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1.
Cell ; 152(3): 519-31, 2013 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-23374347

RESUMO

In stressed cells, apoptosis ensues when Bcl-2 family members Bax or Bak oligomerize and permeabilize the mitochondrial outer membrane. Certain BH3-only relatives can directly activate them to mediate this pivotal, poorly understood step. To clarify the conformational changes that induce Bax oligomerization, we determined crystal structures of BaxΔC21 treated with detergents and BH3 peptides. The peptides bound the Bax canonical surface groove but, unlike their complexes with prosurvival relatives, dissociated Bax into two domains. The structures define the sequence signature of activator BH3 domains and reveal how they can activate Bax via its groove by favoring release of its BH3 domain. Furthermore, Bax helices α2-α5 alone adopted a symmetric homodimer structure, supporting the proposal that two Bax molecules insert their BH3 domain into each other's surface groove to nucleate oligomerization. A planar lipophilic surface on this homodimer may engage the membrane. Our results thus define critical Bax transitions toward apoptosis.


Assuntos
Apoptose , Cristalografia por Raios X , Proteína X Associada a bcl-2/química , Sequência de Aminoácidos , Animais , Citocromos c/metabolismo , Dimerização , Embrião de Mamíferos/metabolismo , Interações Hidrofóbicas e Hidrofílicas , Lipossomos/metabolismo , Fígado/metabolismo , Camundongos , Mitocôndrias/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Estrutura Terciária de Proteína , Alinhamento de Sequência , Proteína X Associada a bcl-2/metabolismo
2.
Eur Biophys J ; 51(3): 193-204, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35380220

RESUMO

Defining protein oligomeric state and/or its changes in solution is of significant interest for many biophysical studies carried out in vitro, especially when the nature of the oligomeric state is crucial in the subsequent interpretation of experimental results and their biological relevance. Nuclear magnetic resonance (NMR) is a well-established methodology for the characterization of protein structure, dynamics, and interactions at the atomic level. As a spectroscopic method, NMR also provides a compelling means for probing both molecular translational and rotational motion, two predominant measures of effective molecular size in solution, under identical conditions as employed for structural, dynamic and interaction studies. Protein translational diffusion is readily measurable by pulse gradient spin echo (PGSE) NMR, whereas its rotational correlation time, or rotational diffusion tensor when its 3D structure is known, can also be quantified from NMR relaxation parameters, such as 15N relaxation parameters of backbone amides which are frequently employed for probing residue-specific protein backbone dynamics. In this article, we present an introductory overview to the NMR measurement of bimolecular translational and rotational motion for assessing changes of protein oligomeric state in aqueous solution, via translational diffusion coefficients measured by PGSE NMR and rotational correlation times derived from composite 15N relaxation parameters of backbone amides, without need for the protein structure being available.


Assuntos
Amidas , Proteínas , Difusão , Espectroscopia de Ressonância Magnética/métodos , Movimento (Física) , Ressonância Magnética Nuclear Biomolecular/métodos
3.
J Chem Phys ; 155(22): 224203, 2021 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-34911323

RESUMO

The interpretation of molecular translational diffusion as measured by pulsed gradient spin-echo NMR (PGSE NMR) can be complicated by the presence of chemical exchange and/or dipolar cross-relaxation (including relayed cross-relaxation via spin diffusion). The magnitude of influence depends on the kinetics of exchange and/or dipolar cross-relaxation present within the system as well as the PGSE NMR sequences chosen for measurements. First, we present an exchange induced zero-crossing phenomenon for signal attenuation of water in lipidic cubic phases (formed by a mixture of monoolein and water) in the presence of pulsed gradients observed using a standard STimulated Echo (STE) sequence. This magnetization exchange induced zero-crossing phenomenon, a pseudo-negative diffraction-like feature, resembles that reported previously for restricted diffusion when locally anisotropic pores are polydisperse or randomly oriented. We then demonstrate the elimination of these exchange and/or dipolar cross-relaxation induced effects with the use of a chemical shift selective STE (CHESS-STE) sequence, adapted from the previously reported band-selective short transient STE sequence, along with results obtained from the bipolar pulse pair STE sequence for comparison. The CHESS-STE sequence introduced here represents a generic form of PGSE NMR sequences for obtaining water diffusion coefficients free from the influence of exchange and/or dipolar cross-relaxation in complex systems. It has potential applications in measuring translational diffusion of water in biopolymer mixtures as well as probing the microscopic structure in materials via water restricted diffusion measured by PGSE NMR, particularly when the potential presence of exchange/cross-relaxation is of concern.

4.
Langmuir ; 36(22): 6254-6260, 2020 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-32418433

RESUMO

Lipidic inverse bicontinuous cubic phases (LCPs), formed via the spontaneous self-assembly of lipids such as monoolein, have found increasing applications in the stabilization and crystallization of integral membrane proteins for structural characterization using X-ray crystallography. Their use as effective drug release matrices has also been demonstrated. Nuclear magnetic resonance (NMR) spectroscopy, both solution and solid state, has previously been employed for the characterization of LCPs and related systems. Herein, we report a number of novel features of solution NMR for probing the fundamental composition and structural properties of monoolein-based LCPs. These include (1) more complete assignments of both 1H and 13C chemical shifts, (2) direct quantification of hydration level in LCPs using one-dimensional (1D) 1H NMR, and (3) monitoring longer-term stability of LCPs and evaluating alterations introduced into standard LCPs at the submolecular level.

5.
Biochem J ; 475(7): 1371-1383, 2018 04 16.
Artigo em Inglês | MEDLINE | ID: mdl-29535276

RESUMO

Bacterial sulfoglycolytic pathways catabolize sulfoquinovose (SQ), or glycosides thereof, to generate a three-carbon metabolite for primary cellular metabolism and a three-carbon sulfonate that is expelled from the cell. Sulfoglycolytic operons encoding an Embden-Meyerhof-Parnas-like or Entner-Doudoroff (ED)-like pathway harbor an uncharacterized gene (yihR in Escherichia coli; PpSQ1_00415 in Pseudomonas putida) that is up-regulated in the presence of SQ, has been annotated as an aldose-1-epimerase and which may encode an SQ mutarotase. Our sequence analyses and structural modeling confirmed that these proteins possess mutarotase-like active sites with conserved catalytic residues. We overexpressed the homolog from the sulfo-ED operon of Herbaspirillum seropedicaea (HsSQM) and used it to demonstrate SQ mutarotase activity for the first time. This was accomplished using nuclear magnetic resonance exchange spectroscopy, a method that allows the chemical exchange of magnetization between the two SQ anomers at equilibrium. HsSQM also catalyzed the mutarotation of various aldohexoses with an equatorial 2-hydroxy group, including d-galactose, d-glucose, d-glucose-6-phosphate (Glc-6-P), and d-glucuronic acid, but not d-mannose. HsSQM displayed only 5-fold selectivity in terms of efficiency (kcat/KM) for SQ versus the glycolysis intermediate Glc-6-P; however, its proficiency [kuncat/(kcat/KM)] for SQ was 17 000-fold better than for Glc-6-P, revealing that HsSQM preferentially stabilizes the SQ transition state.


Assuntos
Carboidratos Epimerases/metabolismo , Herbaspirillum/enzimologia , Espectroscopia de Ressonância Magnética/métodos , Metilglucosídeos/metabolismo , Sequência de Aminoácidos , Carboidratos Epimerases/química , Carboidratos Epimerases/genética , Glicólise , Cinética , Modelos Moleculares , Conformação Proteica , Homologia de Sequência
6.
Eur Biophys J ; 47(8): 891-902, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-29785510

RESUMO

Pulsed-field gradient nuclear magnetic resonance has seen an increase in applications spanning a broad range of disciplines where molecular translational diffusion properties are of interest. The current study introduces and experimentally evaluates the measurement of translational diffusion coefficients of 15N-enriched biomolecules using a 1H-15N HMQC-filtered band-selective excitation short transient (BEST) sequence as an alternative to the previously described SOFAST-XSTE sequence. The results demonstrate that accurate translational diffusion coefficients of 15N-labelled peptides and proteins can be obtained using this alternative 1H-15N HMQC-filtered BEST sequence which is implementable on NMR spectrometers equipped with probes fitted with a single-axis field gradient, including most cryoprobes dedicated to bio-NMR. The sequence is of potential use for direct quantification of protein or peptide translational diffusion within complex systems, such as in mixtures of macromolecules, crowded solutions, membrane-mimicking media and in bicontinuous cubic phases, where conventional sequences may not be readily applicable due to the presence of intense signals arising from sources other than the protein or peptide under investigation.


Assuntos
Ressonância Magnética Nuclear Biomolecular , Sequência de Aminoácidos , Difusão , Fosfopeptídeos/química , Dodecilsulfato de Sódio/química , Soluções
7.
Biochim Biophys Acta ; 1864(9): 1128-1137, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27288992

RESUMO

Beclin 1 is a 450 amino acid protein that plays critical roles in the early stages of autophagosome formation. We recently reported the successful expression, purification and structural characterisation of the entire N-terminal region of Beclin 1 (residues 1-150), including its backbone NMR chemical shift assignments. Based on assigned backbone NMR chemical shifts, it has been established that the N-terminal region of Beclin 1 (1-150), including the BH3 domain (112-123), is intrinsically disordered in the absence of its interaction partners. Here, a detailed study of its conformational preference and backbone dynamics obtained from an analysis of its secondary structure populations using the δ2D method, and the measurements of effective hydrodynamic radius as well as (1)H temperature coefficients, (1)H solvent exchange rates, and (15)N relaxation parameters of backbone amides using NMR spectroscopy is reported. These data provide further evidence for the intrinsically disordered nature of the N-terminal region of Beclin 1 and support the view that the helical conformation adopted by the Beclin 1 BH3 domain upon interaction with binding partners such as BCL-2 pro-survival proteins is likely induced rather than pre-existing.


Assuntos
Proteína Beclina-1/química , Proteínas Intrinsicamente Desordenadas/química , Humanos , Cinética , Espectroscopia de Ressonância Magnética , Isótopos de Nitrogênio , Conformação Proteica em alfa-Hélice , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Coloração e Rotulagem/métodos , Termodinâmica
8.
Chemistry ; 23(2): 390-396, 2017 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-27862429

RESUMO

Two series of branched tetramers of the proline-rich antimicrobial peptide (PrAMP), Chex1-Arg20, were prepared to improve antibacterial selectivity and potency against a panel of Gram-negative nosocomial pathogens including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa. First, tetramerization was achieved by dithiomaleimide (DTM) conjugation of two C-terminal-cysteine bearing dimers that also incorporated C-terminal peptide chemical modification. DTM-linked tetrameric peptides containing a C-terminal hydrazide moiety on each dimer exhibited highly potent activities in the minimum inhibitory concentration (MIC) range of 0.49-2.33 µm. A second series of tetrameric analogues with C-terminal hydrazide modification was prepared by using alternative conjugation linkers including trans-1,4-dibromo-2-butene, α,α'-dibromo-p-xylene, or 6-bismaleimidohexane to determine the effect of length on activity. Each displayed potent and broadened activity against Gram-negative nosocomial pathogens, particularly the butene-linked tetrameric hydrazide. Remarkably, the greatest MIC activity is against P. aeruginosa (0.77 µm/8 µg mL-1 ) where the monomer is inactive. None of these peptides showed any cytotoxicity to mammalian cells up to 25 times the MIC. A diffusion NMR study of the tetrameric hydrazides showed that the more active antibacterial analogues were those with a more compact structure having smaller hydrodynamic radii. The results show that C-terminal PrAMP hydrazidation together with its rational tetramerization is an effective means for increasing both diversity and potency of PrAMP action.


Assuntos
Antibacterianos/química , Peptídeos Catiônicos Antimicrobianos/química , Animais , Antibacterianos/farmacologia , Antibacterianos/toxicidade , Peptídeos Catiônicos Antimicrobianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/toxicidade , Linhagem Celular , Infecção Hospitalar/microbiologia , Bactérias Gram-Negativas/efeitos dos fármacos , Humanos , Hidrocarbonetos Bromados/química , Maleimidas/química , Domínios Proteicos Ricos em Prolina , Multimerização Proteica , Ratos
9.
Biophys J ; 108(8): 1987-96, 2015 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-25902438

RESUMO

Equinatoxin II (EqtII) is a soluble, 20 kDa pore-forming protein toxin isolated from the sea anemone Actinia equina. Although pore formation has long been known to occur in distinct stages, including monomeric attachment to phospholipid membranes followed by detachment of the N-terminal helical domain and oligomerization into the final pore assembly, atomistic-level detail of the protein-lipid interactions underlying these events remains elusive. Using high-resolution solution state NMR of uniformly-(15)N-labeled EqtII at the critical micelle concentration of dodecylphosphocholine, we have mapped the lipid-binding site through chemical shift perturbations. Subsequent docking of an EqtII monomer onto a dodecylphosphocholine micelle, followed by 400 ns of all-atom molecular dynamics simulation, saw several high-occupancy lipid-binding pockets stabilized by cation-π, hydrogen bonding, and hydrophobic interactions; and stabilization of the loop housing the conserved arginine-glycine-aspartate motif. Additional simulation of EqtII with an N-acetyl sphingomyelin micelle, for which high-resolution NMR data cannot be obtained due to aggregate formation, revealed that sphingomyelin specificity might occur via hydrogen bonding to the 3-OH and 2-NH groups unique to the ceramide backbone by side chains of D109 and Y113; and main chains of P81 and W112. Furthermore, a binding pocket formed by K30, K77, and P81, proximate to the hinge region of the N-terminal helix, was identified and may be implicated in triggering pore formation.


Assuntos
Venenos de Cnidários/química , Simulação de Dinâmica Molecular , Esfingomielinas/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Sítios de Ligação , Venenos de Cnidários/metabolismo , Espectroscopia de Ressonância Magnética , Dados de Sequência Molecular , Fosforilcolina/análogos & derivados , Fosforilcolina/química , Fosforilcolina/farmacologia , Ligação Proteica , Esfingomielinas/química
10.
Arch Biochem Biophys ; 545: 33-43, 2014 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-24434006

RESUMO

Activation and oligomerisation of Bax, a key pro-apoptotic Bcl-2 family protein, are key steps in the mitochondrial pathway to apoptosis. The signals for apoptosis are conveyed by the distantly related BH3-only proteins, which use their short BH3 domain, an amphipathic α-helix, to interact with other Bcl-2 family members. Here we report an NMR study of interactions between BaxΔC and BH3 domain-containing peptides in the absence and presence of CHAPS, a zwitterionic detergent. We find for the first time that CHAPS interacts weakly with BaxΔC (fast exchange on the NMR chemical shift timescale), at concentrations below micelle formation and with an estimated Kd in the tens of mM. Direct and relatively strong-interactions (slow exchange on the NMR chemical shift timescale) were also observed for BaxΔC with BaxBH3 (estimated Kd of circa 150µM) or BimBH3 in the absence of CHAPS. The interaction with either peptide alone induced widespread chemical shift perturbations to BaxΔC in solution which implies that BaxΔC might have undergone significant conformation change upon binding the BH3 peptide. However, BaxΔC remained monomeric upon binding either CHAPS or a BH3 peptide alone, but the presence of both provoked it to form a dimer.


Assuntos
Proteínas Reguladoras de Apoptose/metabolismo , Ácidos Cólicos/metabolismo , Detergentes/metabolismo , Proteínas de Membrana/metabolismo , Fragmentos de Peptídeos/metabolismo , Proteínas Proto-Oncogênicas/metabolismo , Proteína X Associada a bcl-2/metabolismo , Apoptose , Proteínas Reguladoras de Apoptose/química , Proteína 11 Semelhante a Bcl-2 , Humanos , Proteínas de Membrana/química , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Fragmentos de Peptídeos/química , Conformação Proteica , Mapas de Interação de Proteínas , Multimerização Proteica , Proteínas Proto-Oncogênicas/química , Proteína X Associada a bcl-2/química
11.
Eur Biophys J ; 43(6-7): 331-9, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24824112

RESUMO

Molecular translational self-diffusion, a measure of diffusive motion, provides information on the effective molecular hydrodynamic radius, as well as information on the properties of media or solution through which the molecule diffuses. Protein translational diffusion measured by pulsed-field gradient nuclear magnetic resonance (PFG-NMR) has seen increased application in structure and interaction studies, as structural changes or protein-protein interactions are often accompanied by alteration of their effective hydrodynamic radii. Unlike the analysis of complex mixtures by PFG-NMR, for monitoring changes of protein translational diffusion under various conditions, such as different stages of folding/unfolding, a partial region of the spectrum or even a single resonance is sufficient. We report translational diffusion coefficients measured by PFG-NMR with a modified stimulated echo (STE) sequence where band-selective pulses are employed for all three (1)H RF pulses. Compared with conventional non-selective sequence, e.g. the BPP-LED sequence, the advantage of this modified band-selective excitation short transient (BEST) version of STE (BEST-STE) sequence is multi-fold, namely: (1) potential sensitivity gain as in generalized BEST-based sequences, (2) water suppression is no longer required as the magnetization of solvent water is not perturbed during the measurement, and (3) dynamic range problems due to the presence of intense resonances from molecules other than the protein or peptide of interest, such as non-deuterated detergent micelles, are avoided.


Assuntos
Peptídeos beta-Amiloides/química , Peptídeos beta-Amiloides/metabolismo , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/metabolismo , Proteína X Associada a bcl-2/química , Proteína X Associada a bcl-2/metabolismo , Difusão , Espectroscopia de Ressonância Magnética , Micelas , Solventes/farmacologia , Tensoativos/farmacologia , Temperatura
12.
Magn Reson Chem ; 52(4): 190-4, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24459096

RESUMO

Solvent exchange properties of protein backbone amide protons provide valuable residue-specific information on protein solvent accessibility, structure stability and flexibility and hence are of significant interest in structural biology. NMR has served as a unique means for the characterization of chemical exchange including proton amide exchange with solvent water at residue-specific levels across a broad range of exchange rates. One of the methods used for the characterization of protein backbone amide exchange by NMR involves the use of progressive selective irradiation of the water resonance. Here, we report the experimental observation of the nutation frequency (strength of RF field used for the irradiation of water resonance) modulation on amide proton signals for those in exchange with the solvent water under the band-selective excitation short transient (BEST) conditions. Compared with conventional saturation transfer of water magnetization experiments, this nutation frequency modulation observed on signal of nuclear spins under the BEST conditions potentially offers a quick identification of protein backbone amides in rapid exchange with solvent water.


Assuntos
Amidas/química , Proteínas/química , Água/química , Espectroscopia de Ressonância Magnética/normas , Prótons , Padrões de Referência , Solventes/química
13.
J Colloid Interface Sci ; 666: 659-669, 2024 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-38616448

RESUMO

Two-dimensional NOE (nuclear Overhauser effect) NMR spectroscopy was employed to investigate the dynamic properties of water within lyotropic bicontinuous lipidic cubic phases (LCPs) formed by monoolein (MO). Experiments observed categorically different effective residence times of water molecules: (i) in proximity to the glycerol moiety of MO, and (ii) adjacent to the hydrophobic chain towards the hydrocarbon tail of MO, as evidenced by the opposite signs of intermolecular NOE cross peaks between protons of water and those of MO in 2D 1H-1H NOESY spectra. Spectroscopic data delineating the different effective residence times of water molecules within both the gyroid (QIIG) and diamond (QIID) phase groups corresponding to hydration levels of 35 and 40 wt%, respectively, are presented. Additionally, an increase in effective residence time of water molecules in proximity to the glycerol moiety of MO in LCPs was observed upon storage at ambient temperature and in the presence of an additive lipid, cholesterol. Atom-specific NOE build-up curves for protons of water and those of MO are also given. The results presented herein provide new insight into the physicochemical properties and behaviour of water in LCPs, and demonstrate an additional avenue for experimental study of water-lipid interactions and hydration dynamics in model membranes and nanomaterials using 2D NOE NMR spectroscopy.

14.
Int J Biol Macromol ; 272(Pt 1): 132845, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38830495

RESUMO

Brown seaweed-derived polysaccharides, notably fucoidan and laminarin, are known for their extensive array of bioactivities and physicochemical properties. However, the effects of upper digestive tract modification on the bioactive performance of fucoidan and laminarin fractions (FLFs) sourced from Australian native species are largely unknown. Here, the digestibility and bioaccessibility of FLFs were evaluated by tracking the dynamic changes in reducing sugar content (CR), profiling the free monosaccharide composition using LC-MS, and comparing high-performance gel permeation chromatography profile variation via LC-SEC-RI. The effects of digestive progression on bioactive performance were assessed by comparing the antioxidant and antidiabetic potential of FLFs and FLF digesta. We observed that molecular weight (Mw) decreased during gastric digestion indicating that FLF aggregates were disrupted in the stomach. During intestinal digestion, Mw gradually decreased and CR increased indicating cleavage of glycosidic bonds releasing free sugars. Although the antioxidant and antidiabetic capacities were not eliminated by the digestion progression, the bioactive performance of FLFs under a digestive environment was reduced contrasting with the same concentration level of the undigested FLFs. These data provide comprehensive information on the digestibility and bioaccessibility of FLFs, and shed light on the effects of digestive progression on bioactive expression.


Assuntos
Antioxidantes , Polissacarídeos , Alga Marinha , Polissacarídeos/química , Polissacarídeos/farmacologia , Alga Marinha/química , Antioxidantes/farmacologia , Antioxidantes/química , Antioxidantes/metabolismo , Trato Gastrointestinal Superior/metabolismo , Trato Gastrointestinal Superior/efeitos dos fármacos , Peso Molecular , Hipoglicemiantes/farmacologia , Hipoglicemiantes/química , Digestão/efeitos dos fármacos , Sulfatos/química , Glucanos/química , Glucanos/farmacologia , Phaeophyceae/química , Humanos
15.
Proc Natl Acad Sci U S A ; 106(13): 5082-7, 2009 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-19289842

RESUMO

Epidermal Growth Factor Receptor (EGFR) is involved in stimulating the growth of many human tumors, but the success of therapeutic agents has been limited in part by interference from the EGFR on normal tissues. Previously, we reported an antibody (mab806) against a truncated form of EGFR found commonly in gliomas. Remarkably, it also recognizes full-length EGFR on tumor cells but not on normal cells. However, the mechanism for this activity was unclear. Crystallographic structures for Fab:EGFR(287-302) complexes of mAb806 (and a second, related antibody, mAb175) show that this peptide epitope adopts conformations similar to those found in the wtEGFR. However, in both conformations observed for wtEGFR, tethered and untethered, antibody binding would be prohibited by significant steric clashes with the CR1 domain. Thus, these antibodies must recognize a cryptic epitope in EGFR. Structurally, it appeared that breaking the disulfide bond preceding the epitope might allow the CR1 domain to open up sufficiently for antibody binding. The EGFR(C271A/C283A) mutant not only binds mAb806, but binds with 1:1 stoichiometry, which is significantly greater than wtEGFR binding. Although mAb806 and mAb175 decrease tumor growth in xenografts displaying mutant, overexpressed, or autocrine stimulated EGFR, neither antibody inhibits the in vitro growth of cells expressing wtEGFR. In contrast, mAb806 completely inhibits the ligand-associated stimulation of cells expressing EGFR(C271A/C283A). Clearly, the binding of mAb806 and mAb175 to the wtEGFR requires the epitope to be exposed either during receptor activation, mutation, or overexpression. This mechanism suggests the possibility of generating antibodies to target other wild-type receptors on tumor cells.


Assuntos
Anticorpos Monoclonais/imunologia , Anticorpos Antineoplásicos/imunologia , Receptores ErbB/imunologia , Proteínas de Neoplasias/imunologia , Animais , Anticorpos Monoclonais/uso terapêutico , Anticorpos Antineoplásicos/uso terapêutico , Complexo Antígeno-Anticorpo/química , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Cristalografia por Raios X , Epitopos , Humanos , Camundongos , Camundongos Nus , Conformação Proteica , Desnaturação Proteica/imunologia , Ensaios Antitumorais Modelo de Xenoenxerto
16.
BBA Adv ; 2: 100062, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-37082598

RESUMO

Nuclear magnetic resonance (NMR) spectroscopy is well-established nowadays for the elucidation of the 3D structures of proteins and protein complexes, the evaluation of biomolecular dynamics with atomistic resolution across a range of time scales, the screening of drug candidates with site specificity, and for the quantitation of molecular translational diffusion. Lyotropic lipidic cubic phases (LCPs) are lipid bilayer-based materials with a complex geometry, formed via the spontaneous self-assembly of certain lipids in an aqueous environment at specific temperature ranges. LCPs have been successfully applied to the in meso crystallization of membrane proteins for structural studies by X-ray crystallography, and have also shown promising potential for serving as matrices for drug and nutrient delivery/release in vivo. The characterization of the structural and dynamics properties of LCPs is of significant interest for the application of these materials. Here we present a systematic review detailing the characterization of LCPs by solution NMR. Using LCPs formed by monoolein (MO) as an example, various aspects of LCPs readily accessible by solution NMR are covered, including spectral perturbation in the presence of additives, quantification of hydration levels, 13C relaxation-based measurements for studying atom-specific dynamics along the MO hydrocarbon chain, PGSE NMR measurement of translational diffusion and its correlation with release profiles, and the encapsulation of soluble proteins in LCPs. A brief discussion of future perspectives for the characterization of LCPs by solution NMR is also presented.

17.
Biophys Rev ; 14(1): 67-74, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35340611

RESUMO

Lipidic cubic phase (LCP) structures have been used for stabilisation and crystallisation of membrane proteins and show promising properties as drug carriers. In this mini-review, we present how NMR spectroscopy has played a major role in understanding the physico-chemical properties of LCPs and how recent advances in pulsed field gradient NMR techniques open new perspectives in characterising encapsulated molecules.

18.
Biochemistry ; 50(13): 2464-77, 2011 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-21329364

RESUMO

Interleukin-3 (IL-3), a cytokine produced primarily by activated T-cells during immune responses, is a crucial regulator of allergic inflammation. The three-dimensional structure of murine IL-3 (mIL-3) has remained elusive owing to its poor solubility and strong tendency toward aggregation under solution conditions typically used for structural studies. Here we describe the solution properties and structure of mIL-3 determined by NMR using an engineered construct of mIL-3 (mIL-3(33-156)). mIL-3 adopts a four-helical bundle fold, typical of proteins belonging to the short-chain cytokine family, and features a core of highly conserved hydrophobic residues. While significant line broadening and peak disappearance were observed in NMR spectra at higher temperatures, there was no evidence for temperature-dependent changes of the oligomeric state of mIL-3(33-156). Further analysis of the temperature dependence of amide (1)H chemical shifts and backbone (15)N relaxation parameters, including (15)N relaxation dispersion, revealed the presence of significant conformational exchange and local conformational heterogeneity. Residues recently shown by mutagenesis to play key roles in ß(IL-3) receptor recognition and activation, which are located within the α(A) and α(C) helices and aligned on one face of the mIL-3(33-156) structure, are relatively rigid. In contrast, pronounced conformational heterogeneity was observed for a cluster of residues located on the opposite side of mIL-3, which corresponds spatially to sites in the related cytokines human IL-3, IL-5, and GM-CSF that are known to mediate interactions with their respective α-receptor subunits. Such conformational heterogeneity may facilitate the interaction of mIL-3 with each of two naturally occurring mIL-3Rα isoforms, leading to structurally distinct high-affinity complexes.


Assuntos
Interleucina-3/química , Fragmentos de Peptídeos/química , Animais , Concentração de Íons de Hidrogênio , Interleucina-3/genética , Camundongos , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Fragmentos de Peptídeos/genética , Conformação Proteica , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Solubilidade , Temperatura
19.
Nat Struct Mol Biol ; 13(1): 77-84, 2006 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-16369487

RESUMO

The four mammalian SPRY domain-containing SOCS box proteins (SSB-1 to SSB-4) are characterized by a C-terminal SOCS box and a central SPRY domain. We have determined the first SPRY-domain structure, as part of SSB-2, by NMR. This domain adopts a novel fold consisting of a beta-sandwich structure formed by two four-stranded antiparallel beta-sheets with a unique topology. We demonstrate that SSB-1, SSB-2 and SSB-4, but not SSB-3, bind prostate apoptosis response protein-4 (Par-4). Mutational analysis of SSB-2 loop regions identified conserved structural determinants for its interaction with Par-4 and the hepatocyte growth factor receptor, c-Met. Mutations in analogous loop regions of pyrin and midline-1 SPRY domains have been shown to cause Mediterranean fever and Opitz syndrome, respectively. Our findings provide a template for SPRY-domain structure and an insight into the mechanism of SPRY-protein interaction.


Assuntos
Proteínas Reguladoras de Apoptose/metabolismo , Sequência Conservada , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Dobramento de Proteína , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Linhagem Celular , Proteínas de Ligação a DNA/classificação , Proteínas de Ligação a DNA/genética , Doença , Humanos , Masculino , Camundongos , Modelos Moleculares , Dados de Sequência Molecular , Mutação/genética , Ressonância Magnética Nuclear Biomolecular , Filogenia , Ligação Proteica , Estrutura Terciária de Proteína , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Homologia Estrutural de Proteína
20.
J Phys Chem B ; 125(2): 571-580, 2021 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-33251799

RESUMO

Proton transportation in proximity to the lipid bilayer membrane surface, where chemical exchange represents a primary pathway, is of significant interest in many applications including cellular energy turnover underlying ATP synthesis, transmembrane mobility, and transport. Lipidic inverse bicontinuous cubic phases (LCPs) are unique membrane structures formed via the spontaneous self-assembly of certain lipids in an aqueous environment. They feature two networks of water channels, separated by a single lipid bilayer which approximates the geometry of a triply periodic minimal surface. When composed of monoolein, the LCP bilayer features two glycerol hydroxyl groups at the lipid-water interface which undergo exchange with water. Depending on the conditions of the aqueous solution used in the formation of LCPs, both resonances of the glycerol hydroxyl groups may be observed by solution 1H NMR. In this study, PFG-NMR and 1D EXSY were employed to gain insight into chemical exchange between the monoolein hydroxyl groups and water in LCPs. Results including the relative population of hydroxyl protons in exchange with water for a number of LCPs at different hydration levels and the exchange rate constants at 35 wt % hydration are reported. Several technical aspects of PFG-NMR and EXSY-NMR for the characterization of chemical exchange in LCPs are discussed, including an alternative way to analyze PFG-NMR data of exchange systems which overcomes the inherent low sensitivity at high diffusion encoding.

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