Nuclear Magnetic Resonance Spectroscopy in Molecular Biology: Proceedings of the Eleventh Jerusalem Symposium on Quantum Chemistry and Biochemistry Held in Jerusalem, Israël, April 3–7, 1978

526 Pages·1978·25.44 MB·English

by  David G. Gorenstein (auth.)

NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
IN MOLECULAR BIOLOGY
THE JERUSALEM SYMPOSIA ON
QUANTUM CHEMISTRY AND BIOCHEMISTRY
PubllMMl by the Ismel ACIIdemy ofS cienca I11III HU1nll1litiel,
distributed by Academic Press (N. Y.)
lit JERUSALEM SYMPOSIUM: Th, Phy,'cocherniCflI A.pect. 0/ Carcinogenllis
(October 1968)
2nd JERUSALEM SYMPOSIUM: Quturtum Asp«t. 0/ H"erocydk Compountb".
Chernutry _ Biochemutry (April 1969)
3rd JERUSALEM SYMPOSIUM: NomtlIlclly, I'I8uJo.Aromtllldly, Antitlromatlclly
(Apri11970)
4th JERUSALEM SYMPOSIUM: The Purine.: Theory and Experiment
(Apri11971)
5th JERUSALEM SYMPOSIUM: The Co'fformation 0/ Biological Molecule. and
Polym• • (April 1972)
PubllWd by the lnel ACIIdemy ofS cienca IIIIIl HU1nII1Iities,
distributed by D. R,idel Publishing Company (Dordrecht, Boston and London)
6th JERUSALEM SYMPOSIUM: Ch,mlCflI and BiochemlCflI Reactivity
(April 1973)
PubllMed and distribuml by D. Reidel Publilhlng Company
(Dordrecht, Boston and London)
7th JERUSALEM SYMPOSIUM: Molecultlr and Quantum Pharmacology
(MarchI April 1974)
8th JERUSALEM SYMPOSIUM: EnvIro",.,.tal FIIect. on Mokcultlr Strucfure _
Pro~t_ (Aprill97')
9th JERUSALEM SYMPOSIUM: M",,~Ligtllld lntertlCtlo",,,. Orpn;c Chemutry
and Bloch,mistry (April 1976)
10th JERUSALEM SYMPOSIUM: Excited States in Organic Chemi,try and
Biochemi,try (March 1977)
VOLUME 11
NUCLEAR MAGNETIC
RESONANCE
SPECTROSCOPY IN
MOLECULAR BIOLOGY
PROCEEDINGS OF THE ELEVENTH JERUSALEM SYMPOSIUM ON
QUANTUM CHEMISTRY AND BIOCHEMISTRY HELD IN
JERUSALEM, ISRAEL, APRIL 3-7, 1978
Edited by
BERNARD PULLMAN
UnlP.n/~ PI.". .t Mart. Curt. (PARIS YI)
In,tlrut d. Blolo,l. Phy,'eo-Ch'miqu.
(Pondiltlon Edmond d. RothrchOd). Part• • P",nc.
D. REIDEL PUBLISHING COMPANY
DORDRECHT : HOLLAND I BQSTON : U.S.A.
LONDON:ENGLAND
Libluy of Coqr:ea Catllosins in PUblication Data
Jerusalem Symposium on Quantum Olemistry and Biochemistry,
llth,1978.
Nuclear magnetic msonance spectroscopy in molecular biology.
(The Jerusalem symposia on quantum chemistry and biochemistry; Y. 11)
Includes bibliographical mfemncel and index.
1. Nuclear magnetic msonance spectroscopy-Congresses. 2. Molecular biology-
Technique-Congresses. I. Pullman, Bernard, 1919- II. Title. III. Series.
QH324.9.N8J47 1978 574.1'92'028 78-13426
ISBN-13: 978-94-009-9884-1 e-ISBN-13:978-94-009-9882-7
DOl: 10.1007/978-94-009-9882-7
Publisbed by D. Reidel PublillhiDa Company,
P.O. Box 17, Dordrecht, Holland
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AU Riahts Reserved
CopyriJhtC1978 by D. Reidel Publilhlq Company, Donlrecht, Holland
Softcover reprint of the hardcover 15t edition 1978
No part or the material protected by tbiI copyript notice may be reproduced or
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PREFACE
The 11th Jeruaalem SympOlium continued the tradition of the pIe __t
and excitiDs meetiDp wbich 0DCe a year &ather dlJtingni,bed ICientiltl, the wodd's most
renowned experts in a specific field of quantum chemistry and biochemistry. in the
impressive IUrroundinp of the Israel Academy of Sciences and Humanities.
We wiah to thank aU those who made this meetiDg pOllible and contributed
to its IUcceSS: the Baron Edmond de Rothschild whOle continuous generosity suarantees
the perenniality of our venture, the Israel Academy of Sciences and Humanities and in
particu1ar its President Professor A. DvoIItIky, the Hebrew UDivenity of Jerusalem, and
Professor David GiDsburg, for their devoted co11aboration. Mn. Abipil Hyam must be
thanked for her decisive contribution to the efficiency and IUCcess of the local
IIIIII1geDleJlts.
Bernard Pulhnan
v
TABLE OF CONTENTS
~~e v
D. G. Gorenstein / P-31 NMR of nucleic acids. Bond angle and torsional effects 1
H. lwahashi and Y. Kyogoku / NMR studies on dynamic properties of nucleic acid
base pairs in nonaqueous solvents 17
M. M. Dhingra and R. H. Sarma / NMR studies and minimum energy confonnation
calculations on the S'-tenninus of mammalian mRNA 31
H.-D. Ludemann and E. Westho/ / Solution confonnations of purine (JJ) nucleosides
and analogs 41
P. Biichner, F. Blomberg, and H. Ruterjans / Nitrogen-IS nuclear magnetic
resonance spectroscopy of lSN-Iabeled nucleotides. Investigations of
Ribonuclease A -Nucleotide interactions S3
D. B. Dallies / Co-operative confonnational properties of nucleosides, nucleotides
and nucleotidyl units in solution 71
C Altona, A. J. Hartel, C S. M. Olsthoom, H. P. M. de Leeuw, and C A. G.
HfJIlsnoot / The quantitative separation of stacking and self-association
phenomena in a dinucleoside monophosphate by means of NMR
51-
concentration-temperature profiles: 6-N{dimethyl) adenyly1{3',
uridine 87
K. G. Wagner, H.-A. Ar[mann, R. Lawaczeck, K. Opatz, I. Schomburg, and V. Wray /
The contn'butions of the purine nitrogens to stacking association 103
S. S. Danyluk, C. F. Ainsworth, and M. MacCoss / Methylation effects on nucleic
acid confonnations 111
viii TABLE OF CONTENTS
P. Davanloo-Ma/herbe, M. Sprinzl, and F. Cramer / Structural studies on the yeast
tRNAPhe by the 1H NMR of modified bases. Effect of removal of the Y base
and anticodon binding 125
T. R. Krugh / Spectroscopic Studies of drug-nucleic acid interactions 137
B. McConnell/ A model for the specifIC site melting of DNA in vivo 147
C Giessner-Prettre and B. Pullman / On the confonnational dependence of the
proton chemical shifts in nucleosides and nucleotides. IV. Proton
chemical shifts in 3'- nucleotides as a function of different confonnational
parameters 161
R. B. Mallion / Some comments and comparisons concerning the use of 'ring-
current' calculations in elucidating molecular confonnations 183
H. GUnther, A. Gronenbom, U. Ewers, and H. Seel (Carbon-13 NMR results
in the freld of nitrogen heterocycles: the detection of proton ation sites 193
K. WUthrich, G. Wagner, and A. Bundi / NMR studies of the molecular dynamics
of peptides and proteins 201
R. Kaptein / Structural infonnation from photo-CIDNP in proteins 211
F. Blombe1g and H. Riiterjaru / Nitrogen 15 nuclear magnetic resonance
investigations on amino acids 231
H. Egli, U. Vogeli, and W. Von Philipsbom / One-bond C, H coupling constants,
a new parameter in confonnational studies of peptides? The cyclo-
s~o~k ~7
D. Cheshnovs/cy and G. Novon / NMR saturation transfer studies of the catalysis
of the reversible hydration of acetaldehyde by carbonic anhydrase 261
y. lmonishi and S. Kimura / Confonnation and interaction with small molecules
of cyclic hexapeptides as studied by nuclear magnetic resonance
spectroscopy and circular dichroism 273
R. Deslauriers, P. Tancrede, W. H. McGregor, D. Sarantakis, R. L. Somorjai,
and I. C P. Smith / 13NMR studies on OPIOID peptides; 13C-enriched
methionine-enkephalin and a-endorpbin 285
J. Feeney / NMR studies of selectively deuteriated and fluorine labelled
dihydrofolate reductase 297
L. J. Berliner and B. H. Landis / Studies of 19F labeled met-192 chymotrypsin:
an NMR study of an activating moiety near the catalytic serine 311
H. Follmann / Principles in substrate and confonnation specificity of
nuc1eotide-convertinS enzymes 323
TABLE OF CONTENTS ix
B. Birdsall/ Cooperativity in the binding of ligands to dihydrofolate
reductase 339
c
W. Hilbers, G. J. Gansen, R. Kaptein, J. G. G. Schoenmtlkers, and J. H.
van Boom / Studies of gene-5 protein nucleic acid interaction 351
T. Schleich, R. G. Gonzalez, and B. J. BlIlckburn / Structural elucidation
studies of aurintrlcarboxylic acid, a potent inhibitor of protein
nucleic acid interactions 365
R. A. Haberkorn, J. Herzfeld, and R. G. Griffin / Magic angle sample spinning
in inhomogeneously broadened spin systems - application to unsonicated
phospholipid bilayers 381
H. Degani / Ionic permeabilities of membranes; NMR kinetic studies 393
L Tamir, D. Lichtenberg, and R. Mechoulam / Interaction of cannabinoids
with model membranes -NMR studies 405
G. Gatti / NMR spectra of mucopolysaccharides 423
A. Lapidot and C S. Irving / An in vivo 15N NMR study of bacterial cell walls 439
R. J. Abraham / The application of aromatic ring currents in the elucidation
of drug-ligand and metallo-porphyrin complexations 461
M. Goldberg and H. Gilboa / Sodium magnetic resonance in biological systems.
Interpretation of the relaxation curves 481
J. A. G. Drake and D. W. Jones / NMR spectroscopy of tricyclic non-altemant
systems containing seven-membered rings, dibenz [b, fJ oxepine and
dibenz [b, fJ azepine: parents of pharmacologically active systems 493
D. B. Davies / Appendix: Discussion document on nomenclature 509
Index of Subjects 517
Index of Namel 524
P-31 IMR 011' IUCLEIC ACIDS. BORD ANGLE .AIm TORSIONAL El'F.l!:CTS
DAVID G. GORENSTED
Department of' Chemistry, University" of' Illinois, Chicaso Circle
Chicago, Illinois 60680, U.S.A.
1. INTRODUCTION
The P-3l Nucleus has preTen to be an extremely usef'ul n.m.r.
probe of' phosphates in biochemical Q'stems. In order to maximize
the amount of information obtainable from a study of' P-3l n.m.r.
spectra, we must be able to assess the extent to which structural
and enviromnental changes perturb P-31 chemical shifts. In this
paper we wish to first discuss those f'actors which alter P-31
chemical shifts and then to use this inf'ormation as a probe of'
the structure of' nucleic acids.
We have recently described an empirical correlation between
P-3l chemical shifts and o-P-O bond angles in phosphates (1). As
shown in Figure 1, f'or a wide variety of dif'f'erent alkyl phosphates
(mono-, di-, and triesters, cyclic and acyclic, neutral, monoanionic,
and dianionic structures) a decrease in the smallest O-P-O bond
ansle in the molecule results in a de shielding of' the 1'-31 nucleus.
The correlation possibly provides an explanation f'or the unusual
downfield shift observed upon ionization of an acyclic monoanion.
The £!. 30 reduction in the O-P-O bond angle of' the dianionic phosphate
is consistent with the 4 ppm dawnf'ield shift. Charge alone is not
responsible for the deshielding since the acyclic mono anion and free
acid have similar chemical shifts (and significantly, similar O-P-O
bond angles).
Pursuing the theoretical foundation f'or this bond angle effect
we have indeed been able to calculate a bond angle sensitivity to the
P-3l shif'ts. Most significantly, however, these calculations also
revealed a torsional. angle sensitivity to these shifts. These semi
empirical molecular orbital, chemical shift calculations (see details
in ref'erence 2) suggested that a phosphate diester in a gauche,gauche
(g,g) contor.mation (structure I Figure 2) should have a P-3l chemical
shift substanti~ upfield (by at least several ppm) from a phosphate
diester in a gauche, trans conf'ormation (g, t i structure II Figure 2)
1
.. "'. .. ,-}. Nut:IIt!tu "..* RatRIIIIIa Spel1Wl:Opy ill ...., ., BIDIDD. 1-15.
M RJ;r,. Rnttnetl. O1P.JIriI#It 0 1'78 by D. R.eItBl "'bIUII",. c:r.r,-".IJordnIt:IJI. HoIIatL
D. G. GORENSTEIN
2
"'\
-10
-10
1
•
I
_.-_
_.,. -
...... 0-"-0 .A. NILI,· ..
.... ' I1p_ .... _ ............ _ ... IW'-O __
__: 0."_ __"
__liii0_ ... ...._ _ ...._ .. .....,-.. . . _.
UaPO.~
Figure 2. Structure of a dinucleoside monophosphate. UpA in the gauche. gauche. I. and
gauche, trans, I~ phosphate ester conformations. From Sundaralingam (21).
Actually the bond angle effect and torsional angle effect are
not unrelated phenomena sinc.e Gorenstein, et al (3-5) and Perahia and
Pullman (6) have established a coupling of phosphate ester bond angles
with these torsional angles. As shown in Figure 3 a bond angle/
torsional angle energy surface for dimethyl phosphate was computed
with the eRDO molecular orbital method (see computational details in