A protein structure from nuclear magnetic resonance data

Kaptein, Robert; Zuiderweg, E.R.P.; Scheek, Ruud M.; Boelens, Rolf; Gunsteren, Wilfred F. van

doi:10.1016/0022-2836(85)90036-1

Cited by 468 publications

(230 citation statements)

References 13 publications

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“…(b and c) The short-and long-range interproton distance restraints shown as dashed lines, respectively, superimposed on a framework comprising a smoothed backbone (C, C", N) atom representation of the restrained energy minimized average structure (RDDG)m. minimization and restrained molecular dynamics in which the NOE interproton distances are incorporated into the total energy function of the system in the form of effective potentials (Kaptein et al, 1985;Clore et al, , 1986bBriinger et al, 1986).…”

Section: B I O C H E M I S T R Y (A)mentioning

confidence: 99%

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Clore¹,

Gronenborn²,

Nilges³

et al. 1987

Biochemistry

276

179

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The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 'H N M R spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional N M R techniques to identify through-bond and through-space (C5 A) connectivities. A set of 309 approximate interproton distance restraints is derived from the two-dimensional nuclear Overhauser enhancement spectra and used as the basis of a three-dimensional structure determination by a combination of metric matrix distance geometry and restrained molecular dynamics calculations. A total of 1 1 converged distance geometry structures were computed and refined by using restrained molecular dynamics. The average atomic root mean square (rms) difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 f 0.3 8, for residues 2-39 and 0.9 f 0.2 %, for residues 5-37. The corresponding values for all atoms are 1.9 f 0.3 and 1.4 f 0.2 A, respectively. The larger values for residues 2-38 relative to those for residues 5-37 arise from the fact that the positions of the N -(residues 1-4) and C-(residues 38-39) terminal tails are rather poorly determined, whereas those of the core of the protein (residues 5-37) are well determined by the experimental interproton distance data. The computed structures are very close to the X-ray structure of CPI in its complex with carboxypeptidase, and the backbone atomic rms difference between the mean of the computed structures and the X-ray structure is only 1.2 A. Nevertheless, there are some real differences present which are evidenced by significant deviations between the experimental upper interproton distance limits and the corresponding interproton distances derived from the X-ray structure. These principally occur in two regions, residues 18-20 and residues 28-30, the latter comprising part of the region of secondary contacts between CPI and carboxypeptidase in the X-ray structure.Carboxypeptidase inhibitor (CPI)' is a small 39-residue protein that binds tightly to both carboxypeptidase A (Kl -5 X

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Section: B I O C H E M I S T R Y (A)mentioning

confidence: 99%

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Clore¹,

Gronenborn²,

Nilges³

et al. 1987

Biochemistry

276

179

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“…u-helices or [3-turn. The other ones are located in highly structured parts of the protein: G11 and V12 are components of the turn in the helix-turn-helix motif typical of this DNAbinding protein family [18]; G23, R29 and V30 are involved in the rather tight segment connecting helices 2 and 3 [2]. (ii) amide protons exchanging on the intermediate time scale (ms to s) can be divided into two classes: not surprisingly, the first one is found either in the N-terminal flexible part of FruR(1-57)*, (residue 3) and close to its C-terminal part (residues 47 to 59).…”

Section: A Brckmann Et Al/febs Letters 383mentioning

confidence: 99%

Rapid estimation of relative amide proton exchange rates of ¹⁵N‐labelled proteins by a straightforward water selective NOESY‐HSQC experiment

1996

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A straightforward heteronuclear pseudo-3D NOESY-HSQC pulse sequence using radiation damping to selectively invert magnetization at the water frequency was developed to estimate the amide proton exchange rates in lSN-labelled proteins. The peak intensities in the resultant 2D spectrum allow a direct classification of amide proton exchange rates according to short (ms), intermediate (ms to s) or long (---s) residence times. This method was successfully used for the analysis of amide proton exchange rates in the mSN-labelled FruR DNAbinding domain and pertinent information about its dynamics was obtained.

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“…Nuclear Overhauser Effect (NOE) intensities can be converted to a set of upper bounds {ry 6 } to the distances between atoms (hydrogens) 1 and j , which leads to a socalled distance restraining function (Kaptein et al 1985).…”

Section: W F Van Gunsteren Et Almentioning

confidence: 99%

Fundamentals of drug design from a biophysical viewpoint

Gunsteren¹,

King²,

Mark³

1994

Quart. Rev. Biophys.

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A protein structure from nuclear magnetic resonance data

Cited by 468 publications

References 13 publications

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Rapid estimation of relative amide proton exchange rates of ¹⁵N‐labelled proteins by a straightforward water selective NOESY‐HSQC experiment

Fundamentals of drug design from a biophysical viewpoint

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A protein structure from nuclear magnetic resonance data

Cited by 468 publications

References 13 publications

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Rapid estimation of relative amide proton exchange rates of 15N‐labelled proteins by a straightforward water selective NOESY‐HSQC experiment

Fundamentals of drug design from a biophysical viewpoint

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Rapid estimation of relative amide proton exchange rates of ¹⁵N‐labelled proteins by a straightforward water selective NOESY‐HSQC experiment