Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 47
Filtrar
Mais filtros

Base de dados
País/Região como assunto
Tipo de documento
Intervalo de ano de publicação
1.
Mol Cell Biochem ; 2023 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-37902886

RESUMO

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.
Anal Biochem ; 567: 82-84, 2019 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-30571946

RESUMO

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.


Assuntos
Cromatografia Líquida de Alta Pressão , Glicosaminoglicanos/líquido cefalorraquidiano , Espectrometria de Massas em Tandem , Biomarcadores/líquido cefalorraquidiano , Doenças do Sistema Nervoso Central/diagnóstico , Sulfatos de Condroitina/líquido cefalorraquidiano , Heparitina Sulfato/líquido cefalorraquidiano , Humanos , Ácido Hialurônico/líquido cefalorraquidiano
3.
Anal Biochem ; 571: 21-24, 2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30779907

RESUMO

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.


Assuntos
Detergentes/química , Eletroforese em Gel de Poliacrilamida/métodos , Proteínas/análise , Proteínas/química , Sarcosina/análogos & derivados , Dodecilsulfato de Sódio/química , Cinética , Estrutura Molecular , Estabilidade Proteica , Sarcosina/química
4.
Proc Natl Acad Sci U S A ; 112(47): 14605-10, 2015 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-26554002

RESUMO

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.


Assuntos
Engenharia de Proteínas/métodos , Proteínas/química , Sítios de Ligação , Simulação por Computador , Detergentes/farmacologia , Cinética , Ligantes , Modelos Moleculares , Peptídeo Hidrolases/metabolismo , Dobramento de Proteína/efeitos dos fármacos , Estabilidade Proteica/efeitos dos fármacos , Termodinâmica
5.
Biochemistry ; 56(47): 6179-6186, 2017 11 28.
Artigo em Inglês | MEDLINE | ID: mdl-29087706

RESUMO

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.


Assuntos
Conformação Proteica , Dobramento de Proteína , Estabilidade Proteica , Proteínas/química , Humanos , Cinética , Desnaturação Proteica , Multimerização Proteica , Termodinâmica
6.
Biochem Biophys Res Commun ; 491(4): 994-999, 2017 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-28774556

RESUMO

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.


Assuntos
Fabaceae/química , Extratos Vegetais/química , Proteínas de Plantas/química , Dodecilsulfato de Sódio/química , Cinética , Extratos Vegetais/análise , Proteínas de Plantas/análise , Estabilidade Proteica , Temperatura , Fatores de Tempo
7.
Adv Exp Med Biol ; 855: 117-34, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26149928

RESUMO

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.


Assuntos
Amiloide/biossíntese , Biopolímeros/metabolismo , Proteína Amiloide A Sérica/metabolismo , Animais , HDL-Colesterol/metabolismo , Modelos Animais de Doenças , Humanos , Camundongos , Conformação Proteica , Proteína Amiloide A Sérica/química
8.
J Biol Chem ; 288(4): 2744-55, 2013 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-23223242

RESUMO

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.


Assuntos
Amiloidose/metabolismo , Proteína Amiloide A Sérica/química , Animais , Biofísica/métodos , Dicroísmo Circular , Células HEK293 , Humanos , Inflamação , Cinética , Camundongos , Microscopia de Força Atômica/métodos , Ligação Proteica , Desnaturação Proteica , Dobramento de Proteína , Isoformas de Proteínas , Proteínas Recombinantes/química , Proteína Amiloide A Sérica/metabolismo , Espectrofotometria Ultravioleta/métodos
9.
Proc Natl Acad Sci U S A ; 108(6): 2210-5, 2011 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-21257910

RESUMO

Protein aggregation is a hallmark of many diseases, including amyotrophic lateral sclerosis (ALS), where aggregation of Cu/Zn superoxide dismutase (SOD1) is implicated in causing neurodegeneration. Recent studies have suggested that destabilization and aggregation of the most immature form of SOD1, the disulfide-reduced, unmetallated (apo) protein is particularly important in causing ALS. We report herein in depth analyses of the effects of chemically and structurally diverse ALS-associated mutations on the stability and aggregation of reduced apo SOD1. In contrast with previous studies, we find that various reduced apo SOD1 mutants undergo highly reversible thermal denaturation with little aggregation, enabling quantitative thermodynamic stability analyses. In the absence of ALS-associated mutations, reduced apo SOD1 is marginally stable but predominantly folded. Mutations generally result in slight decreases to substantial increases in the fraction of unfolded protein. Calorimetry, ultracentrifugation, and light scattering show that all mutations enhance aggregation propensity, with the effects varying widely, from subtle increases in most cases, to pronounced formation of 40-100 nm soluble aggregates by A4V, a mutation that is associated with particularly short disease duration. Interestingly, although there is a correlation between observed aggregation and stability, there is minimal to no correlation between observed aggregation, predicted aggregation propensity, and disease characteristics. These findings suggest that reduced apo SOD1 does not play a dominant role in modulating disease. Rather, additional and/or multiple forms of SOD1 and additional biophysical and biological factors are needed to account for the toxicity of mutant SOD1 in ALS.


Assuntos
Esclerose Lateral Amiotrófica/enzimologia , Mutação , Dobramento de Proteína , Superóxido Dismutase/química , Esclerose Lateral Amiotrófica/genética , Estabilidade Enzimática/genética , Temperatura Alta , Humanos , Desnaturação Proteica , Superóxido Dismutase/genética , Superóxido Dismutase/metabolismo , Superóxido Dismutase-1
10.
Biochemistry ; 52(36): 6275-85, 2013 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-23952613

RESUMO

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.


Assuntos
Dependovirus/metabolismo , Glicosaminoglicanos/metabolismo , Heparina/metabolismo , Animais , Heparina/análogos & derivados , Microscopia de Força Atômica , Ressonância de Plasmônio de Superfície , Suínos
11.
Mol Cell Proteomics ; 10(9): M110.006718, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21606484

RESUMO

There is growing evidence supporting the need for a broad scale investigation of the proteins and protein modifications in the organic matrix of bone and the use of these measures to predict fragility fractures. However, limitations in sample availability and high heterogeneity of bone tissue cause unique experimental and/or diagnostic problems. We addressed these by an innovative combination of laser capture microscopy with our newly developed liquid chromatography separation methods, followed by gel electrophoresis and mass spectrometry analysis. Our strategy allows in-depth analysis of very limited amounts of bone material, and thus, can be important to medical sciences, biology, forensic, anthropology, and archaeology. The developed strategy permitted unprecedented biochemical analyses of bone-matrix proteins, including collagen modifications, using nearly nanoscale amounts of exceptionally homogenous bone tissue. Dissection of fully mineralized bone-tissue at such degree of homogeneity has not been achieved before. Application of our strategy established that: (1) collagen in older interstitial bone contains higher levels of an advanced glycation end product pentosidine then younger osteonal tissue, an observation contrary to the published data; (2) the levels of two enzymatic crosslinks (pyridinoline and deoxypiridinoline) were higher in osteonal than interstitial tissue and agreed with data reported by others; (3) younger osteonal bone has higher amount of osteopontin and osteocalcin then older interstitial bone and this has not been shown before. Taken together, these data show that the level of fluorescent crosslinks in collagen and the amount of two major noncollagenous bone matrix proteins differ at the level of osteonal and interstitial tissue. We propose that this may have important implications for bone remodeling processes and bone microdamage formation.


Assuntos
Arginina/análogos & derivados , Matriz Óssea/metabolismo , Cromatografia Líquida/métodos , Dissecação/métodos , Ósteon/metabolismo , Lisina/análogos & derivados , Microscopia Confocal/métodos , Osteopontina/análise , Proteômica/métodos , Fatores Etários , Aminoácidos/análise , Aminoácidos/química , Antropologia/métodos , Arginina/análise , Arginina/química , Matriz Óssea/química , Remodelação Óssea , Calcificação Fisiológica , Colágeno/química , Colágeno/metabolismo , Ciências Forenses/métodos , Ósteon/química , Humanos , Lisina/análise , Lisina/química , Espectrometria de Massas , Nanopartículas , Osteocalcina/química , Osteocalcina/metabolismo , Osteopontina/química
12.
J Cardiovasc Transl Res ; 16(3): 698-714, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36271180

RESUMO

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.


Assuntos
Insuficiência Cardíaca , Humanos , Volume Sistólico , Agregados Proteicos
13.
Biochemistry ; 51(1): 100-7, 2012 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-22106876

RESUMO

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.


Assuntos
Eletroforese em Gel de Poliacrilamida/métodos , Estabilidade Proteica/efeitos dos fármacos , Dodecilsulfato de Sódio , Termodinâmica , Animais , Proteínas de Bactérias/química , Bromelaínas/química , Catalase/química , Bovinos , Celulases/química , Dicroísmo Circular , Proteínas Fúngicas/química , Glucose Oxidase/química , Humanos , Proteínas de Plantas/química , Pré-Albumina/química , Desnaturação Proteica , Desdobramento de Proteína/efeitos dos fármacos , Detecção de Spin/métodos , Estreptavidina/química , Fatores de Tempo , Inibidores da Tripsina/química
14.
Biochemistry ; 51(14): 3092-9, 2012 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-22448726

RESUMO

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.


Assuntos
Amiloide/química , Dobramento de Proteína , Proteína Amiloide A Sérica/química , Amiloide/metabolismo , Animais , Cinética , Camundongos , Microscopia de Força Atômica , Peso Molecular , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteína Amiloide A Sérica/genética , Proteína Amiloide A Sérica/metabolismo
15.
Proteins ; 80(3): 920-34, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22189917

RESUMO

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.


Assuntos
Dissulfetos/química , Desdobramento de Proteína , Proteínas/química , Software , Bacillus/enzimologia , Bacillus/genética , Proteínas de Bactérias , Bacteriófago T4/enzimologia , Bacteriófago T4/genética , Entropia , Escherichia coli/enzimologia , Escherichia coli/genética , Cinética , Modelos Moleculares , Muramidase/química , Muramidase/genética , Mutação , Conformação Proteica , Estabilidade Proteica , Proteínas/genética , Ribonucleases/química , Ribonucleases/genética , Tetra-Hidrofolato Desidrogenase/química , Tetra-Hidrofolato Desidrogenase/genética
16.
Biochemistry ; 50(43): 9184-91, 2011 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-21942925

RESUMO

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.


Assuntos
Amiloide/metabolismo , Proteína Amiloide A Sérica/metabolismo , Amiloide/química , Amiloide/ultraestrutura , Amiloidose/metabolismo , Animais , Benzotiazóis , Eletroforese em Gel de Poliacrilamida , Camundongos , Ligação Proteica , Estabilidade Proteica , Estrutura Secundária de Proteína , Proteína Amiloide A Sérica/química , Temperatura , Tiazóis/metabolismo
17.
Biochem Biophys Res Commun ; 407(4): 725-9, 2011 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-21439938

RESUMO

Serum amyloid A (SAA) is an inflammatory protein predominantly bound to high-density lipoprotein in plasma and presumed to play various biological and pathological roles. We previously found that the murine isoform SAA2.2 exists in aqueous solution as a marginally stable hexamer at 4-20°C, but becomes an intrinsically disordered protein at 37°C. Here we show that when urea-denatured SAA2.2 is dialyzed into buffer (pH 8.0, 4°C), it refolds mostly into an octameric species. The octamer transitions to the hexameric structure upon incubation from days to weeks at 4°C, depending on the SAA2.2 concentration. Thermal denaturation of the octamer and hexamer monitored by circular dichroism showed that the octamer is ∼10°C less stable, with a denaturation mid point of ∼22°C. Thus, SAA2.2 becomes kinetically trapped by refolding into a less stable, but more kinetically accessible octameric species. The ability of SAA2.2 to form different oligomeric species in vitro along with its marginal stability, suggest that the structure of SAA might be modulated in vivo to form different biologically relevant species.


Assuntos
Proteína Amiloide A Sérica/química , Animais , Isoenzimas/química , Camundongos , Desnaturação Proteica , Dobramento de Proteína , Multimerização Proteica , Ureia/química
18.
Biochemistry ; 49(34): 7239-41, 2010 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-20677776

RESUMO

Upon folding, some proteins become conformationally trapped, presumably to protect against aggregation or premature degradation. To probe the occurrence of this property, known as kinetic stability, we used a diagonal two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis method to probe biologically diverse organisms. The results show that kinetic stability is prevalent in prokaryotes, especially thermophiles, but uncommon in eukaryotic organisms, thereby suggesting that this property might be crucial for the adaptation and survival of less complex prokaryotic organisms.


Assuntos
Proteínas/química , Proteínas/isolamento & purificação , Eletroforese em Gel de Poliacrilamida/métodos , Eucariotos , Células Procarióticas , Proteínas/genética
19.
Small ; 5(4): 470-6, 2009 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19189325

RESUMO

The structure, thermodynamic and kinetic stability, and activity of cytochrome c (cyt c) on silica nanoparticles (SNPs) of different sizes have been studied. Adsorption of cyt c onto larger SNPs results in both greater disruption of the cyt c global structure and more significant changes of the local heme microenvironment than upon adsorption onto smaller SNPs. The disruption of the heme microenvironment leads to a more solvent-accessible protein active site, as suggested by Soret circular dichroism spectroscopy and through an increase in peroxidase activity as a function of increased SNP size. Similarly, the stability of cyt c decreases more dramatically upon adsorption onto larger SNPs. These results are consistent with changes in protein-nanoparticle interactions that depend on the size or surface curvature of the supporting nanostructure. This study provides further fundamental insights into the effects of nanoscale surfaces on adsorbed protein structure and function.


Assuntos
Citocromos c/química , Nanopartículas , Dióxido de Silício , Adsorção , Estabilidade Enzimática , Tamanho da Partícula , Conformação Proteica
20.
Biochim Biophys Acta ; 1774(1): 78-85, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17118726

RESUMO

Factor for inversion stimulation (FIS) is a 98-residue homodimeric DNA-binding protein involved in several different cellular processes including DNA inversion and the regulation of multiple genes. FIS contains a flexible and functionally important N-terminus followed by four helices (A-D), the last two of which consist of the DNA-binding region. Helix B, which comprises the main dimerization interface has a 20 degrees kink at its center that was originally thought to be caused by the presence of a proline at position 61. However, it was later shown that the kink remained largely intact and that FIS retained its native-like function when the proline was mutated to an alanine. We previously showed that the P61A mutation increased the stability of FIS, but decreased its equilibrium denaturation cooperativity apparently due to preferential stabilization of the B-helix. Here we studied a peptide of P61A FIS, corresponding to residues 26-71 (26-71(A3) FIS), which encompasses the dimer interface (helices A and B). Circular dichroism (CD) and size-exclusion chromatography/multi-angle light scattering showed that the peptide was alpha-helical and dimeric, respectively, as expected based on the 3D structure of FIS. Urea-induced equilibrium denaturation experiments monitored by far-UV CD revealed a concentration-dependent transition, and data analysis based on a N2<-->2U model yielded a DeltaG of approximately -10 kcal/mol. Our results suggest that 26-71(A3) FIS can form a stable dimeric structure despite lacking the N- and C-terminus of native FIS.


Assuntos
Fator Proteico para Inversão de Estimulação/química , Fator Proteico para Inversão de Estimulação/genética , Fragmentos de Peptídeos/química , Sequência de Aminoácidos , Substituição de Aminoácidos , Dicroísmo Circular , Dimerização , Modelos Moleculares , Dados de Sequência Molecular , Desnaturação Proteica , Estrutura Secundária de Proteína
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA