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1.
Mol Cell Biochem ; 2023 Oct 30.
Article in English | MEDLINE | ID: mdl-37902886

ABSTRACT

BACKGROUND: Heart failure (HF) often disrupts the protein quality control (PQC) system leading to protein aggregate accumulation. Evidence from tissue biopsies showed that exercise restores PQC system in HF; however, little is known about its effects on plasma proteostasis. AIM: To determine the effects of exercise training on the load and composition of plasma SDS-resistant protein aggregates (SRA) in patients with HF with reduced ejection fraction (HFrEF). METHODS: Eighteen patients with HFrEF (age: 63.4 ± 6.5 years; LVEF: 33.4 ± 11.6%) participated in a 12-week combined (aerobic plus resistance) exercise program (60 min/session, twice per week). The load and content of circulating SRA were assessed using D2D SDS-PAGE and mass spectrometry. Cardiorespiratory fitness, quality of life, and circulating levels of high-sensitive C-reactive protein, N-terminal pro-B-type natriuretic peptide (NT-proBNP), haptoglobin and ficolin-3, were also evaluated at baseline and after the exercise program. RESULTS: The exercise program decreased the plasma SRA load (% SRA/total protein: 38.0 ± 8.9 to 36.1 ± 9.7%, p = 0.018; % SRA/soluble fraction: 64.3 ± 27.1 to 59.8 ± 27.7%, p = 0.003). Plasma SRA of HFrEF patients comprised 31 proteins, with α-2-macroglobulin and haptoglobin as the most abundant ones. The exercise training significantly increased haptoglobin plasma levels (1.03 ± 0.40 to 1.11 ± 0.46, p = 0.031), while decreasing its abundance in SRA (1.83 ± 0.54 × 1011 to 1.51 ± 0.59 × 1011, p = 0.049). Cardiorespiratory fitness [16.4(5.9) to 19.0(5.2) ml/kg/min, p = 0.002], quality of life, and circulating NT-proBNP [720.0(850.0) to 587.0(847.3) pg/mL, p = 0.048] levels, also improved after the exercise program. CONCLUSION: Exercise training reduced the plasma SRA load and enhanced PQC, potentially via haptoglobin-mediated action, while improving cardiorespiratory fitness and quality of life of patients with HFrEF.

2.
J Cardiovasc Transl Res ; 16(3): 698-714, 2023 06.
Article in English | MEDLINE | ID: mdl-36271180

ABSTRACT

This study characterizes the plasma levels and composition of SDS-resistant aggregates (SRAs) in patients with heart failure with preserved ejection fraction (HFpEF) to infer molecular pathways associated with disease and/or proteostasis disruption. Twenty adults (ten with HFpEF and ten age-matched individuals) were included. Circulating SRAs were resolved by diagonal two-dimensional SDS-PAGE, and their protein content was identified by mass spectrometry. Protein carbonylation, ubiquitination and ficolin-3 were evaluated. Patients with HFpEF showed higher SRA/total (36.6 ± 4.9% vs 29.6 ± 2.2%, p = 0.009) and SRA/soluble levels (58.6 ± 12.7% vs 40.6 ± 5.8%, p = 0.008). SRAs were carbonylated and ubiquitinated, suggesting they are composed of dysfunctional proteins resistant to degradation. SRAs were enriched in proteins associated with cardiovascular function/disease and with proteostasis machinery. Total ficolin-3 levels were decreased (0.77 ± 0.22, p = 0.041) in HFpEF, suggesting a reduced proteostasis capacity to clear circulating SRA. Thus, the higher accumulation of SRA in HFpEF may result from a failure or overload of the protein clearance machinery.


Subject(s)
Heart Failure , Humans , Stroke Volume , Protein Aggregates
3.
Anal Biochem ; 571: 21-24, 2019 04 15.
Article in English | MEDLINE | ID: mdl-30779907

ABSTRACT

Sodium dodecyl sulfate (SDS) is a detergent used as a strong denaturant of proteins in gel electrophoresis. It has previously been shown that certain hyperstable, also known as kinetically stable, proteins are resistant to SDS and thus require heating for their denaturation in the presence of SDS. Because of its high denaturing strength, relatively few proteins are resistant to SDS thereby limiting the current use of SDS-PAGE for identifying hyperstable degradation-resistant proteins. In this study, we show that sarkosyl, a milder detergent than SDS, is able to identify proteins with moderately high kinetic stability that lack SDS-resistance. Our assay involves running and subsequently comparing boiled and unheated protein samples containing sarkosyl, instead of SDS, on PAGE gels and identifying subsequent differences in protein migration. Our results also show that sarkosyl and SDS may be combined in PAGE experiments at varying relative percentages to obtain semi-quantitative information about a protein's kinetic stability in a range inaccessible by probing through native- or SDS-PAGE. Using protein extracts from various legumes as model systems, we detected proteins with a range of protein stability from nearly SDS-resistant to barely sarkosyl resistant.


Subject(s)
Detergents/chemistry , Electrophoresis, Polyacrylamide Gel/methods , Proteins/analysis , Proteins/chemistry , Sarcosine/analogs & derivatives , Sodium Dodecyl Sulfate/chemistry , Kinetics , Molecular Structure , Protein Stability , Sarcosine/chemistry
4.
Anal Biochem ; 567: 82-84, 2019 02 15.
Article in English | MEDLINE | ID: mdl-30571946

ABSTRACT

Glycosaminoglycans (GAGs) were recovered from human cerebral spinal fluid (CSF) and after their conversion to disaccharides using polysaccharide lyases were analyzed by liquid chromatography tandem mass spectrometry using multiple reaction monitoring. CSF showed ng/mL levels of heparan sulfate, chondroitin sulfates and hyaluronan. The amounts and disaccharide composition of these GAGs differed from those found in human plasma. This approach may offer a new method for the discovery of biomarkers for diseases of the central nervous system.


Subject(s)
Chromatography, High Pressure Liquid , Glycosaminoglycans/cerebrospinal fluid , Tandem Mass Spectrometry , Biomarkers/cerebrospinal fluid , Central Nervous System Diseases/diagnosis , Chondroitin Sulfates/cerebrospinal fluid , Heparitin Sulfate/cerebrospinal fluid , Humans , Hyaluronic Acid/cerebrospinal fluid
5.
Biochemistry ; 56(47): 6179-6186, 2017 11 28.
Article in English | MEDLINE | ID: mdl-29087706

ABSTRACT

A protein's stability may range from nonexistent, as in the case of intrinsically disordered proteins, to very high, as indicated by a protein's resistance to degradation, even under relatively harsh conditions. The stability of this latter group is usually under kinetic control because of a high activation energy for unfolding that virtually traps the protein in a specific conformation, thereby conferring resistance to proteolytic degradation and misfolding aggregation. The usual outcome of kinetic stability is a longer protein half-life. Thus, the protective role of protein kinetic stability is often appreciated, but relatively little is known about the extent of biological roles related to this property. In this Perspective, we will discuss several known or putative biological roles of protein kinetic stability, including protection from stressors to avoid aggregation or premature degradation, achieving long-term phenotypic change, and regulating cellular processes by controlling the trigger and timing of molecular motion. The picture that emerges from this analysis is that protein kinetic stability is involved in a myriad of known and yet to be discovered biological functions via its ability to confer degradation resistance and control the timing, extent, and permanency of molecular motion.


Subject(s)
Protein Conformation , Protein Folding , Protein Stability , Proteins/chemistry , Humans , Kinetics , Protein Denaturation , Protein Multimerization , Thermodynamics
6.
Ageing Res Rev ; 40: 1-10, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28757291

ABSTRACT

Cells ensure their protein quality control through the proteostasis network. Aging and age-related diseases, such as neurodegenerative and cardiovascular diseases, have been associated to the reduction of proteostasis network efficiency and, consequently, to the accumulation of protein misfolded aggregates. The decline in protein homeostasis has been associated with the development and progression of atherosclerotic cardiovascular disease, cardiac hypertrophy, cardiomyopathies, and heart failure. Exercise training is a key component of the management of patients with cardiovascular disease, consistently improving quality of life and prognosis. In this review, we give an overview on age-related protein aggregation, the role of the increase of misfolded protein aggregates on cardiovascular pathophysiology, and describe the beneficial or deleterious effects of the proteostasis network on the development of cardiovascular disease. We subsequently discuss how exercise training, a key lifestyle intervention in those with cardiovascular disease, could restore proteostasis and improve disease status.


Subject(s)
Cardiovascular Diseases/metabolism , Exercise/physiology , Protein Aggregates/physiology , Protein Folding , Cardiovascular Diseases/prevention & control , Humans , Life Style , Proteins/metabolism , Quality of Life
7.
Biochem Biophys Res Commun ; 491(4): 994-999, 2017 09 30.
Article in English | MEDLINE | ID: mdl-28774556

ABSTRACT

In common beans and lima bean, the storage protein phaseolin is difficult to degrade and SDS-resistant, a sign of kinetic stability. Kinetically stable proteins (KSPs) are characterized by having a high-energy barrier between the native and denatured states that results in very slow unfolding. Such proteins are resistant to proteolytic degradation and detergents, such as SDS. Here the method SDS-Trapping of Proteins (S-TraP) is applied directly on bean extracts to quantify the kinetic stability of phaseolin in lima bean and several common beans, including black bean, navy bean, and small red bean. The bean extracts were incubated in SDS at various temperatures (60-75 °C) for different time periods, followed by SDS-PAGE analysis at room temperature, and subsequent band quantification to determine the kinetics of phaseolin unfolding. Eyring plot analysis showed that the phaseolin from each bean has high kinetic stability, with an SDS-trapping (i.e. unfolding) half-life ranging from about 20-100 years at 24 °C and 2-7 years at 37 °C. The remarkably high kinetic stability of these phaseolin proteins is consistent with the low digestibility of common beans and lima bean, as well as their relatively high germination temperatures. From a practical perspective, this work exemplifies that S-TraP is a useful and cost-effective method for quantifying the kinetic stability of proteins in biological extracts or lysates. Depending on the protein to be studied and its abundance, S-TraP may be performed directly on the extract without need for protein purification.


Subject(s)
Fabaceae/chemistry , Plant Extracts/chemistry , Plant Proteins/chemistry , Sodium Dodecyl Sulfate/chemistry , Kinetics , Plant Extracts/analysis , Plant Proteins/analysis , Protein Stability , Temperature , Time Factors
8.
J Agric Food Chem ; 64(40): 7649-7657, 2016 Oct 12.
Article in English | MEDLINE | ID: mdl-27643830

ABSTRACT

Kinetically stable proteins (KSPs) are resistant to the denaturing detergent sodium dodecyl sulfate (SDS). Such resilience makes KSPs resistant to proteolytic degradation and may have arisen in nature as a mechanism for organismal adaptation and survival against harsh conditions. Legumes are well-known for possessing degradation-resistant proteins that often diminish their nutritional value. Here we applied diagonal two-dimensional (D2D) SDS-polyacrylamide gel electrophoresis (PAGE), a method that allows for the proteomics-level identification of KSPs, to a group of 12 legumes (mostly beans and peas) of agricultural and nutritional importance. Our proteomics results show beans that are more difficult to digest, such as soybean, lima beans, and various common beans, have high contents of KSPs. In contrast, mung bean, red lentil, and various peas that are highly digestible contain low amounts of KSPs. Identified proteins with high kinetic stability are associated with warm-season beans, which germinate at higher temperatures. In contrast, peas and red lentil, which are cool-season legumes, contain low levels of KSPs. Thus, our results show protein kinetic stability is an important factor in the digestibility of legume proteins and may relate to nutrition efficiency, timing of seed germination, and legume resistance to biotic stressors. Furthermore, we show D2D SDS-PAGE is a powerful method that could be applied for determining the abundance and identity of KSPs in engineered and wild legumes and for advancing basic research and associated applications.


Subject(s)
Germination , Plant Proteins/chemistry , Adaptation, Biological , Electrophoresis, Polyacrylamide Gel , Fabaceae , Pisum sativum , Phaseolus/chemistry , Plant Proteins/analysis , Plant Proteins/metabolism , Seeds/chemistry , Temperature
9.
Age (Dordr) ; 38(3): 56, 2016 Jun.
Article in English | MEDLINE | ID: mdl-27179971

ABSTRACT

Proteins that misfold into hyper-stable/degradation-resistant species during aging may accumulate and disrupt protein homeostasis (i.e., proteostasis), thereby posing a survival risk to any organism. Using the method diagonal two-dimensional (D2D) SDS-PAGE, which separates hyper-stable SDS-resistant proteins at a proteomics level, we analyzed the plasma of healthy young (<30 years) and older (60-80 years) adults. We discovered the presence of soluble SDS-resistant protein aggregates in the plasma of older adults, but found significantly lower levels in the plasma of young adults. We identified the inflammation-related chaperone protein haptoglobin as the main component of the hyper-stable aggregates. This observation is consistent with the growing link between accumulations of protein aggregates and aging across many organisms. It is plausible higher amounts of SDS-resistant protein aggregates in the plasma of older adults may reflect a compromise in proteostasis that may potentially indicate cellular aging and/or disease risk. The results of this study have implications for further understanding the link between aging and the accumulation of protein aggregates, as well as potential for the development of aging-related biomarkers. More broadly, this novel application of D2D SDS-PAGE may be used to identify, quantify, and characterize the degradation-resistant protein aggregates in human plasma or any biological system.


Subject(s)
Aging/blood , Proteasome Endopeptidase Complex/blood , Protein Aggregates/physiology , Proteins/metabolism , Adult , Aged , Aged, 80 and over , Electrophoresis, Polyacrylamide Gel , Female , Homeostasis , Humans , Male , Middle Aged , Young Adult
10.
Proc Natl Acad Sci U S A ; 112(47): 14605-10, 2015 Nov 24.
Article in English | MEDLINE | ID: mdl-26554002

ABSTRACT

The design of stable, functional proteins is difficult. Improved design requires a deeper knowledge of the molecular basis for design outcomes and properties. We previously used a bioinformatics and energy function method to design a symmetric superfold protein composed of repeating structural elements with multivalent carbohydrate-binding function, called ThreeFoil. This and similar methods have produced a notably high yield of stable proteins. Using a battery of experimental and computational analyses we show that despite its small size and lack of disulfide bonds, ThreeFoil has remarkably high kinetic stability and its folding is specifically chaperoned by carbohydrate binding. It is also extremely stable against thermal and chemical denaturation and proteolytic degradation. We demonstrate that the kinetic stability can be predicted and modeled using absolute contact order (ACO) and long-range order (LRO), as well as coarse-grained simulations; the stability arises from a topology that includes many long-range contacts which create a large and highly cooperative energy barrier for unfolding and folding. Extensive data from proteomic screens and other experiments reveal that a high ACO/LRO is a general feature of proteins with strong resistances to denaturation and degradation. These results provide tractable approaches for predicting resistance and designing proteins with sufficient topological complexity and long-range interactions to accommodate destabilizing functional features as well as withstand chemical and proteolytic challenge.


Subject(s)
Protein Engineering/methods , Proteins/chemistry , Binding Sites , Computer Simulation , Detergents/pharmacology , Kinetics , Ligands , Models, Molecular , Peptide Hydrolases/metabolism , Protein Folding/drug effects , Protein Stability/drug effects , Thermodynamics
11.
Adv Exp Med Biol ; 855: 117-34, 2015.
Article in English | MEDLINE | ID: mdl-26149928

ABSTRACT

Serum amyloid A (SAA) is an acute-phase reactant protein predominantly bound to high-density lipoprotein in serum and presumed to play various biological and pathological roles. Upon tissue trauma or infection, hepatic expression of SAA increases up to 1,000 times the basal levels. Prolonged increased levels of SAA may lead to amyloid A (AA) amyloidosis, a usually fatal systemic disease in which the amyloid deposits are mostly comprised of the N-terminal 1-76 fragment of SAA. SAA isoforms may differ across species in their ability to cause AA amyloidosis, and the mechanism of pathogenicity remains poorly understood. In vitro studies have shown that SAA is a marginally stable protein that folds into various oligomeric species at 4 °C. However, SAA is largely disordered at 37 °C, reminiscent of intrinsically disordered proteins. Non-pathogenic murine (m)SAA2.2 spontaneously forms amyloid fibrils in vitro at 37 °C whereas pathogenic mSAA1.1 has a long lag (nucleation) phase, and eventually forms fibrils of different morphology than mSAA2.2. Remarkably, human SAA1.1 does not form mature fibrils in vitro. Thus, it appears that the intrinsic amyloidogenicity of SAA is not a key determinant of pathogenicity, and that other factors, including fibrillation kinetics, ligand binding effects, fibril stability, nucleation efficiency, and SAA degradation may play key roles. This chapter will focus on the known structural and biophysical properties of SAA and discuss how these properties may help better understand the molecular mechanism of AA amyloidosis.


Subject(s)
Amyloid/biosynthesis , Biopolymers/metabolism , Serum Amyloid A Protein/metabolism , Animals , Cholesterol, HDL/metabolism , Disease Models, Animal , Humans , Mice , Protein Conformation , Serum Amyloid A Protein/chemistry
12.
Biochimie ; 104: 70-80, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24878279

ABSTRACT

Serum amyloid A (SAA) is an apolipoprotein involved in poorly understood roles in inflammation. Upon trauma, hepatic expression of SAA rises 1000 times the basal levels. In the case of inflammatory diseases like rheumatoid arthritis, there is a risk for deposition of SAA fibrils in various organs leading to Amyloid A (AA) amyloidosis. Although the amyloid deposits in AA amyloidosis accumulate with the glycosaminoglycan (GAG) heparan sulfate, the role GAGs play in the function and pathology of SAA is an enigma. It has been shown that GAG sulfation is a contributing factor in protein fibrillation and for co-aggregating with a plethora of amyloidogenic proteins. Herein, the effects of heparin, heparan sulfate, hyaluronic acid, chondroitin sulfate A, and heparosan on the oligomerization and aggregation properties of pathogenic mouse SAA1.1 were investigated. Delipidated SAA was used to better understand the interactions between SAA and GAGs without the complicating involvement of lipids. The results revealed-to varying degrees-that all GAGs accelerated SAA1.1 aggregation, but had variable effects on its fibrillation. Heparan sulfate, hyaluronic acid, and heparosan did not affect much the fibrillation of SAA1.1. In contrast, chondroitin sulfate A blocked SAA fibril formation and facilitated the formation of spherical aggregates of various sizes. Interestingly, heparin caused formation of spherical SAA1.1 aggregates of various sizes, vast amounts of thin protofibrils, and few long fibrils of various heights. These results suggest that GAGs may have an intrinsic and divergent influence on the aggregation and fibrillation of HDL-free SAA1.1 in vivo, with functional and pathological implications.


Subject(s)
Glycosaminoglycans/pharmacology , Protein Multimerization/drug effects , Serum Amyloid A Protein/chemistry , Amino Acid Sequence , Animals , Glycosaminoglycans/metabolism , Heparin/metabolism , Kinetics , Mice , Models, Molecular , Molecular Sequence Data , Protein Refolding/drug effects , Protein Structure, Secondary , Serum Amyloid A Protein/metabolism
13.
Protein Sci ; 23(4): 400-10, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24408076

ABSTRACT

Wild-type green fluorescent protein (GFP) folds on a time scale of minutes. The slow step in folding is a cis-trans peptide bond isomerization. The only conserved cis-peptide bond in the native GFP structure, at P89, was remodeled by the insertion of two residues, followed by iterative energy minimization and side chain design. The engineered GFP was synthesized and found to fold faster and more efficiently than its template protein, recovering 50% more of its fluorescence upon refolding. The slow phase of folding is faster and smaller in amplitude, and hysteresis in refolding has been eliminated. The elimination of a previously reported kinetically trapped state in refolding suggests that X-P89 is trans in the trapped state. A 2.55 Å resolution crystal structure revealed that the new variant contains only trans-peptide bonds, as designed. This is the first instance of a computationally remodeled fluorescent protein that folds faster and more efficiently than wild type.


Subject(s)
Green Fluorescent Proteins/chemistry , Green Fluorescent Proteins/metabolism , Peptides/chemistry , Protein Engineering , Protein Folding , Crystallography, X-Ray , Green Fluorescent Proteins/genetics , Kinetics , Models, Molecular , Peptides/metabolism , Protein Refolding , Stereoisomerism
14.
Biochemistry ; 52(36): 6275-85, 2013 Sep 10.
Article in English | MEDLINE | ID: mdl-23952613

ABSTRACT

Adeno-associated virus (AAV) is a key candidate in the development of gene therapy. In this work, we used surface plasmon resonance spectroscopy to study the interaction between AAV and heparin and other glycosaminoglycans (GAGs). Surface plasmon resonance results revealed that heparin binds to AAV with an extremely high affinity. Solution competition studies showed that binding of AAV to heparin is chain length-dependent. AAV prefers to bind full chain heparin. All sulfo groups (especially N-sulfo and 6-O-sulfo groups) on heparin are important for the AAV-heparin interaction. Higher levels of sulfo group substitution in GAGs enhance their binding affinities. Atomic force microscopy was also performed to image AAV-2 in a complex with heparin.


Subject(s)
Dependovirus/metabolism , Glycosaminoglycans/metabolism , Heparin/metabolism , Animals , Heparin/analogs & derivatives , Microscopy, Atomic Force , Surface Plasmon Resonance , Swine
15.
PLoS One ; 8(6): e64974, 2013.
Article in English | MEDLINE | ID: mdl-23750222

ABSTRACT

The fibrillation of Serum Amyloid A (SAA) - a major acute phase protein - is believed to play a role in the disease Amyloid A (AA) Amyloidosis. To better understand the amyloid formation pathway of SAA, we characterized the oligomerization, misfolding, and aggregation of a disease-associated isoform of human SAA - human SAA1.1 (hSAA1.1) - using techniques ranging from circular dichroism spectroscopy to atomic force microscopy, fluorescence spectroscopy, immunoblot studies, solubility measurements, and seeding experiments. We found that hSAA1.1 formed alpha helix-rich, marginally stable oligomers in vitro on refolding and cross-beta-rich aggregates following incubation at 37°C. Strikingly, while hSAA1.1 was not highly amyloidogenic in vitro, the addition of a single N-terminal methionine residue significantly enhanced the fibrillation propensity of hSAA1.1 and modulated its fibrillation pathway. A deeper understanding of the oligomerization and fibrillation pathway of hSAA1.1 may help elucidate its pathological role.


Subject(s)
Protein Multimerization , Serum Amyloid A Protein/chemistry , Humans , Methionine , Models, Molecular , Protein Isoforms/chemistry , Protein Refolding , Protein Structure, Secondary , Solubility
16.
J Biol Chem ; 288(4): 2744-55, 2013 Jan 25.
Article in English | MEDLINE | ID: mdl-23223242

ABSTRACT

Serum amyloid A (SAA) is best known for being the main component of amyloid in the inflammation-related disease amyloid A (AA) amyloidosis. Despite the high sequence identity among different SAA isoforms, not all SAA proteins are pathogenic. In most mouse strains, the AA deposits mostly consist of SAA1.1. Conversely, the CE/J type mouse expresses a single non-pathogenic SAA2.2 protein that is 94% identical to SAA1.1. Here we show that SAA1.1 and SAA2.2 differ in their quaternary structure, fibrillation kinetics, prefibrillar oligomers, and fibril morphology. At 37 °C and inflammation-related SAA concentrations, SAA1.1 exhibits an oligomer-rich fibrillation lag phase of a few days, whereas SAA2.2 shows virtually no lag phase and forms small fibrils within a few hours. Deep UV resonance Raman, far UV-circular dichroism, atomic force microscopy, and fibrillation cross-seeding experiments suggest that SAA1.1 and SAA2.2 fibrils possess different morphology. Both the long-lived oligomers of pathogenic SAA1.1 and the fleeting prefibrillar oligomers of non-pathogenic SAA2.2, but not their respective amyloid fibrils, permeabilized synthetic bilayer membranes in vitro. This study represents the first comprehensive comparison between the biophysical properties of SAA isoforms with distinct pathogenicities, and the results suggest that structural and kinetic differences in the oligomerization-fibrillation of SAA1.1 and SAA2.2, more than their intrinsic amyloidogenicity, may contribute to their diverse pathogenicity.


Subject(s)
Amyloidosis/metabolism , Serum Amyloid A Protein/chemistry , Animals , Biophysics/methods , Circular Dichroism , HEK293 Cells , Humans , Inflammation , Kinetics , Mice , Microscopy, Atomic Force/methods , Protein Binding , Protein Denaturation , Protein Folding , Protein Isoforms , Recombinant Proteins/chemistry , Serum Amyloid A Protein/metabolism , Spectrophotometry, Ultraviolet/methods
17.
Biochemistry ; 51(14): 3092-9, 2012 Apr 10.
Article in English | MEDLINE | ID: mdl-22448726

ABSTRACT

The fibrillar deposition of serum amyloid A (SAA) has been linked to the disease amyloid A (AA) amyloidosis. We have used the SAA isoform, SAA2.2, from the CE/J mouse strain, as a model system to explore the inherent structural and biophysical properties of SAA. Despite its nonpathogenic nature in vivo, SAA2.2 spontaneously forms fibrils in vitro, suggesting that SAA proteins are inherently amyloidogenic. However, whereas the importance of the amino terminus of SAA for fibril formation has been well documented, the influence of the proline-rich and presumably disordered carboxy terminus remains poorly understood. To clarify the inherent role of the carboxy terminus in the oligomerization and fibrillation of SAA, we truncated the proline-rich final 13 residues of SAA2.2. We found that unlike full-length SAA2.2, the carboxy-terminal truncated SAA2.2 (SAA2.2ΔC) did not oligomerize to a hexamer or octamer, but formed a high molecular weight soluble aggregate. Moreover, SAA2.2ΔC also exhibited a pronounced decrease in the rate of fibril formation. Intriguingly, when equimolar amounts of denatured SAA2.2 and SAA2.2ΔC were mixed and allowed to refold together, the mixture formed an octamer and exhibited rapid fibrillation kinetics, similar to those for full-length SAA2.2. These results suggest that the carboxy terminus of SAA, which is highly conserved among SAA sequences in all vertebrates, might play important structural roles, including modulating the folding, oligomerization, misfolding, and fibrillation of SAA.


Subject(s)
Amyloid/chemistry , Protein Folding , Serum Amyloid A Protein/chemistry , Amyloid/metabolism , Animals , Kinetics , Mice , Microscopy, Atomic Force , Molecular Weight , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , Serum Amyloid A Protein/genetics , Serum Amyloid A Protein/metabolism
18.
Proteins ; 80(3): 920-34, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22189917

ABSTRACT

Protein unfolding is modeled as an ensemble of pathways, where each step in each pathway is the addition of one topologically possible conformational degree of freedom. Starting with a known protein structure, GeoFold hierarchically partitions (cuts) the native structure into substructures using revolute joints and translations. The energy of each cut and its activation barrier are calculated using buried solvent accessible surface area, side chain entropy, hydrogen bonding, buried cavities, and backbone degrees of freedom. A directed acyclic graph is constructed from the cuts, representing a network of simultaneous equilibria. Finite difference simulations on this graph simulate native unfolding pathways. Experimentally observed changes in the unfolding rates for disulfide mutants of barnase, T4 lysozyme, dihydrofolate reductase, and factor for inversion stimulation were qualitatively reproduced in these simulations. Detailed unfolding pathways for each case explain the effects of changes in the chain topology on the folding energy landscape. GeoFold is a useful tool for the inference of the effects of disulfide engineering on the energy landscape of protein unfolding.


Subject(s)
Disulfides/chemistry , Protein Unfolding , Proteins/chemistry , Software , Bacillus/enzymology , Bacillus/genetics , Bacterial Proteins , Bacteriophage T4/enzymology , Bacteriophage T4/genetics , Entropy , Escherichia coli/enzymology , Escherichia coli/genetics , Kinetics , Models, Molecular , Muramidase/chemistry , Muramidase/genetics , Mutation , Protein Conformation , Protein Stability , Proteins/genetics , Ribonucleases/chemistry , Ribonucleases/genetics , Tetrahydrofolate Dehydrogenase/chemistry , Tetrahydrofolate Dehydrogenase/genetics
19.
Biochemistry ; 51(1): 100-7, 2012 Jan 10.
Article in English | MEDLINE | ID: mdl-22106876

ABSTRACT

Globular proteins are usually in equilibrium with unfolded conformations, whereas kinetically stable proteins (KSPs) are conformationally trapped by their high unfolding transition state energy. Kinetic stability (KS) could allow proteins to maintain their activity under harsh conditions, increase a protein's half-life, or protect against misfolding-aggregation. Here we show the development of a simple method for quantifying a protein's KS that involves incubating a protein in SDS at high temperature as a function of time, running the unheated samples on SDS-PAGE, and quantifying the bands to determine the time-dependent loss of a protein's SDS resistance. Six diverse proteins, including two monomer, two dimers, and two tetramers, were studied by this method, and the kinetics of the loss of SDS resistance correlated linearly with their unfolding rate determined by circular dichroism. These results imply that the mechanism by which SDS denatures proteins involves conformational trapping, with a trapping rate that is determined and limited by the rate of protein unfolding. We applied the SDS trapping of proteins (S-TraP) method to superoxide dismutase (SOD) and transthyretin (TTR), which are highly KSPs with native unfolding rates that are difficult to measure by conventional spectroscopic methods. A combination of S-TraP experiments between 75 and 90 °C combined with Eyring plot analysis yielded an unfolding half-life of 70 ± 37 and 18 ± 6 days at 37 °C for SOD and TTR, respectively. The S-TraP method shown here is extremely accessible, sample-efficient, cost-effective, compatible with impure or complex samples, and will be useful for exploring the biological and pathological roles of kinetic stability.


Subject(s)
Electrophoresis, Polyacrylamide Gel/methods , Protein Stability/drug effects , Sodium Dodecyl Sulfate , Thermodynamics , Animals , Bacterial Proteins/chemistry , Bromelains/chemistry , Catalase/chemistry , Cattle , Cellulases/chemistry , Circular Dichroism , Fungal Proteins/chemistry , Glucose Oxidase/chemistry , Humans , Plant Proteins/chemistry , Prealbumin/chemistry , Protein Denaturation , Protein Unfolding/drug effects , Spin Trapping/methods , Streptavidin/chemistry , Time Factors , Trypsin Inhibitors/chemistry
20.
Biochemistry ; 50(43): 9184-91, 2011 Nov 01.
Article in English | MEDLINE | ID: mdl-21942925

ABSTRACT

For nearly four decades, the formation of amyloid fibrils by the inflammation-related protein serum amyloid A (SAA) has been pathologically linked to the disease amyloid A (AA) amyloidosis. However, here we show that the nonpathogenic murine SAA2.2 spontaneously forms marginally stable amyloid fibrils at 37 °C that exhibit cross-beta structure, binding to thioflavin T, and fibrillation by a nucleation-dependent seeding mechanism. In contrast to the high stability of most known amyloid fibrils to thermal and chemical denaturation, experiments monitored by glutaraldehyde cross-linking/SDS-PAGE, thioflavin T fluorescence, and light scattering (OD(600)) showed that the mature amyloid fibrils of SAA2.2 dissociate upon incubation in >1.0 M urea or >45 °C. When considering the nonpathogenic nature of SAA2.2 and its ~1000-fold increased concentration in plasma during an inflammatory response, its extreme in vitro amyloidogenicity under physiological-like conditions suggest that SAA amyloid might play a functional role during inflammation. Of general significance, the combination of methods used here is convenient for exploring the stability of amyloid fibrils that are sensitive to urea and temperature. Furthermore, our studies imply that analogous to globular proteins, which can possess structures ranging from intrinsically disordered to extremely stable, amyloid fibrils formed in vivo might have a broader range of stabilities than previously appreciated with profound functional and pathological implications.


Subject(s)
Amyloid/metabolism , Serum Amyloid A Protein/metabolism , Amyloid/chemistry , Amyloid/ultrastructure , Amyloidosis/metabolism , Animals , Benzothiazoles , Electrophoresis, Polyacrylamide Gel , Mice , Protein Binding , Protein Stability , Protein Structure, Secondary , Serum Amyloid A Protein/chemistry , Temperature , Thiazoles/metabolism
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