A PFG NMR experiment for accurate diffusion and flow studies in the presence of eddy currents

Gibbs, S. Julian; Johnson, Charles S.

doi:10.1016/0022-2364(91)90014-k

Cited by 302 publications

(256 citation statements)

References 8 publications

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“…Amide exchange rates were monitored by dissolving freeze-dried peptide in 2 H 2 O at pH 4.9 and then recording a series of one-dimensional spectra at 5°C followed by 60-ms TOCSY and 250-ms NOE spectroscopy spectra at 600 MHz. Diffusion measurements were performed using a pulsed-field-gradient longitudinal eddy-current delay pulse sequence (12,15), as implemented by Yao et al (53). Spectra were processed using XWINNMR (version 3.5; Bruker Biospin) and analyzed using XEASY (version 1.3.13).…”

Section: Methodsmentioning

confidence: 99%

Binding Hot Spot for Invasion Inhibitory Molecules on Plasmodium falciparum Apical Membrane Antigen 1

et al. 2005

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Apical membrane antigen 1 (AMA1) is expressed in schizont-stage malaria parasites and sporozoites and is thought to be involved in the invasion of host red blood cells. AMA1 is an important vaccine candidate, as immunization with this antigen induces a protective immune response in rodent and monkey models of human malaria. Additionally, anti-AMA1 polyclonal and monoclonal antibodies inhibit parasite invasion in vitro. We have isolated a 20-residue peptide (R1) from a random peptide library that binds to native AMA1 as expressed by Plasmodium falciparum parasites. Binding of R1 peptide is dependent on AMA1 having the proper conformation, is strain specific, and results in the inhibition of merozoite invasion of host erythrocytes. The solution structure of R1, as determined by nuclear magnetic resonance spectroscopy, contains two structured regions, both involving turns, but the first region, encompassing residues 5 to 10, is hydrophobic and the second, at residues 13 to 17, is more polar. Several lines of evidence reveal that R1 targets a "hot spot" on the AMA1 surface that is also recognized by other peptides and monoclonal antibodies that have previously been shown to inhibit merozoite invasion. The functional consequence of binding to this region by a variety of molecules is the inhibition of merozoite invasion into host erythrocytes. The interaction between these peptides and AMA1 may further our understanding of the molecular mechanisms of invasion by identifying critical functional regions of AMA1 and aid in the development of novel antimalarial strategies.

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Section: Methodsmentioning

confidence: 99%

Binding Hot Spot for Invasion Inhibitory Molecules on Plasmodium falciparum Apical Membrane Antigen 1

et al. 2005

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“…The translational diffusion rates were measured by monitoring 1D 1 H signal decay due to molecular diffusion in the z-direction of the sample using PFGs (18,33) at variable concentrations of b30-82. In each experiment, the PFG strength was linearly increased from 2 to 95 G/cm, with a translational diffusion delay of 200 ms and total encoding and decoding gradient durations of 5 ms.…”

Section: Biochemicals Pfumentioning

confidence: 99%

Solution Structure, Determined by Nuclear Magnetic Resonance, of the b30-82 Domain of Subunit b of Escherichia coli F ₁ F _o ATP Synthase

et al. 2009

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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 ␦-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 ␣-helix between residues 39 and 72. In the solution structure, b30-82 has a length of 48.07 Å. 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 ␣-helices in b22-156.ATP synthesis by oxidative phosphorylation or photophosphorylation is a multistep membrane-located process that provides the bulk of cellular energy in eukaryotes and many prokaryotes. The majority of ATP synthesis is accomplished by the enzyme ATP synthase (EC 3.6.1.34), also called F 1 F o ATP synthase, which, in its simplest form, as in bacteria, is composed of eight different subunits (␣ 3 , ␤ 3 , ␥, ␦, ε, a, b 2 , and c 9-12 ). This multisubunit complex is divided into the F 1 headpiece, ␣ 3 :␤ 3 , and a membrane-embedded ion-translocating part known as F o , to which F 1 is attached by a central and a peripheral stalk (1,5,25). ATP is synthesized or hydrolyzed on the ␣ 3 :␤ 3 hexamer, and the energy provided for or released during that process is transmitted to the membrane-bound F o sector, consisting of subunits a and c and part of subunit b (30, 31). The energy coupling between the two active domains occurs via the stalk part(s) (6). The central stalk is made of subunits ␥ and ε, and the peripheral stalk is formed by subunits ␦ and b. The peripheral stalk, which lies at the edge of the multisubunit assembly of the F 1 F o ATP synthase, acts as a stator to counter the tendency of the ␣ 3 :␤ 3 hexamer to follow the rotation of the central stalk and the attached c-ring, and to anchor the membrane-embedded a subunit (17, 36).In Escherichia coli, subunit b with its 156 residues extends with its soluble part (b sol ; b21-156) from the top of the F 1 sector down, into, and across the membrane, where it is associated with subunit a (2, 15, 32, 34). The 156-residue b subunit has been divided into four functional domains (28). They are, in order from the N to the C terminus; the membrane domain, the tether region, the dimerization domain, and the ␦-binding

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“…The linearity of the gradient was checked by performing diffusion measurements on water over different ranges of the gradient. The PFG longitudinal eddy-current delay pulse sequence (Gibbs & Johnson, 1991) was used for all self-diffusion measurements that were performed in D 2 0 over the temperature range 278 to 3 13 K. Peptide concentrations ranged from 0.05 to 20 mg/mL.…”

Section: Pulsed-field Gradient Nmr Self-difision Measurementsmentioning

confidence: 99%

A folding pathway for βpep‐4 peptide 33mer: From unfolded monomers and β‐sheet sandwich dimers to well‐structured tetramers

Mayo

Ilyina

1998

Protein Science

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It was recently reported that a de novo designed peptide 33mer, Ppep-4, can form well-structured P-sheet sandwich tetramers (Ilyina E, Roongta V, Mayo KH, 1997b, Biochemistry 36:5245-5250). For insight into the pathway of Ppep-4 folding, the present study investigates the concentration dependence of Ppep-4 self-association by using 'H-NMR pulsedfield gradient (PFG)-NMR diffusion measurements, and circular dichroism. Downfield chemically shifted a H resonances, found to arise only from the well-structured Ppep-4 tetramer state, yield the fraction of tetramer within the oligomer equilibrium distribution. PFG-NMR-derived diffusion coefficients, D, provide a means for deriving the contribution of monomer and other oligomer states to this distribution. These data indicate that tetramer is the highest oligomer state formed, and that inclusion of monomer and dimer states in the oligomer distribution is sufficient to explain the concentration dependence of D values for /.?pep-4. Equilibrium constants calculated from these distributions [2.5 X lo5 M" for M-D and 1.2 X lo4 M-' for D-T at 31 3 K] decrease only slightly, if at all, with decreasing temperature indicating a hydrophobically mediated, entropy-driven association/folding process. Conformational analyses using NMR and CD provide a picture where "random coil" monomers associate to form molten globule-like P-sheet sandwich dimers that further associate and fold as well-structured tetramers. /.?pep-4 folding is thermodynamically linked to self-association. As with folding of singlechain polypeptides, the final folding step to well-structured tetramer ppep-4 is rate limiting.

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A PFG NMR experiment for accurate diffusion and flow studies in the presence of eddy currents

Cited by 302 publications

References 8 publications

Binding Hot Spot for Invasion Inhibitory Molecules on Plasmodium falciparum Apical Membrane Antigen 1

Binding Hot Spot for Invasion Inhibitory Molecules on Plasmodium falciparum Apical Membrane Antigen 1

Solution Structure, Determined by Nuclear Magnetic Resonance, of the b30-82 Domain of Subunit b of Escherichia coli F ₁ F _o ATP Synthase

A folding pathway for βpep‐4 peptide 33mer: From unfolded monomers and β‐sheet sandwich dimers to well‐structured tetramers

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A PFG NMR experiment for accurate diffusion and flow studies in the presence of eddy currents

Cited by 302 publications

References 8 publications

Binding Hot Spot for Invasion Inhibitory Molecules on Plasmodium falciparum Apical Membrane Antigen 1

Binding Hot Spot for Invasion Inhibitory Molecules on Plasmodium falciparum Apical Membrane Antigen 1

Solution Structure, Determined by Nuclear Magnetic Resonance, of the b30-82 Domain of Subunit b of Escherichia coli F 1 F o ATP Synthase

A folding pathway for βpep‐4 peptide 33mer: From unfolded monomers and β‐sheet sandwich dimers to well‐structured tetramers

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Solution Structure, Determined by Nuclear Magnetic Resonance, of the b30-82 Domain of Subunit b of Escherichia coli F ₁ F _o ATP Synthase