scholarly journals Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3607
Author(s):  
Olena Dobrovolska ◽  
Øyvind Strømland ◽  
Ørjan Sele Handegård ◽  
Martin Jakubec ◽  
Morten L. Govasli ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Misfolding ◽  
Driving Forces ◽  
Conformational Space ◽  
Supported Bilayers ◽  
Conformational Ensembles ◽  
Protein Membrane ◽  
Chimeric Polypeptide ◽  
Protein Misfolding And Aggregation ◽  
In Silico Analyses

The driving forces and conformational pathways leading to amphitropic protein-membrane binding and in some cases also to protein misfolding and aggregation is the subject of intensive research. In this study, a chimeric polypeptide, A-Cage-C, derived from α-Lactalbumin is investigated with the aim of elucidating conformational changes promoting interaction with bilayers. From previous studies, it is known that A-Cage-C causes membrane leakages associated with the sporadic formation of amorphous aggregates on solid-supported bilayers. Here we express and purify double-labelled A-Cage-C and prepare partially deuterated bicelles as a membrane mimicking system. We investigate A-Cage-C in the presence and absence of these bicelles at non-binding (pH 7.0) and binding (pH 4.5) conditions. Using in silico analyses, NMR, conformational clustering, and Molecular Dynamics, we provide tentative insights into the conformations of bound and unbound A-Cage-C. The conformation of each state is dynamic and samples a large amount of overlapping conformational space. We identify one of the clusters as likely representing the binding conformation and conclude tentatively that the unfolding around the central W23 segment and its reorientation may be necessary for full intercalation at binding conditions (pH 4.5). We also see evidence for an overall elongation of A-Cage-C in the presence of model bilayers.

Osmolytes as Modulators of Conformational Changes in Serpins

2001 ◽  
Vol 382 (11) ◽  
pp. 1593-1599 ◽  
Author(s):  
Michelle K.M. Chow ◽  
Glyn L. Devlin ◽  
Stephen P. Bottomley
Keyword(s):  
Conformational Changes ◽  
Protein Misfolding ◽  
Structural Changes ◽  
Serine Proteinase ◽  
Thermally Induced ◽  
Naturally Occurring ◽  
Antitrypsin Deficiency ◽  
Integral Role ◽  
Protein Misfolding And Aggregation ◽  
Insoluble Polymers

Abstract Protein misfolding and aggregation play an integral role in many diseases. The misfolding of the serpin (SERine Proteinase INhibitor) α1-antitrypsin results in the accumulation of insoluble polymers within hepatocytes and α1-antitrypsin deficiency in plasma, predisposing patients to liver cirrhosis and emphysema. We have examined the effect of three naturally occurring osmolytes, sarcosine, glycine betaine and trimethylamine Noxide, on conformational changes in α1-antitrypsin. All three solutes protected native α1-antitrypsin against thermally induced polymerisation and inactivation in a concentrationdependent manner. Further spectroscopic analysis showed that sarcosine stabilises the native conformation of α1-antitrypsin, thus hindering its conversion to an intermediate state and subsequent polymerisation. On refolding in the presence of sarcosine, α1-antitrypsin formed a heterogeneous population, with increasing proportions of molecules adopting an inactive conformation in higher concentrations of the osmolyte. These data show that sarcosine can be used to prevent abnormal structural changes in native α1-antitrypsin, but is ineffective in facilitating the correct folding of the protein. The implications of these results in the context of conformational changes and states adopted by α1-antitrypsin are discussed.

scholarly journals The Pah-R261Q mouse reveals oxidative stress associated with amyloid-like hepatic aggregation of mutant phenylalanine hydroxylase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Oscar Aubi ◽  
Karina S. Prestegård ◽  
Kunwar Jung-KC ◽  
Tie-Jun Sten Shi ◽  
Ming Ying ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Protein Misfolding ◽  
Phenylalanine Hydroxylase ◽  
Hepatic Tissue ◽  
Loss Of Function ◽  
Advantageous Position ◽  
Protein Misfolding And Aggregation ◽  
Activity Decrease ◽  
Systemic Accumulation ◽  
Altered Lipid

AbstractPhenylketonuria (PKU) is caused by autosomal recessive variants in phenylalanine hydroxylase (PAH), leading to systemic accumulation of L-phenylalanine (L-Phe) that may reach neurotoxic levels. A homozygous Pah-R261Q mouse, with a highly prevalent misfolding variant in humans, reveals the expected hepatic PAH activity decrease, systemic L-Phe increase, L-tyrosine and L-tryptophan decrease, and tetrahydrobiopterin-responsive hyperphenylalaninemia. Pah-R261Q mice also present unexpected traits, including altered lipid metabolism, reduction of liver tetrahydrobiopterin content, and a metabolic profile indicative of oxidative stress. Pah-R261Q hepatic tissue exhibits large ubiquitin-positive, amyloid-like oligomeric aggregates of mutant PAH that colocalize with selective autophagy markers. Together, these findings reveal that PKU, customarily considered a loss-of-function disorder, can also have toxic gain-of-function contribution from protein misfolding and aggregation. The proteostasis defect and concomitant oxidative stress may explain the prevalence of comorbid conditions in adult PKU patients, placing this mouse model in an advantageous position for the discovery of mutation-specific biomarkers and therapies.

scholarly journals Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs

2021 ◽  
Vol 22 (3) ◽  
pp. 1364
Author(s):  
V. V. Krishnan ◽  
Timothy Bentley ◽  
Alina Xiong ◽  
Kalyani Maitra
Keyword(s):  
Principal Component ◽  
Md Simulations ◽  
Conformational Space ◽  
Random Coil ◽  
Radius Of Gyration ◽  
Small Peptides ◽  
Conformational Ensembles ◽  
Solution State ◽  
Peptide Motifs ◽  
Explicit Solvent

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.

scholarly journals The Non-Protein Amino Acid BMAA Is Misincorporated into Human Proteins in Place of l-Serine Causing Protein Misfolding and Aggregation

PLoS ONE ◽  
2013 ◽  
Vol 8 (9) ◽  
pp. e75376 ◽  
Author(s):  
Rachael Anne Dunlop ◽  
Paul Alan Cox ◽  
Sandra Anne Banack ◽  
Kenneth John Rodgers
Keyword(s):  
Amino Acid ◽  
Protein Misfolding ◽  
Protein Amino Acid ◽  
Human Proteins ◽  
Protein Misfolding And Aggregation

Glutamine repeats: structural hypotheses and neurodegeneration

2002 ◽  
Vol 30 (4) ◽  
pp. 548-551 ◽  
Author(s):  
L. Masino ◽  
A. Pastore
Keyword(s):  
Protein Misfolding ◽  
Trinucleotide Repeats ◽  
Intranuclear Inclusions ◽  
The Past ◽  
Cag Trinucleotide Repeats ◽  
Protein Misfolding And Aggregation ◽  
Polyglutamine Protein ◽  
Molecular Bases ◽  
Protein Models

A growing number of neurodegenerative diseases are caused by expansion of CAG trinucleotide repeats coding for polyglutamine. The presence of intranuclear inclusions in the affected neuronal cells has suggested a mechanism for pathogenesis based on protein misfolding and aggregation. Detailed understanding of these phenomena is therefore crucial in order to rationalize different phases of the diseases. In the past decade, a few studies have focused on the structural properties of polyglutamine and on the molecular bases of the aggregation process. Most of these studies have been performed on polyglutamine peptides and protein models. Only one report is currently available on the characterization of a full-length polyglutamine protein. The structural hypotheses resulting from these studies are reviewed here.

Amyloidosis

2013 ◽  
pp. 1397-1409
Author(s):  
Philip N. Hawkins
Keyword(s):  
Protein Misfolding ◽  
Solid Organ Transplantation ◽  
The Body ◽  
Solid Organ ◽  
Body Protein ◽  
Amyloid Deposits ◽  
Life Threatening ◽  
And Function ◽  
Protein Misfolding And Aggregation ◽  
The Brain

Amyloidosis is a disorder of protein folding in which normally soluble proteins are deposited in the interstitial space as insoluble and remarkably stable fibrils that progressively disrupt tissue structure and function of organs throughout the body. Protein misfolding and aggregation have increasingly been recognized in the pathogenesis of various other diseases, but amyloidosis—the disease directly caused by extracellular amyloid deposition—is a precise term with critical implications for patients with a specific group of life-threatening disorders. Amyloidosis may be acquired or hereditary and the pattern of organ involvement varies within and between types, though clinical phenotypes overlap greatly. Virtually any tissue other than the brain may be directly involved. Although histology remains the diagnostic gold standard, developments in scintigraphy and MRI technology often produce pathognomonic findings. Systemic amyloidosis is usually fatal, but the prognosis has improved as the result of increasingly effective treatments for many of the conditions that underlie it, notably the use of biologic anti-inflammatory agents in patients with AA amyloidosis and new immunomodulatory agents in patients with AL type. Better supportive care, including dialysis and solid organ transplantation, have also influenced the prognosis favourably. A range of specific novel therapies are currently in clinical development, including RNA inhibitors that suppress production of amyloid precursor proteins, drugs that promote their normal soluble conformation in the plasma, and immunotherapy approaches that directly target the amyloid deposits.

scholarly journals Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases

2020 ◽  
Vol 53 ◽  
Author(s):  
Tessa Sinnige ◽  
Karen Stroobants ◽  
Christopher M. Dobson ◽  
Michele Vendruscolo
Keyword(s):  
Protein Misfolding ◽  
Molecular Mechanisms ◽  
Amyloid Β ◽  
Therapeutic Interventions ◽  
In Vivo Models ◽  
Disease Modifying Drugs ◽  
Parkinson’S Diseases ◽  
Protein Misfolding And Aggregation

Abstract Neurodegenerative disorders, including Alzheimer's (AD) and Parkinson's diseases (PD), are characterised by the formation of aberrant assemblies of misfolded proteins. The discovery of disease-modifying drugs for these disorders is challenging, in part because we still have a limited understanding of their molecular origins. In this review, we discuss how biophysical approaches can help explain the formation of the aberrant conformational states of proteins whose neurotoxic effects underlie these diseases. We discuss in particular models based on the transgenic expression of amyloid-β (Aβ) and tau in AD, and α-synuclein in PD. Because biophysical methods have enabled an accurate quantification and a detailed understanding of the molecular mechanisms underlying protein misfolding and aggregation in vitro, we expect that the further development of these methods to probe directly the corresponding mechanisms in vivo will open effective routes for diagnostic and therapeutic interventions.

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