligase

Biotin protein ligase catalyses the post-translational modification of biotin carboxyl carrier protein (BCCP) domains, a modification that is crucial for the function of several carboxylases. It is a two-step process that results in the covalent attachment of biotin to the ɛ-amino group of a conserved lysine of the BCCP domain of a carboxylase in an ATP-dependent manner. In Leishmania, three mitochondrial enzymes, acetyl-CoA carboxylase, methylcrotonyl-CoA carboxylase and propionyl-CoA carboxylase, depend on biotinylation for activity. In view of the indispensable role of the biotinylating enzyme in the activation of these carboxylases, crystal structures of L. major biotin protein ligase complexed with biotin and with biotinyl-5′-AMP have been solved. L. major biotin protein ligase crystallizes as a unique dimer formed by cross-handshake interactions of the hinge region of the two monomers formed by partial unfolding of the C-terminal domain. Interestingly, the substrate (BCCP domain)-binding site of each monomer is occupied by its own C-terminal domain in the dimer structure. This was observed in all of the crystals that were obtained, suggesting a closed/inactive conformation of the enzyme. Size-exclusion chromatography studies carried out using high protein concentrations (0.5 mM) suggest the formation of a concentration-dependent dimer that exists in equilibrium with the monomer.

scholarly journals The Driving Force: Nuclear Mechanotransduction in Cellular Function, Fate, and Disease

2019 ◽  
Vol 21 (1) ◽  
pp. 443-468 ◽  
Author(s):  
Melanie Maurer ◽  
Jan Lammerding
Keyword(s):  
Cell Fate ◽  
Conformational Changes ◽  
Current Evidence ◽  
Mechanical Stimuli ◽  
Cellular Behavior ◽  
Biochemical Responses ◽  
Technological Developments ◽  
Transcriptional Changes ◽  
Partial Unfolding ◽  
New Treatment

Cellular behavior is continuously affected by microenvironmental forces through the process of mechanotransduction, in which mechanical stimuli are rapidly converted to biochemical responses. Mounting evidence suggests that the nucleus itself is a mechanoresponsive element, reacting to cytoskeletal forces and mediating downstream biochemical responses. The nucleus responds through a host of mechanisms, including partial unfolding, conformational changes, and phosphorylation of nuclear envelope proteins; modulation of nuclear import/export; and altered chromatin organization, resulting in transcriptional changes. It is unclear which of these events present direct mechanotransduction processes and which are downstream of other mechanotransduction pathways. We critically review and discuss the current evidence for nuclear mechanotransduction, particularly in the context of stem cell fate, a largely unexplored topic, and in disease, where an improved understanding of nuclear mechanotransduction is beginning to open new treatment avenues. Finally, we discuss innovative technological developments that will allow outstanding questions in the rapidly growing field of nuclear mechanotransduction to be answered.

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