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1.
Phys Chem Chem Phys ; 24(36): 22250-22262, 2022 Sep 21.
Article in English | MEDLINE | ID: mdl-36098073

ABSTRACT

Targeting amyloidosis requires high-resolution insight into the underlying mechanisms of amyloid aggregation. The sequence-specific intrinsic properties of a peptide or protein largely govern the amyloidogenic propensity. Thus, it is essential to delineate the structural motifs that define the subsequent downstream amyloidogenic cascade of events. Additionally, it is important to understand the role played by extrinsic factors, such as temperature or sample agitation, in modulating the overall energy barrier that prompts divergent nucleation events. Consequently, these changes can affect the fibrillation kinetics, resulting in structurally and functionally distinct amyloidogenic conformers associated with disease pathogenesis. Here, we have focused on human Islet Polypeptide (hIAPP) amyloidogenesis for the full-length peptide along with its N- and C-terminal fragments, under different temperatures and sample agitation conditions. This helped us to gain a comprehensive understanding of the intrinsic role of specific functional epitopes in the primary structure of the peptide that regulates amyloidogenesis and subsequent cytotoxicity. Intriguingly, our study involving an array of biophysical experiments and ex vivo data suggests a direct influence of external changes on the C-terminal fibrillating sequence. Furthermore, the observations indicate a possible collaborative role of this segment in nucleating hIAPP amyloidogenesis in a physiological scenario, thus making it a potential target for future therapeutic interventions.


Subject(s)
Amyloidosis , Islet Amyloid Polypeptide , Amyloid/chemistry , Amyloidogenic Proteins , Epitopes , Humans , Islet Amyloid Polypeptide/chemistry
2.
Proc Natl Acad Sci U S A ; 110(10): 3743-8, 2013 Mar 05.
Article in English | MEDLINE | ID: mdl-23426629

ABSTRACT

Despite the significance of Alzheimer's disease, the link between metal-associated amyloid-ß (metal-Aß) and disease etiology remains unclear. To elucidate this relationship, chemical tools capable of specifically targeting and modulating metal-Aß species are necessary, along with a fundamental understanding of their mechanism at the molecular level. Herein, we investigated and compared the interactions and reactivities of the green tea extract, (-)-epigallocatechin-3-gallate [(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate; EGCG], with metal [Cu(II) and Zn(II)]-Aß and metal-free Aß species. We found that EGCG interacted with metal-Aß species and formed small, unstructured Aß aggregates more noticeably than in metal-free conditions in vitro. In addition, upon incubation with EGCG, the toxicity presented by metal-free Aß and metal-Aß was mitigated in living cells. To understand this reactivity at the molecular level, structural insights were obtained by ion mobility-mass spectrometry (IM-MS), 2D NMR spectroscopy, and computational methods. These studies indicated that (i) EGCG was bound to Aß monomers and dimers, generating more compact peptide conformations than those from EGCG-untreated Aß species; and (ii) ternary EGCG-metal-Aß complexes were produced. Thus, we demonstrate the distinct antiamyloidogenic reactivity of EGCG toward metal-Aß species with a structure-based mechanism.


Subject(s)
Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/drug effects , Catechin/analogs & derivatives , Metals/chemistry , Alzheimer Disease/etiology , Alzheimer Disease/metabolism , Alzheimer Disease/prevention & control , Amyloid beta-Peptides/toxicity , Camellia sinensis/chemistry , Catechin/chemistry , Catechin/pharmacology , Copper/chemistry , Copper/pharmacology , Copper/toxicity , Humans , Metals/pharmacology , Metals/toxicity , Models, Molecular , Neuroprotective Agents/chemistry , Neuroprotective Agents/pharmacology , Nuclear Magnetic Resonance, Biomolecular , Peptide Fragments/chemistry , Peptide Fragments/drug effects , Peptide Fragments/toxicity , Plant Extracts/chemistry , Plant Extracts/pharmacology , Protein Binding , Protein Conformation/drug effects , Protein Multimerization/drug effects , Tandem Mass Spectrometry , Zinc/chemistry , Zinc/pharmacology , Zinc/toxicity
3.
J Biol Chem ; 288(30): 22080-95, 2013 Jul 26.
Article in English | MEDLINE | ID: mdl-23709268

ABSTRACT

Microsomal cytochrome b5 (cytb5) is a membrane-bound protein that modulates the catalytic activity of its redox partner, cytochrome P4502B4 (cytP450). Here, we report the first structure of full-length rabbit ferric microsomal cytb5 (16 kDa), incorporated in two different membrane mimetics (detergent micelles and lipid bicelles). Differential line broadening of the cytb5 NMR resonances and site-directed mutagenesis data were used to characterize the cytb5 interaction epitope recognized by ferric microsomal cytP450 (56 kDa). Subsequently, a data-driven docking algorithm, HADDOCK (high ambiguity driven biomolecular docking), was used to generate the structure of the complex between cytP4502B4 and cytb5 using experimentally derived restraints from NMR, mutagenesis, and the double mutant cycle data obtained on the full-length proteins. Our docking and experimental results point to the formation of a dynamic electron transfer complex between the acidic convex surface of cytb5 and the concave basic proximal surface of cytP4502B4. The majority of the binding energy for the complex is provided by interactions between residues on the C-helix and ß-bulge of cytP450 and residues at the end of helix α4 of cytb5. The structure of the complex allows us to propose an interprotein electron transfer pathway involving the highly conserved Arg-125 on cytP450 serving as a salt bridge between the heme propionates of cytP450 and cytb5. We have also shown that the addition of a substrate to cytP450 likely strengthens the cytb5-cytP450 interaction. This study paves the way to obtaining valuable structural, functional, and dynamic information on membrane-bound complexes.


Subject(s)
Cytochrome P-450 Enzyme System/chemistry , Cytochromes b5/chemistry , Models, Molecular , Multiprotein Complexes/chemistry , Amino Acid Sequence , Animals , Arginine/chemistry , Arginine/genetics , Arginine/metabolism , Binding Sites/genetics , Biocatalysis , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Cytochromes b5/genetics , Cytochromes b5/metabolism , Electron Transport/genetics , Heme/analogs & derivatives , Heme/chemistry , Heme/metabolism , Kinetics , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Mutagenesis, Site-Directed , Mutation , Oxidation-Reduction , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Rabbits , Sequence Homology, Amino Acid , Substrate Specificity
4.
Biochim Biophys Acta ; 1808(10): 2337-42, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21723249

ABSTRACT

Human islet amyloid polypeptide is a hormone coexpressed with insulin by pancreatic beta-cells. For reasons not clearly understood, hIAPP aggregates in type II diabetics to form oligomers that interfere with beta-cell function, eventually leading to the loss of insulin production. The cellular membrane catalyzes the formation of amyloid deposits and is a target of amyloid toxicity through disruption of the membrane's structural integrity. Therefore, there is considerable current interest in solving the 3D structure of this peptide in a membrane environment. NMR experiments could not be directly utilized in lipid bilayers due to the rapid aggregation of the peptide. To overcome this difficulty, we have solved the structure of the naturally occurring peptide in detergent micelles at a neutral pH. The structure has an overall kinked helix motif, with residues 7-17 and 21-28 in a helical conformation, and with a 3(10) helix from Gly 33-Asn 35. In addition, the angle between the N- and C-terminal helices is constrained to 85°. The greater helical content of human IAPP in the amidated versus free acid form is likely to play a role in its aggregation and membrane disruptive activity.


Subject(s)
Amides/chemistry , Hydrogen-Ion Concentration , Islet Amyloid Polypeptide/chemistry , Amino Acid Sequence , Cell Membrane/chemistry , Lipid Bilayers , Molecular Sequence Data , Nuclear Magnetic Resonance, Biomolecular , Protein Conformation
5.
Biochem Biophys Res Commun ; 411(2): 312-6, 2011 Jul 29.
Article in English | MEDLINE | ID: mdl-21726530

ABSTRACT

Aggregation of the Aß(1-40) peptide is linked to the development of extracellular plaques characteristic of Alzheimer's disease. While previous studies commonly show the Aß(1-40) is largely unstructured in solution, we show that Aß(1-40) can adopt a compact, partially folded structure. In this structure (PDB ID: 2LFM), the central hydrophobic region of the peptide forms a 3(10) helix from H13 to D23 and the N- and C-termini collapse against the helix due to the clustering of hydrophobic residues. Helical intermediates have been predicted to be crucial on-pathway intermediates in amyloid fibrillogenesis, and the structure presented here presents a new target for investigation of early events in Aß(1-40) fibrillogenesis.


Subject(s)
Amyloid beta-Peptides/chemistry , Peptide Fragments/chemistry , Water/chemistry , Amino Acid Sequence , Cold Temperature , Humans , Hydrogen-Ion Concentration , Hydrophobic and Hydrophilic Interactions , Molecular Sequence Data , Nuclear Magnetic Resonance, Biomolecular , Protein Folding , Protein Structure, Secondary , Sodium Chloride/chemistry
6.
Biochim Biophys Acta ; 1787(4): 242-51, 2009 Apr.
Article in English | MEDLINE | ID: mdl-19344662

ABSTRACT

Understanding the structural traits of subunit G is essential, as it is needed for V(1)V(O) assembly and function. Here solution NMR of the recombinant N- (G(1-59)) and C-terminal segment (G(61-114)) of subunit G, has been performed in the absence and presence of subunit d of the yeast V-ATPase. The data show that G does bind to subunit d via its N-terminal part, G(1-59) only. The residues of G(1-59) involved in d binding are Gly7 to Lys34. The structure of G(1-59) has been solved, revealing an alpha-helix between residues 10 and 56, whereby the first nine- and the last three residues of G(1-59) are flexible. The surface charge distribution of G(1-59) reveals an amphiphilic character at the N-terminus due to positive and negative charge distribution at one side and a hydrophobic surface on the opposite side of the structure. The C-terminus exhibits a strip of negative residues. The data imply that G(1-59)-d assembly is accomplished by hydrophobic interactions and salt-bridges of the polar residues. Based on the recently determined NMR structure of segment E(18-38) of subunit E of yeast V-ATPase and the presently solved structure of G(1-59), both proteins have been docked and binding epitopes have been analyzed.


Subject(s)
Protein Subunits/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Vacuolar Proton-Translocating ATPases/chemistry , Vacuolar Proton-Translocating ATPases/metabolism , Amino Acid Sequence , Circular Dichroism , Kinetics , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Sequence Data , Protein Binding , Protein Structure, Secondary , Protein Subunits/chemistry , Solutions , Surface Plasmon Resonance , Time Factors , Titrimetry
7.
J Am Chem Soc ; 132(26): 8973-83, 2010 Jul 07.
Article in English | MEDLINE | ID: mdl-20536124

ABSTRACT

Human Islet Amyloid Polypeptide (hIAPP) is a highly amyloidogenic protein found in islet cells of patients with type II diabetes. Because hIAPP is highly toxic to beta-cells under certain conditions, it has been proposed that hIAPP is linked to the loss of beta-cells and insulin secretion in type II diabetics. One of the interesting questions surrounding this peptide is how the toxic and aggregation prone hIAPP peptide can be maintained in a safe state at the high concentrations that are found in the secretory granule where it is stored. We show here zinc, which is found at millimolar concentrations in the secretory granule, significantly inhibits hIAPP amyloid fibrillogenesis at concentrations similar to those found in the extracellular environment. Zinc has a dual effect on hIAPP fibrillogenesis: it increases the lag-time for fiber formation and decreases the rate of addition of hIAPP to existing fibers at lower concentrations, while having the opposite effect at higher concentrations. Experiments at an acidic pH which partially neutralizes the change in charge upon zinc binding show inhibition is largely due to an electrostatic effect at His18. High-resolution structures of hIAPP determined from NMR experiments confirm zinc binding to His18 and indicate zinc induces localized disruption of the secondary structure of IAPP in the vicinity of His18 of a putative helical intermediate of IAPP. The inhibition of the formation of aggregated and toxic forms of hIAPP by zinc provides a possible mechanism between the recent discovery of linkage between deleterious mutations in the SLC30A8 zinc transporter, which transports zinc into the secretory granule, and type II diabetes.


Subject(s)
Amyloid/chemistry , Amyloid/metabolism , Protein Multimerization/drug effects , Zinc/pharmacology , Amino Acid Sequence , Dose-Response Relationship, Drug , Histidine/metabolism , Humans , Hydrogen-Ion Concentration , Islet Amyloid Polypeptide , Kinetics , Ligands , Models, Molecular , Molecular Sequence Data , Protein Structure, Quaternary , Protein Structure, Secondary
8.
J Am Chem Soc ; 132(1): 96-105, 2010 Jan 13.
Article in English | MEDLINE | ID: mdl-19958024

ABSTRACT

The cyclic peptides c-(LSETTl) and c-(RTLPFS) are of potential clinical interest--they stimulate neurite outgrowth in a way that is similar to the effects of the HNK-1 (human natural killer cell-1) antigenic carbohydrate chains, which are terminated by 3'-sulfated glucuronic acid attached to an N-acetyllactosamine unit. To investigate the structure-activity relationships of the ability of the cyclic peptides to mimic HNK-1 carbohydrates, conformational analysis and examination of hydrophobic and hydrophilic patterns were performed and compared with the characteristics of a synthetic HNK-1 trisaccharide derivative. Data obtained demonstrate that both the trisaccharide and the glycomimetic peptide c-(LSETTl) exhibit a similar relationship between their hydrophobic moieties and their negatively charged sites. However, the second cyclic glycomimetic peptide investigated here, c-(RTLPFS), has a positively charged group as a potential contact point due to its Arg residue. Therefore, we studied the amino acid composition of all known receptor structures in the Protein Data Bank that are in contact with uronic acid and/or sulfated glycans. Interactions of the HNK-1 trisaccharide, c-(LSETTl), and c-(RTLPFS) with a laminin fragment involved in HNK-1 carbohydrate binding (i.e., the 21mer peptide: KGVSSRSYVGCIKNLEISRST) were also analyzed. Because the structure of the HNK-1-binding laminin domain is not available in the Protein Data Bank, we used the HNK-1-binding 21mer peptide fragment of laminin for the construction of a model receptor that enabled us to compare the molecular interplay of the HNK-1 trisaccharide and the two cyclopeptides c-(LSETTl) and c-(RTLPFS) with a reliable receptor structure in considerable detail.


Subject(s)
Antigens/chemistry , Carbohydrates/chemistry , Killer Cells, Natural , Molecular Mimicry , Peptides, Cyclic/chemistry , Peptides, Cyclic/metabolism , Amino Acid Motifs , Amino Acid Sequence , Animals , Antigens/metabolism , Binding Sites , Carbohydrate Conformation , Carbohydrate Metabolism , Computational Biology , Dimethyl Sulfoxide/chemistry , Humans , Laminin/chemistry , Laminin/metabolism , Magnetic Resonance Spectroscopy , Mice , Molecular Dynamics Simulation , Molecular Sequence Data , Protein Structure, Tertiary , Uronic Acids/chemistry , Water/chemistry
9.
J Bacteriol ; 191(24): 7538-44, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19820091

ABSTRACT

Subunit b, the peripheral stalk of bacterial F(1)F(o) ATP synthases, is composed of a membrane-spanning and a soluble part. The soluble part is divided into tether, dimerization, and delta-binding domains. The first solution structure of b30-82, including the tether region and part of the dimerization domain, has been solved by nuclear magnetic resonance, revealing an alpha-helix between residues 39 and 72. In the solution structure, b30-82 has a length of 48.07 A. The surface charge distribution of b30-82 shows one side with a hydrophobic surface pattern, formed by alanine residues. Alanine residues 61, 68, 70, and 72 were replaced by single cysteines in the soluble part of subunit b, b22-156. The cysteines at positions 61, 68, and 72 showed disulfide formation. In contrast, no cross-link could be formed for the A70C mutant. The patterns of disulfide bonding, together with the circular dichroism spectroscopy data, are indicative of an adjacent arrangement of residues 61, 68, and 72 in both alpha-helices in b22-156.


Subject(s)
Bacterial Proton-Translocating ATPases/chemistry , Escherichia coli/chemistry , Protein Subunits/chemistry , Circular Dichroism , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Protein Structure, Secondary , Protein Structure, Tertiary , Static Electricity
10.
J Am Chem Soc ; 131(49): 17972-9, 2009 Dec 16.
Article in English | MEDLINE | ID: mdl-19995078

ABSTRACT

Semen is the main vector for HIV transmission worldwide. Recently, a peptide fragment (PAP(248-286)) has been isolated from seminal fluid that dramatically enhances HIV infectivity by up to 4-5 orders of magnitude. PAP(248-286) appears to enhance HIV infection by forming amyloid fibers known as SEVI, which are believed to enhance the attachment of the virus by bridging interactions between virion and host-cell membranes. We have solved the atomic-level resolution structure of the SEVI precursor PAP(248-286) using NMR spectroscopy in SDS micelles, which serve as a model membrane system. PAP(248-286), which does not disrupt membranes like most amyloid proteins, binds superficially to the surface of the micelle, in contrast to other membrane-disruptive amyloid peptides that generally penetrate into the core of the membrane. The structure of PAP(248-286) is unlike most amyloid peptides in that PAP(248-286) is mostly disordered when bound to the surface of the micelle, as opposed to the alpha-helical structures typically found of most amyloid proteins. The highly disordered nature of the SEVI peptide may explain the unique ability of SEVI amyloid fibers to enhance HIV infection as partially disordered amyloid fibers will have a greater capture radius for the virus than compact amyloid fibers. Two regions of nascent structure (an alpha-helix from V262-H270 and a dynamic alpha/3(10) helix from S279-L283) match the prediction of highly amyloidogenic sequences and may serve as nuclei for aggregation and amyloid fibril formation. The structure presented here can be used for the rational design of mutagenesis studies on SEVI amyloid formation and viral infection enhancement.


Subject(s)
Amyloid/chemistry , Membranes, Artificial , Peptide Fragments/chemistry , Semen/chemistry , HIV Infections/virology , Magnetic Resonance Spectroscopy , Semen/virology
11.
J Am Chem Soc ; 131(46): 16663-5, 2009 Nov 25.
Article in English | MEDLINE | ID: mdl-19877631

ABSTRACT

Our design of bifunctional metal chelators as chemical probes and potential therapeutics for Alzheimer's disease (AD) is based on the incorporation of a metal binding moiety into structural frameworks of Abeta aggregate-imaging agents. Using this strategy, two compounds 2-[4-(dimethylamino)phenyl]imidazo[1,2-a]pyridine-8-ol (1) and N(1),N(1)-dimethyl-N(4)-(pyridin-2-ylmethylene)benzene-1,4-diamine (2) were prepared and characterized. The bifunctionality for metal chelation and Abeta interaction of 1 and 2 was verified by spectroscopic methods. Furthermore, the reactivity of 1 and 2 with Cu(II)-associated Abeta aggregates was investigated. The modulation of Cu(II)-triggered Abeta aggregation by 1 and 2 was found to be more effective than that by the known metal chelating agents CQ, EDTA, and phen. These studies suggest a new class of multifunctional molecules for the development of chemical tools to unravel metal-associated events in AD and potential therapeutic agents for metal-ion chelation therapy.


Subject(s)
Alzheimer Disease/metabolism , Amyloid beta-Peptides/drug effects , Chelating Agents/pharmacology , Copper/metabolism , Imidazoles/pharmacology , Phenylenediamines/pharmacology , Pyridines/pharmacology , Alzheimer Disease/drug therapy , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/metabolism , Cell Line, Tumor , Chelating Agents/chemistry , Chelating Agents/therapeutic use , Copper/chemistry , Drug Design , Humans , Imidazoles/chemistry , Imidazoles/therapeutic use , Phenylenediamines/chemistry , Phenylenediamines/therapeutic use , Pyridines/chemistry , Pyridines/therapeutic use
12.
J Am Chem Soc ; 130(14): 4660-8, 2008 Apr 09.
Article in English | MEDLINE | ID: mdl-18341335

ABSTRACT

Biomineral matrix formation and molecular recognition are two important processes associated with eggshell biomineralization. To understand these two processes, a major intracrystalline peptide, pelovaterin, was isolated from turtle (Pelodiscus sinensis) eggshell and its tertiary and quaternary structures were established. The global fold of pelovaterin is similar to that of human beta-defensins but has a large hydrophobic core and a short hydrophilic N-terminal segment, which is not preserved in defensins. Pelovaterin exhibits strong antimicrobial activity against two pathogenic gram-negative bacteria, Pseudomonas aeruginosa and Proteus vulgaris, and stabilizes a thin film of metastable vaterite. We show that pelovaterin self-aggregates in the form of micellar nanospheres and the aggregation in solution is entropy-driven. It is suggested that the micellar aggregation of pelovaterin is responsible for the induction and stabilization of the metastable phase by altering the interfacial energy. The results demonstrate the adaptability of an extracellular matrix protein to perform multiple tasks: polymorph discrimination and protection of the contents of the egg against bacterial invasion.


Subject(s)
Anti-Infective Agents/chemistry , Egg Proteins/chemistry , Turtles , beta-Defensins/chemistry , Animals , Anti-Infective Agents/isolation & purification , Anti-Infective Agents/pharmacology , Calcium Carbonate/chemistry , Calorimetry , Chromatography, Gel , Egg Proteins/isolation & purification , Egg Proteins/pharmacology , Light , Microbial Sensitivity Tests , Microscopy, Atomic Force , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Proteus vulgaris/drug effects , Pseudomonas aeruginosa/drug effects , Scattering, Radiation , Thermodynamics , beta-Defensins/pharmacology
13.
Biophys J ; 93(11): 3963-76, 2007 Dec 01.
Article in English | MEDLINE | ID: mdl-17704148

ABSTRACT

Hemextin AB complex from the venom of Hemachatus haemachatus is the first known natural anticoagulant that specifically inhibits the enzymatic activity of blood coagulation factor VIIa in the absence of factor Xa. It is also the only known heterotetrameric complex of two three-finger toxins. Individually only hemextin A has mild anticoagulant activity, whereas hemextin B is inactive. However, hemextin B synergistically enhances the anticoagulant activity of hemextin A and their complex exhibits potent anticoagulant activity. In this study we characterized the nature of molecular interactions leading to the complex formation. Circular dichroism studies indicate the stabilization of beta-sheet in the complex. Hemextin AB complex has an increased apparent molecular diameter in both gas and liquid phase techniques. The complex formation is enthalpically favorable and entropically unfavorable with a negative change in the heat capacity. Thus, the anticoagulant complex shows less structural flexibility than individual subunits. Both electrostatic and hydrophobic interactions are important for the complexation; the former driving the process and the latter helping in the stabilization of the tetramer. The tetramer dissociates into dimers and monomers with the increase in the ionic strength of the solution and also with increase in the glycerol concentration in the buffer. The two dimers formed under each of these conditions display distinct differences in their apparent molecular diameters and anticoagulant properties. Based on these results, we have proposed a model for this unique anticoagulant complex.


Subject(s)
Elapid Venoms/chemistry , Factor VIIa/antagonists & inhibitors , Protein Conformation
14.
J Phys Chem B ; 119(7): 2886-96, 2015 Feb 19.
Article in English | MEDLINE | ID: mdl-25645610

ABSTRACT

The aggregation of amyloidogenic proteins is infamous for being highly chaotic, with small variations in conditions sometimes leading to large changes in aggregation rates. Using the amyloidogenic protein IAPP (islet amyloid polypeptide protein, also known as amylin) as an example, we show that a part of this phenomenon may be related to the formation of micellelike oligomers at specific critical concentrations and temperatures. We show that pyrene fluorescence can sensitively detect micellelike oligomer formation by IAPP and discriminate between micellelike oligomers from fibers and monomers, making pyrene one of the few chemical probes specific to a prefibrillar oligomer. We further show that oligomers of this type reversibly form at critical concentrations in the low micromolar range and at specific critical temperatures. Micellelike oligomer formation has several consequences for amyloid formation by IAPP. First, the kinetics of fiber formation increase substantially as the critical concentration is approached but are nearly independent of concentration below it, suggesting a direct role for the oligomers in fiber formation. Second, the critical concentration is strongly correlated with the propensity to form amyloid: higher critical concentrations are observed for both IAPP variants with lower amyloidogenicity and for native IAPP at acidic pH in which aggregation is greatly slowed. Furthermore, using the DEST NMR technique, we show that the pathway of amyloid formation switches as the critical point is approached, with self-interactions primarily near the N-terminus below the critical temperature and near the central region above the critical temperature, reconciling two apparently conflicting views of the initiation of IAPP aggregation.


Subject(s)
Islet Amyloid Polypeptide/chemistry , Fluorescence , Hydrogen-Ion Concentration , Kinetics , Micelles , Protein Multimerization , Pyrenes , Spectrum Analysis , Temperature
15.
Sci Rep ; 5: 11811, 2015 Jul 03.
Article in English | MEDLINE | ID: mdl-26138908

ABSTRACT

Alzheimer's disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-ß (Aß). The aggregation of Aß leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aß oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling (1)H-(1)H NMR experiments to overcome many of these limitations. Using (1)H-(1)H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aß1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time (1)H-(1)H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aß1-40 oligomer 5-15 nm in diameter can form and coexist in parallel with the well-known cross-ß-sheet fibrils.


Subject(s)
Alzheimer Disease/metabolism , Amyloid beta-Peptides/chemistry , Amyloid/chemistry , Nuclear Magnetic Resonance, Biomolecular , Alzheimer Disease/pathology , Amino Acid Sequence , Humans , Macromolecular Substances/chemistry , Peptide Fragments/chemistry , Protein Aggregation, Pathological/metabolism , Protein Conformation
16.
Biomol NMR Assign ; 8(2): 409-13, 2014 Oct.
Article in English | MEDLINE | ID: mdl-24105099

ABSTRACT

Microsomal cytochrome b5 plays a key role in the oxidation of a variety of exogenous and endogenous compounds, including drugs, fatty acids, cholesterol and steroid hormones. To better understand its functional properties in a membrane mimic environment, we carried out high-resolution solution NMR studies. Here we report resonance assignments for full-length rabbit cytochrome b5 embedded in dodecylphosphocholine micelles.


Subject(s)
Cell Membrane/enzymology , Cytochromes b5/chemistry , Nuclear Magnetic Resonance, Biomolecular , Animals , Cell Membrane/chemistry , Micelles , Phosphorylcholine/analogs & derivatives , Phosphorylcholine/chemistry , Rabbits
17.
J Magn Reson ; 242: 169-79, 2014 May.
Article in English | MEDLINE | ID: mdl-24657390

ABSTRACT

Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled ((13)C, (15)N and (2)H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged (1)H-(1)H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time - obtained from 2D (1)H-(1)H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure (1)H-(1)H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent (1)H-(1)H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from (1)H-(1)H RFDR experiments. The appearance of resonances with distinct chemical shift values in (1)H-(1)H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.


Subject(s)
Cytochromes b5/chemistry , Cytochromes b5/ultrastructure , Proton Magnetic Resonance Spectroscopy/methods , Signal Processing, Computer-Assisted , Amino Acid Sequence , Animals , Micelles , Molecular Sequence Data , Protein Conformation , Rabbits
18.
Chem Commun (Camb) ; 49(32): 3339-41, 2013 Apr 25.
Article in English | MEDLINE | ID: mdl-23505632

ABSTRACT

The aggregation of human islet amyloid polypeptide (hIAPP) has been linked to beta-cell death in type II diabetes. Zinc present in secretory granules has been shown to affect this aggregation. A combination of EXAFS, NMR, and AFM experiments shows that the influence of zinc is most likely due to the stabilization of prefibrillar aggregates of hIAPP.


Subject(s)
Islet Amyloid Polypeptide/chemistry , Zinc/chemistry , Humans , Microscopy, Atomic Force , X-Ray Absorption Spectroscopy
19.
J Phys Chem B ; 117(44): 13851-60, 2013 Nov 07.
Article in English | MEDLINE | ID: mdl-24107224

ABSTRACT

It has been well realized that the dependence of chemical shift anisotropy (CSA) tensors on the amino acid sequence, secondary structure, dynamics, and electrostatic interactions can be utilized in the structural and dynamic studies of proteins by NMR spectroscopy. In addition, CSA tensors could also be utilized to measure the structural interactions between proteins in a protein-protein complex. To this end, we report the experimentally measured backbone amide-(15)N CSA tensors for a membrane-bound 16.7 kDa full-length rabbit cytochrome-b5 (cytb5), in complexation with a 55.8 kDa microsomal rabbit cytochrome P450 2B4 (cytP4502B4). The (15)N-CSAs, determined using the (15)N CSA/(15)N-(1)H dipolar coupling transverse cross-correlated rates, for free cytb5 are compared with those for the cytb5 bound to cytP4502B4. An overall increase in backbone amide-(15)N transverse cross-correlated rates for the cytb5 residues in the cytb5-cytP450 complex is observed as compared to the free cytb5 residues. Due to fast spin-spin relaxation (T2) and subsequent broadening of the signals in the complex, we could measure amide-(15)N CSAs only for 48 residues of cytb5 as compared to 84 residues of free cytb5. We observed a change in (15)N CSA for most residues of cytb5 in the complex, as compared to free cytb5, suggesting a dynamic interaction between the oppositely charged surfaces of anionic cytb5 and cationic cytP450. The mean values of (15)N CSA determined for residues in helical, sheet, and turn regions of cytb5 in the complex are -184.5, -146.8, and -146.2 ppm, respectively, with an overall average value of -165.5 ppm (excluding the values from residues in more flexible termini). The measured CSA value for residues in helical conformation is slightly larger as compared to previously reported values. This may be attributed to the paramagnetic effect from Fe(III) of the heme in cytb5, which is similar to our previously reported values for the free cytb5.


Subject(s)
Cytochrome P-450 Enzyme System/metabolism , Cytochromes b5/metabolism , Amides/chemistry , Animals , Cytochrome P-450 Enzyme System/chemistry , Cytochromes b5/chemistry , Nitrogen Isotopes/chemistry , Nuclear Magnetic Resonance, Biomolecular , Protein Interaction Domains and Motifs , Protein Structure, Tertiary , Rabbits
20.
J Mol Biol ; 416(1): 108-20, 2012 Feb 10.
Article in English | MEDLINE | ID: mdl-22200484

ABSTRACT

Calcitonin is a 32-residue peptide hormone known for its hypocalcemic effect and its inhibition of bone resorption. While calcitonin has been used in therapy for osteoporosis and Paget's disease for decades, human calcitonin (hCT) forms fibrils in aqueous solution that limit its therapeutic application. The molecular mechanism of fiber formation by calcitonin is not well understood. Here, high-resolution structures of hCT at concentrations of 0.3 mM and 1 mM have been investigated using NMR spectroscopy. Comparing the structures of hCT at different concentrations, we discovered that the peptide undergoes a conformational transition from an extended to a ß-hairpin structure in the process of molecular association. This conformational transition locates the aromatic side chains of Tyr12 and Phe16 in a favorable way for intermolecular π-π stacking, which is proposed to be a crucial interaction for peptide association and fibrillation. One-dimensional (1)H NMR experiments confirm that oligomerization of hCT accompanies the conformational transition at 1 mM concentration. The effect of the polyphenol epigallocatechin 3-gallate (EGCG) on hCT fibrillation was also investigated by NMR and electron microscopy, which show that EGCG efficiently inhibits fibril formation of hCT by preventing the initial association of hCT before fiber formation. The NMR experiments also indicate that the interaction between aromatic rings of EGCG and the aromatic side chains of the peptide may play an important role in inhibiting fibril formation of hCT.


Subject(s)
Calcitonin/chemistry , Calcitonin/metabolism , Catechin/analogs & derivatives , Amino Acid Sequence , Catechin/chemistry , Catechin/metabolism , Humans , Microscopy, Electron/methods , Molecular Sequence Data , Nuclear Magnetic Resonance, Biomolecular/methods , Protein Binding , Protein Structure, Secondary
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