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1.
Phys Chem Chem Phys ; 21(41): 22679-22694, 2019 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-31595905

RESUMO

Peptide misfolding and aberrant assembly in membranous micro-environments have been associated with numerous neurodegenerative diseases. The biomolecular mechanisms and biophysical implications of these amyloid membrane interactions have been under extensive research and can assist in understanding disease pathogenesis and potential development of rational therapeutics. But, the complex nature and diversity of biomolecular interactions, structural transitions, and dependence on local environmental conditions have made accurate microscopic characterization challenging. In this review, using cases of Alzheimer's disease (amyloid-beta peptide), Parkinson's disease (alpha-synuclein peptide) and Huntington's disease (huntingtin protein), we illustrate existing challenges in experimental investigations and summarize recent relevant numerical simulation studies into amyloidogenic peptide-membrane interactions. In addition we project directions for future in silico studies and discuss shortcomings of current computational approaches.


Assuntos
Biologia Computacional , Lipídeos/química , Doenças Neurodegenerativas , Dobramento de Proteína , Proteínas Amiloidogênicas/metabolismo , Membrana Celular/metabolismo , Simulação por Computador , Humanos , Metabolismo dos Lipídeos , Doenças Neurodegenerativas/fisiopatologia , Peptídeos/metabolismo
2.
Phys Chem Chem Phys ; 21(41): 23162-23168, 2019 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-31612180

RESUMO

Here we present a theoretical-computational study of the thermodynamics and kinetics of an aqueous Trp-cage, a 20-residue long miniprotein. The combined use of accurate molecular dynamics simulations rigorously reconstructing the proper isobar of the system and a sound statistical-mechanical model provides a quantitative description of the temperature dependence of the relevant physical-chemical properties and insights into the detailed mechanisms regulating the folding-unfolding properties.


Assuntos
Modelos Teóricos , Peptídeos/química , Dobramento de Proteína , Temperatura Ambiente , Termodinâmica , Cinética , Simulação de Dinâmica Molecular
3.
J Chem Phys ; 151(10): 104309, 2019 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-31521069

RESUMO

Specific folded structures of peptides and proteins depend on the sequence of various amino acid residues as well as different types of noncovalent interactions induced by the backbone as well as side-chains of those residues. In general, secondary structures of peptides and proteins are stabilized by C6 (δ-turn), C7 (γ-turn), C10 (ß-turn), C13 (α-turn), and C15 (π-turn) hydrogen-bonded rings formed through inter-residue interactions. However, it has been reported recently that an intraresidue C5 hydrogen-bond, which is relatively weak in strength, can contribute significantly to the stability of peptides and proteins. The C5 hydrogen-bond is mostly present in the ß-sheet structures of peptides and proteins along with other inter-residue noncovalent interactions. In this work, we have studied structures and conformational preferences of a dipeptide Z-Gly-Pro-OH (Z = benzyloxycarbonyl) using mass-selected vibrationally resolved electronic spectroscopy and IR-UV double resonance spectroscopy coupled with quantum chemistry calculations. Two conformers of the peptide are observed in the experiment. One of the conformers has an extended ß-strand type structure stabilized by C5 hydrogen-bonding, while the other one is folded through O-H ⋯ π interaction. The noncovalent interactions present in the two observed structures of the peptide are validated by natural bond orbital and noncovalent interaction calculations.


Assuntos
Dipeptídeos/química , Peptídeos/química , Ligações de Hidrogênio , Dobramento de Proteína , Estrutura Secundária de Proteína
4.
J Phys Chem Lett ; 10(19): 5815-5822, 2019 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-31525988

RESUMO

The topological knot is thought to play a stabilizing role in maintaining the global fold and nature of proteins with the underlying mechanism yet to be elucidated. Given that most proteins containing trefoil knots exist and function as homodimers with a large part of the dimer interface occupied by the knotted region, we reason that the knotted conformation cooperates with dimerization in protein stabilization. Here, we take YbeA from Escherichia coli as the knotted protein model, using molecular dynamics (MD) simulations to compare the stability of two pairs of dimeric proteins having the same sequence and secondary structures but differing in the presence or absence of a trefoil knot in each subunit. The dimer interface of YbeA is identified to involve favorable contacts among three α-helices (α1, α3, and α5), one of which (α5) is threaded through a loop connected with α3 to form the knot. Upon removal of the knot by appropriate change of the knot-making crossing of the polypeptide chain, relevant domains are less constrained and exhibit enhanced fluctuations to decrease contacts at the interface. Unknotted subunits are less compact and undergo structural changes to ease the dimer separation. Such a stabilizing effect is evidenced by steered MD simulations, showing that the mechanical force required for dimer separation is significantly reduced by removing the knot. In addition to the knotted conformation, dimerization further improves the protein stability by restricting the α1-α5 separation, which is defined as a leading step for protein unfolding. These results provide important insights into the structure-function relationship of dimerization in knotted proteins.


Assuntos
Simulação de Dinâmica Molecular , Multimerização Proteica , Estabilidade Proteica , Proteínas/química , Proteínas de Escherichia coli/química , Metiltransferases/química , Peptídeos/química , Conformação Proteica , Dobramento de Proteína , Termodinâmica
5.
BMC Bioinformatics ; 20(1): 455, 2019 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-31492097

RESUMO

BACKGROUND: Evolutionary information contained in the amino acid sequences of proteins specifies the biological function and fold, but exactly what information contained in the protein sequence drives both of these processes? Considerable progress has been made to answer this fundamental question, but it remains challenging to explore the potential space of cooperative interactions between amino acids. Statistical analysis plays a significant role in studying such interactions and its use has expanded in recent years to studies ranging from coevolution-guided rational protein design to protein folding in silico. RESULTS: Here we describe a computational tool named Sibe for use in studies of protein sequence, folding, and design using evolutionary coupling between amino acids as a driving factor. In this study, Sibe is used to identify positionally conserved couplings between pairwise amino acids and aid rational protein design. In this process, pairwise couplings are filtered according to the relative entropy computed from the positional conservations and grouped into several 'blocks', which could contribute to driving protein folding and design. A human ß2-adrenergic receptor (ß2AR) was used to demonstrate that those 'blocks' contribute the rational design for specifying functional residues. Sibe also provides folding modules based on both the positionally conserved couplings and well-established statistical potentials for simulating protein folding in silico and predicting tertiary structure. Our results show that statistically inferences of basic evolutionary principles, such as conservations and coupled-mutations, can be used to rapidly design a diverse set of proteins and study protein folding. CONCLUSIONS: The developed software Sibe provides a computational tool for systematical analysis from protein primary to its tertiary structure using the evolutionary couplings as a driving factor. Sibe, written in C++, accounts for compatibility with the 'big data' era in biological science, and it primarily focuses on protein sequence analysis, but it is also applicable to extend to other modeling and predictions of experimental measurements.


Assuntos
Biologia Computacional/métodos , Simulação por Computador , Engenharia de Proteínas , Dobramento de Proteína , Proteínas/química , Proteínas/genética , Sequência de Aminoácidos , Entropia , Humanos , Mutação , Receptores Adrenérgicos beta 2/química , Receptores Adrenérgicos beta 2/genética , Análise de Sequência , Software
6.
Phys Chem Chem Phys ; 21(32): 17950-17958, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31384849

RESUMO

The A. aeolicus intrinsically disordered protein FlgM has four well-defined α-helices when bound to σ28, but in water FlgM undergoes a change in tertiary structure. In this work, we investigate the structure of FlgM in aqueous solutions of the ionic liquid [C4mpy][Tf2N]. We find that FlgM is induced to fold by the addition of the ionic liquid, achieving average α-helicity values similar to the bound state. Analysis of secondary structure reveals significant similarity with the bound state, but the tertiary structure is found to be more compact. Interestingly, the ionic liquid is not homogeneously dispersed in the water, but instead aggregates near the protein. Separate simulations of aqueous ionic liquid do not show ion clustering, which suggests that FlgM stabilizes ionic liquid aggregation.


Assuntos
Proteínas de Bactérias/química , Imidas/química , Proteínas Intrinsicamente Desordenadas/química , Líquidos Iônicos/química , Modelos Moleculares , Pirrolidinas/química , Bases de Dados de Proteínas , Conformação Proteica em alfa-Hélice , Dobramento de Proteína , Termodinâmica , Água
7.
BMC Evol Biol ; 19(1): 158, 2019 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-31362700

RESUMO

BACKGROUND: There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding. RESULTS: Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure to assess how well the prebiotic amino acid set preserves fold information against all other possible ten-amino acid sets. An extensive virtual mutagenesis procedure revealed that the prebiotic set excellently preserves sequence-dependent information regarding both backbone conformation and tertiary contact matrix of proteins. We observed that information retention is fold-class dependent: the prebiotic set sufficiently encodes the structure space of α/ß and α + ß folds, and to a lesser extent, of all-α and all-ß folds. The prebiotic set appeared insufficient to encode the small proteins. Assessing how well the prebiotic set discriminates native vs. incorrect sequence-structure matches, we found that α/ß and α + ß folds exhibit more pronounced energy gaps with the prebiotic set than with nearly all alternatives. CONCLUSIONS: The prebiotic set optimally encodes local backbone structures that appear in the folded environment and near-optimally encodes the tertiary contact matrix of extant proteins. The fold-class-specific patterns observed from our structural analysis confirm the postulated timeline of fold appearance in proteogenesis derived from proteomic sequence analyses. Polypeptides arising in a prebiotic environment will likely form α/ß and α + ß-like folds if any at all. We infer that the progressive expansion of the alphabet allowed the increased conformational stability and functional specificity of later folds, including all-α, all-ß, and small proteins. Our results suggest that prebiotic sequences are amenable to mutations that significantly lower native conformational energies and increase discrimination amidst incorrect folds. This property may have assisted the genesis of functional proto-enzymes prior to the expansion of the full amino acid alphabet.


Assuntos
Aminoácidos/metabolismo , Origem da Vida , Proteínas/química , Sequência de Aminoácidos , Método de Monte Carlo , Mutagênese/genética , Conformação Proteica , Domínios Proteicos , Dobramento de Proteína , Proteínas/genética
8.
Phys Chem Chem Phys ; 21(33): 18219-18226, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31389931

RESUMO

The villin headpiece subdomain (HP35) is a fast-folding protein with 35 residues and its folding pathways have been extensively studied experimentally and theoretically but remain controversial. While experiments showed that HP35 might have multiple folding pathways, most theoretical studies only found one major pathway, although a few theoretical studies revealed two. Here we report our results of molecular dynamics simulations of HP35 folding by using the newest AMBER ff14SB force field and show that HP35 has a novel folding pathway in addition to the two pathways shown previously. We also study the mechanism of determining the folding pathways and found that the dynamics of Helix2 may play a special role in the folding of HP35. Our results may be helpful to understand the folding mechanism of HP35 further.


Assuntos
Proteínas dos Microfilamentos/química , Simulação de Dinâmica Molecular , Peptídeos/química , Dobramento de Proteína , Domínios Proteicos , Termodinâmica
9.
Chem Commun (Camb) ; 55(70): 10392-10395, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31407730

RESUMO

The preference of N,N-aryl, alkyl tertiary amides for cis conformations has been exploited through the use of tertiary squaramides as hairpin turn units that promote the folding of aromatic ß-sheets. Head-to-head aromatic arrangements were shown to prevail in sufficiently long bent aromatic sequences.


Assuntos
Dobramento de Proteína , Proteínas/química , Quinina/análogos & derivados , Cristalografia por Raios X , Conformação Proteica em Folha beta , Quinina/química
10.
Yakugaku Zasshi ; 139(7): 1015-1019, 2019.
Artigo em Japonês | MEDLINE | ID: mdl-31257248

RESUMO

Amyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease that is characterized by the loss of motor neurons, which results in progressive muscle atrophy. The pathology spreads from the initial site of onset to contiguous anatomic regions. Mutations in the gene encoding Cu/Zn-superoxide dismutase (SOD1) have been identified in a dominantly inherited form of ALS (ALS-SOD1). A major hallmark of ALS-SOD1 is the abnormal accumulation of conformationally aberrant SOD1 protein (i.e., misfolded SOD1) within motor neurons. Emerging experimental evidence has suggested that misfolded proteins associated with neurodegenerative diseases exhibit prion-like properties, i.e., misfolded proteins act as conformational templates that convert normal proteins into a pathogenic form. Possibly as a result of this prion-like self-propagation property, misfolded forms of pathological proteins are considered to accumulate in the central nervous system and cause neurodegeneration. In this article, we review recent evidence for the role of prion-like mechanisms in ALS-SOD1. In particular, we discuss the propensity of misfolded SOD1 to act as a pathological seed, spread between cells, and propagate neuroanatomically.


Assuntos
Esclerose Amiotrófica Lateral/genética , Superóxido Dismutase-1/genética , Humanos , Neurônios Motores/metabolismo , Mutação , Príons , Agregação Patológica de Proteínas , Dobramento de Proteína , Superóxido Dismutase-1/metabolismo
11.
Yakugaku Zasshi ; 139(7): 999-1005, 2019.
Artigo em Japonês | MEDLINE | ID: mdl-31257259

RESUMO

Pathological α-synuclein (αSyn) has been shown to retain the ability to propagate as prions in humans and animals. However, the molecular basis underlying the prion-like properties of αSyn remains poorly understood. We examined whether brain tissues from cases of dementia with Lewy bodies (DLB), which contain serine 129 (Ser129)-phosphorylated insoluble aggregates of αSyn, exhibit prion-like seeding activity in vitro using the real-time quaking-induced conversion (RT-QuIC) seeding assay. Brain tissues from cases of diffuse neocortical DLB yielded a 50% seeding dose of 107.3-109.8/g brain. The RT-QuIC assay could discriminate between DLB and other neurological and neurodegenerative disorders, suggesting its potential applicability for differential diagnosis. Insoluble aggregates of αSyn>250 kDa detected only in DLB brain tissues by Western blotting analysis were specifically phosphorylated at Ser129. Therefore, we postulated that Ser129-phosphorylated insoluble aggregates of αSyn have prion-like seeding activity. However, insoluble aggregates of recombinant human αSyn (rSyn) with increased ß-sheet structures showed little seeding activity in either the phosphorylated or nonphosphorylated state. In contrast, prefibrillar oligomers of rSyn showed seeding activity both with and without phosphorylation. The findings of the present study suggested that soluble oligomeric αSyn, but not the fully fibrillary form, is a seeding species in vitro.


Assuntos
Encéfalo/metabolismo , Agregação Patológica de Proteínas , alfa-Sinucleína/metabolismo , Humanos , Técnicas In Vitro , Doença por Corpos de Lewy/genética , Doença por Corpos de Lewy/metabolismo , Príons/metabolismo , Dobramento de Proteína
12.
J Sci Food Agric ; 99(14): 6500-6508, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31321768

RESUMO

BACKGROUND: Emulsification is important for food quality and processing functionality. Most emulsification occurs under high-fat conditions that eventually cause health concerns. Protein emulsifiers also have drawbacks such as lower dispersity. This study considered the effects of different high-speed shear homogenization (HSH) speeds on the emulsifying and structural properties of myofibrillar proteins (MPs) under low-fat conditions. RESULTS: High-speed shear homogenization significantly increased the emulsifying activity and emulsifying stability of MPs at lower speeds (8000 to 14 500 rpm). The primary structure of MP was not altered significantly by HSH, whereas its secondary, tertiary, and quaternary structures were changed. Particle size decreased first and then increased significantly, and reached a minimum when the HSH speed was 14 500 rpm. The absolute zeta potential values increased significantly and the dendritic fibrous structure of sample was destroyed when the speed exceeded 14 500 rpm. High-speed shear homogenization (14 500 rpm) decreased the particle size and unfolded the protein, which improved the emulsifying properties of MPs. Excessive HSH speeds (20 500 rpm or higher) caused an aggregation of MP molecules, which was not conducive to improving their emulsifying properties. CONCLUSION: Optimal HSH speed was achieved at 14 500 rpm to modify MPs' emulsifying and structural properties under low-fatconditions. © 2019 Society of Chemical Industry.


Assuntos
Gorduras/análise , Manipulação de Alimentos/métodos , Proteínas Musculares/química , Animais , Galinhas , Emulsões/química , Emulsões/isolamento & purificação , Manipulação de Alimentos/instrumentação , Carne/análise , Proteínas Musculares/isolamento & purificação , Tamanho da Partícula , Pressão , Dobramento de Proteína
13.
Phys Chem Chem Phys ; 21(29): 16198-16206, 2019 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-31298234

RESUMO

The secondary structure of proteins is of prime importance to their proper functioning and protein misfolding may cause serious disorders in the human body. Here, the electric field influence on the conformational stability of model alpha helical peptides is studied by employing density functional theory calculations combined with continuum dielectric method computations. Our results show that the basic parameters of the electric field - its strength and directionality - are determinative for the alpha helix stability. An electric field strength of 0.005 a.u. (2.5 V nm-1) applied along the X coordinate axis (the long axis of the helix) in the direction of the µx component of the molecular dipole moment does affect the peptide conformation, destroys the helix, and leads to the formation of a cyclic-peptide-like structure. Interestingly, the process of denaturation can be reversible when the electric field is switched-off. The reversibility of the process of the electric field induced disruption of the peptide secondary structure suggests a possible mechanism for the healing of misfolded proteins.


Assuntos
Fenômenos Eletromagnéticos , Modelos Químicos , Peptídeos/química , Peptídeos/efeitos da radiação , Conformação Proteica em alfa-Hélice , Dobramento de Proteína/efeitos da radiação
14.
BMC Bioinformatics ; 20(1): 299, 2019 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-31159742

RESUMO

BACKGROUND: The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as decoy discrimination. However, these two aspects are found to be mutually exclusive in many statistical potentials. RESULTS: We developed an atomic ANgle- and DIStance-dependent (ANDIS) statistical potential for protein structure quality assessment with distance cutoff being a tunable parameter. When distance cutoff is ≤9.0 Å, "effective atomic interaction" is employed to enhance the ability of native recognition. For a distance cutoff of ≥10 Å, the distance-dependent atom-pair potential with random-walk reference state is combined to strengthen the ability of decoy discrimination. Benchmark tests on 632 structural decoy sets from diverse sources demonstrate that ANDIS outperforms other state-of-the-art potentials in both native recognition and decoy discrimination. CONCLUSIONS: Distance cutoff is a crucial parameter for distance-dependent statistical potentials. A lower distance cutoff is better for native recognition, while a higher one is favorable for decoy discrimination. The ANDIS potential is freely available as a standalone application at http://qbp.hzau.edu.cn/ANDIS/ .


Assuntos
Biologia Computacional/métodos , Proteínas/química , Software , Estatística como Assunto , Bases de Dados de Proteínas , Conformação Proteica , Dobramento de Proteína
15.
Phys Chem Chem Phys ; 21(24): 12806-12817, 2019 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-31165827

RESUMO

We present a study of the combined effects of natural cosolvents (TMAO, glycine, urea) and pressure on the activity of the tetrameric enzyme lactate dehydrogenase (LDH). To this end, high-pressure stopped-flow methodology in concert with fast UV/Vis spectroscopic detection of product formation was applied. To reveal possible pressure effects on the stability and dynamics of the enzyme, FTIR spectroscopic and neutron scattering measurements were carried out. In neat buffer solution, the catalytic turnover number of the enzyme, kcat, increases up to 1000 bar, the pressure range where dissociation of the tetrameric species to dimers sets in. Accordingly, we obtain a negative activation volume, ΔV# = -45.3 mL mol-1. Further, the enzyme substrate complex has a larger volume compared to the enzyme and substrate in the unbound state. The neutron scattering data show that changes in the fast internal dynamics of the enzyme are not responsible for the increase of kcat upon compression. Whereas the magnitude of kcat is similar in the presence of the osmolytes, the pressure of deactivation is modulated by the addition of cosolvents. TMAO and glycine increase the pressure of deactivation, and in accordance with the observed stabilizing effect both cosolvents exhibit against denaturation and/or dissociation of proteins. While urea does not markedly affect the magnitude of the Michaelis constant, KM, both 1 M TMAO and 1 M glycine exhibit smaller KM values of about 0.07 mM and 0.05 mM below about 1 kbar. Such positive effect on the substrate affinity could be rationalized by the effect the two cosolutes impose on the thermodynamic activities of the reactants, which reflect changes in water-mediated intermolecular interactions. Our data show that the intracellular milieu, i.e., the solution conditions that have evolved, may be sufficient to maintain enzymatic activity under extreme environmental conditions, including the whole pressure range encountered on Earth.


Assuntos
L-Lactato Desidrogenase/química , Solventes/química , Glicina/química , Cinética , Metilaminas/química , Modelos Moleculares , Pressão , Desnaturação Proteica , Dobramento de Proteína , Multimerização Proteica , Termodinâmica , Ureia/química , Água/química
16.
Chem Commun (Camb) ; 55(51): 7366-7369, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31172994

RESUMO

The tolerance of ribosomal peptide translation for helical aromatic oligoamide foldamers appended as initiators has been investigated. Small cationic foldamer side-chains were shown to expand the range of foldamer-peptide hybrids that can be produced by the ribosome to more rigid sequences.


Assuntos
Amidas/química , Peptídeos/química , Ribossomos/metabolismo , Aminoácidos/química , Modelos Moleculares , Conformação Molecular , Fatores de Alongamento de Peptídeos/química , Biossíntese de Proteínas , Dobramento de Proteína , Ribossomos/química
17.
Nat Commun ; 10(1): 2865, 2019 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-31253771

RESUMO

The mechanistic target of rapamycin (mTOR) kinase forms two multi-protein signaling complexes, mTORC1 and mTORC2, which are master regulators of cell growth, metabolism, survival and autophagy. Two of the subunits of these complexes are mLST8 and Raptor, ß-propeller proteins that stabilize the mTOR kinase and recruit substrates, respectively. Here we report that the eukaryotic chaperonin CCT plays a key role in mTORC assembly and signaling by folding both mLST8 and Raptor. A high resolution (4.0 Å) cryo-EM structure of the human mLST8-CCT intermediate isolated directly from cells shows mLST8 in a near-native state bound to CCT deep within the folding chamber between the two CCT rings, and interacting mainly with the disordered N- and C-termini of specific CCT subunits of both rings. These findings describe a unique function of CCT in mTORC assembly and a distinct binding site in CCT for mLST8, far from those found for similar ß-propeller proteins.


Assuntos
Chaperonina com TCP-1/fisiologia , Homólogo LST8 da Proteína Associada a MTOR/metabolismo , Proteína Regulatória Associada a mTOR/metabolismo , Serina-Treonina Quinases TOR/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Microscopia Crioeletrônica , Regulação da Expressão Gênica/fisiologia , Técnicas de Silenciamento de Genes , Células HEK293 , Células Hep G2 , Humanos , Homólogo LST8 da Proteína Associada a MTOR/genética , Espectrometria de Massas , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Dobramento de Proteína , Proteína Regulatória Associada a mTOR/genética , Serina-Treonina Quinases TOR/genética
18.
Nat Commun ; 10(1): 2472, 2019 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-31171781

RESUMO

The evolution of microbial and viral organisms often generates clonal interference, a mode of competition between genetic clades within a population. Here we show how interference impacts systems biology by constraining genetic and phenotypic complexity. Our analysis uses biophysically grounded evolutionary models for molecular phenotypes, such as fold stability and enzymatic activity of genes. We find a generic mode of phenotypic interference that couples the function of individual genes and the population's global evolutionary dynamics. Biological implications of phenotypic interference include rapid collateral system degradation in adaptation experiments and long-term selection against genome complexity: each additional gene carries a cost proportional to the total number of genes. Recombination above a threshold rate can eliminate this cost, which establishes a universal, biophysically grounded scenario for the evolution of sex. In a broader context, our analysis suggests that the systems biology of microbes is strongly intertwined with their mode of evolution.


Assuntos
Bactérias/genética , Evolução Biológica , Dobramento de Proteína , Estabilidade Proteica , Vírus/genética , Bactérias/metabolismo , Evolução Molecular , Aptidão Genética , Fenótipo , Recombinação Genética , Seleção Genética , Biologia de Sistemas , Vírus/metabolismo
19.
Nat Methods ; 16(7): 611-614, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31235884

RESUMO

The study of the aggregation of soluble proteins into highly ordered, insoluble amyloid fibrils is fundamental for the understanding of neurodegenerative disorders. Here, we present a method for the observation of single amyloid fibrils that allows the investigation of fibril growth, secondary nucleation or fibril breakup that is typically hidden in the average ensemble. Our approach of thermophoretic trapping and rotational diffusion measurements is demonstrated for single Aß40, Aß42 and pyroglutamyl-modified amyloid-ß variant (pGlu3-Aß3-40) amyloid fibrils.


Assuntos
Amiloide/química , Agregados Proteicos , Difusão , Dobramento de Proteína
20.
Nat Commun ; 10(1): 2636, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-31201318

RESUMO

The leading cause of cystic fibrosis (CF) is the deletion of phenylalanine 508 (F508del) in the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR). The mutation affects the thermodynamic stability of the domain and the integrity of the interface between NBD1 and the transmembrane domain leading to its clearance by the quality control system. Here, we develop nanobodies targeting NBD1 of human CFTR and demonstrate their ability to stabilize both isolated NBD1 and full-length protein. Crystal structures of NBD1-nanobody complexes provide an atomic description of the epitopes and reveal the molecular basis for stabilization. Furthermore, our data uncover a conformation of CFTR, involving detachment of NBD1 from the transmembrane domain, which contrast with the compact assembly observed in cryo-EM structures. This unexpected interface rearrangement is likely to have major relevance for CF pathogenesis but also for the normal function of CFTR and other ABC proteins.


Assuntos
Regulador de Condutância Transmembrana em Fibrose Cística/genética , Fibrose Cística/genética , Modelos Moleculares , Cristalografia por Raios X , Regulador de Condutância Transmembrana em Fibrose Cística/isolamento & purificação , Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Humanos , Dobramento de Proteína , Domínios e Motivos de Interação entre Proteínas/genética , Estabilidade Proteica , Estrutura Terciária de Proteína/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Deleção de Sequência , Anticorpos de Domínio Único/metabolismo
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