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Kinetic study of the linear ising chain. comparison with ultrasonic absorption measurements in solutions of
polypeptides
Y. Dormoy, R. Cerf
To cite this version:
Y. Dormoy, R. Cerf. Kinetic study of the linear ising chain. comparison with ultrasonic absorption
measurements in solutions of polypeptides. Journal de Physique Lettres, Edp sciences, 1976, 37 (10),
pp.265-270. �10.1051/jphyslet:019760037010026500�. �jpa-00231289�
L-265
LE JOURNAL DE PHYSIQUE - LETTRES TOME 37, OCTOBRE 1976, PAGI
Classification Physics Abstra,~ts ’ 1.660 - 5.660 - 7.270
KINETIC STUDY OF THE LINEAR ISING CHAIN.
COMPARISON WITH ULTRASONIC ABSORPTION MEASUREMENTS
IN SOLUTIONS OF POLYPEPTIDES
Y. DORMOY and R. CERF
Laboratoire
d’Acoustique
Moléculaire(*)
UniversitéLouis-Pasteur, 4,
rueBlaise-Pascal,
67070Strasbourg Cedex,
France(Re.Vu
le6 fevrier 1976,
revise le28 juin 1976, accepte
le8 juillet 1976)
Résumé. 2014 La cinétique de la chaîne linéaire d’Ising a été traitée sans autre approximation que la
fermeture aux triplets et la réduction à quatre des équations cinétiques. On a étudié plus particulière-
ment l’influence des fluctuations du nombre
de séquences
ininterrompues d’élémentsidentiques
enintroduisant une variation de volume molaire 0394V liée à ces fluctuations. Par un choix
adéquat
des paramètres cinétiques, il est possible de prendre en compte au moins partiellement des interactions àlongue
distance et des effets de bouts de chaine. La théorie estappliquée
à l’étudecinétique
de latransition hélice-pelote des
polypeptides.
Pour une chaîne relativement courte d’acidepoly-1-glu-
tamique de masse moléculaire M = 12 000, qui est encore longue devant la distance de coopérativité,le déplacement du pic
d’absorption
ultrasonore dû à la relaxation 1 vers les hélicités élevées va depair avec
l’apparition
d’une contribution nonnégligeable
de l’absorption due à une seconde relaxa- tion.Les résultats
de la théorie sont en accord avec les mesures existantes, et l’on a pu évaluer le volume A V.Abstract. 2014 A study of the kinetics of the linear Ising chain has been carried out using as sole
approximations
the triplet closure and four kinetic equations. In particular, we have examined the effect of fluctuationsof the
number of uninterrupted sequences of the like elements by introducing amolar volume change 0394V associated with these fluctuations. Long range interactions and end effects
can be partially accounted for by a suitable choice of the kinetic parameters. The theory is
applied
to the kinetic study of the helix-coil transition of
polypeptides.
For arelatively
shortpoly-1-glutamic
acid chain of molecular weight M = 12 000 (which is still long compared with the
cooperativity
length) the shift of the ultrasonicabsorption
peak due to relaxation 1 isaccompanied by
a non- negligible contribution of the absorption associated with a secondrelaxation.
The theoretical results agree with existing measurements, and we have evaluated the volume 0394 V.1. Introduction :
time-dependent
statistics of the linearIsing
chain. - It is well known that variousbiological
functions of nucleic acids andproteins
are
governed by
conformations which are extre-mely
sensitive to small external effects. Suchhigh sensitivity
is the result of thecooperative
nature ofthe
elementary
steps of conformationalchanges.
The
importance
of the kineticaspects
of confor- mationalchanges
isequally
wellknown,
e.g., in the transfer ofgenetic
information or in the process ofenzymatic
reactions.Thus,
it isinteresting
to carryout kinetic studies based on
simple
models thatexhibit the
cooperative
aspects of theproblem.
Linear systems are
commonly
found among bio-polymers
andthey
furnishgood examples
thatreadily
lend themselves to both theoretical and expe-(*) E.R.A. au C.N.R.S.
’
rimental studies. Efforts have therefore been directed
by
many authors towards anunderstanding
of thetime-dependent
statistics of thesimplest cooperative
linear chain in which the interactions occur between
next-neighbors, i.e.,
the one dimensionalIsing
lattice.We shall denote
by
A and B the twopossible
statesof each element of the chain. An
example
of an A ~ Bconformational
change
will be discussed in section 3.In Schwarz’s model
[1] propagation
steps(AAB ~ ABB)
and nucleation steps(AAA ~ ABA;
BBB ~
BAB)
areconsidered
and a molar volumechange
6V is associated with the A ~ B conforma- tionalchange. Consequently,
fluctuations of the fractionp(B)
of elements in the B-formproduce
anoverall volume
change
and hence loss of energy inan ultrasonic wave. In aqueous
solutions,
the corres-ponding
attenuation coefficient isproportional
to[1] :
Article published online by EDP Sciences and available at http://dx.doi.org/10.1051/jphyslet:019760037010026500
L-266 JOURNAL DE PHYSIQUE - LETTRES N~ 10
where s is the
equilibrium
constant associated with the A ~ Bchange.
For along, highly cooperative chain, expression (1)
is maximum for s =1, i.e.,
forp(B)
= 0.5.In the present context we shall use a more
general scheme, proposed by
one of us[2, 3],
and in whichfluctuations of the number v of
uninterrupted
Aor
B-sequences
per molecule are also taken into account. This isdone by introducing
an average molar volumechange AV,
which is associated with the loss of oneuninterrupted A-sequence
per chain.It can be shown
by simple reasoning [2]
that thefluctuations of v contribute to the energy loss in an
ultrasonic wave and that for
relatively large
valuesof
p(B)
thecorresponding
attenuation is propor- tional to :where N is the number of elements
(A
orB)
per chain.The kinetic
theory
of the model considered herecan be
developed quantitatively
if thetriplet
closureapproximation recently proposed by
Schwarz[4, 5]
is used. Within this
approximation,
theprobability
of any sequence of elements of the chain is
expressed
in terms of
probabilities
of doublets andtriplets [4].
When the chain is very
long,
thetriplet
closureresults in the reduction of the number of rate equa-
tions,
which is apriori
of the order of2N,
toonly 4, i.e.,
thoseequations
which govern theprobabilities
of
singlets,
doublets andtriplets [4].
The kinetics is then described in terms of four relaxation times and of thecorresponding amplitude
factors.For
the model that includes the volumechange
AV the
triplet
closure has been shown[3]
to leadto
explicit expressions
both of the relaxationampli-
tude
A 1
associatedwith Schwarz’s longest
relaxationtime T 1 and of the
(A V) 2-proportional
contribution to theamplitude A2
associated with the second relaxation time T2[6].
Additional information can be obtained
by
nume-rical calculations. This will be shown in section 2 to furnish the contributions to
A2
that are propor- tional to(~ V )2
and to 6 V. A V. It alsopermits
avariation in the values of the three kinetic parameters of the model. This
possibility
will beexploited
insection 3 when the model is
applied
to a concreteexample.
2. Results of numerical calculations. - It is recalled that
according
to Schwarz[1]
three kinetic parametersare considered :
kD,
associated with thepropagation
step ABB -+AAB; o-/B A~,
associated with the nucleation step AAA --+ ABA andr/p kD
associatedwith the nucleation step BBB -+
BAB ;
a is theequilibrium
nucleation parameter of Zimm andBragg [7]
andkF
=skD. Except
infigures
5 and6,
the kinetic parameters
f A
andf B
are chosen to beequal
to 1.The
non-negligible
contributions to the ultrasonicabsorption
areproduced by
the relaxations associated with the twolongest
times’rl.and
i2.Figure
1 showsthe contributions
A 1
andA2
of relaxations 1 and 2 to thequantity :
for a constant
frequency
such that W7: 1M =2.5 ;
úJ is the circular
frequency
and 1’lM the maximum value reachedby 7:1
whenp(B)
is varied.FIG. 1. - Ultrasonic absorption per wavelenght A and A2 for the
two relaxation processes 1 and 2, and sum A 1 + A2 plotted against p(B) for or = 5 x 10 - 3, N = 100, A~/5~= 15, rotUI = 2.5,
In
expression (3),
A is thewavelength
of the ultra-sound, v
itspropagation velocity,
R the gas constant, T the absolutetemperature,
p thedensity
of themedium and c the concentration of chain elements in moles per unit volume.. The
quantities ~4i, A2
and
A 1 + A2
areplotted against p(B)
for the above value of cor lm and for a = 5 x10 - 3,
N =100, AV16V =
15. Thefigure
shows thedisplacement
ofthe
absorption peak
towards values ofp(B) larger
than
0.5,
asalready
discussed in references[2]
and[3].
It is seen that thedisplacement
is due to relaxa-tion 1.
Figure
2 illustrates and compares three differentapproximations
ofB1
=A l ~c~il/(1
+c~2 il)~ -1,
asdeduced from the
expression
for theamplitude
factor
A1
= 2013(bV)2 B1/(RT)
of relaxation1, given
FIG. 2. - Value of B =
A 1 I (J)t 1/(1
+ c~2’t"î) 1-1
as a functionof p(B) for the values of the parameters as in figure 1 : Curve I : approximate value of B1 ~iven by expression (4); Curve II : sum
of the (A~/5~)o and (A~~). proportional terms, calculated
numerically; Curve III : exact value of B 1.
L-267
N~ 10 KINETICS OF THE LINEAR ISING CHAIN
in reference
[3].
Atrelatively large
values ofp(B)
we
have,
to a firstapproximation [3] :
i.e., BI
is the sum of two terms that areproportional
to
(1)
and(2), respectively.
Thequantity (4)
is repre- sented infigure
2(curve I)
as a function ofp(B)
forthe
preceding
values of a,N and ~ V/8 V.
Curve IIrepresents
2?i
when the exact values of the termsproportional
to(4 V J~ Y)°
and to(AF/5F)
areretained,
and Curve III is calculatedusing
thecomplete
expres- sion ofBI
mentionedabove, i.e.,
in which the termproportional
to(t1 Y/b Y)2
is also retained. It is seenthat the
(e V/b V ) 2-term
enhances thedisplacement
of the
absorption peak
towardshigh
values ofp(B).
For A~/5~
10expression (4)
is anacceptable approximation
forB1.
Figure
3 represents the valuepm(B)
ofp(B)
forwhich
A 1
islargest
at agiven
value of thefrequency F, plotted against AV16V
for various values of W7:IM.The parameters have the same values as before.
The dotted lines
represent
the results of a firstapproxi-
mation
published
earlier[3].
FIG. 3. - Value of /?m(B) (at which A 1 is a maximum) plotted against A~75~ for different values of oTiM’ The parameters have the same values as in figures 1 and 2. Dotted straight lines represent
first approximation results (see reference [3]).
Figure
4 representskD(A1
+A2) jc~
which is pro-portional
tocxlf 2 plotted
as a functionof p(B)
forvarious values of DT~
(i.e.,
for variousfrequencies)
and for the values of the parameters
already
usedin the
previous figures.
3. Kinetics of the helix-coil transition of
poly-L- glutamic
acid. - The helix-coil transition ofpoly-a-
aminoacids
composed
of like units(i.e., polypep-
tides in which each amino acid residue
bears the same side groupe
R)
has beenthoroughly investigated
withregard
to both statistical and kinetic aspects. When dissolved in anappropriate solvent,
a helical
polypeptide
canundergo
asharp
transitionFIG. 4. - A quantity proportional to the amplitude of ex/ F2 due to
relaxations 1 and 2 is plotted against p(B) for ro’t 1M = 1, 2, 3, 4.
The parameters have the same values as in the, preceding figures.
to a
randomly
coiled chainwhen,
forexample,
thepH
is variedthrough
a certain range.In the a-helical
conformation,
thepeptide nitrogen
atom is
hydrogen-bonded
to thepeptide (carbonyl)
oxygen atom of the fourth residue down the chain.
The
randomly
coiled conformation results if thehydrogen
bonds aresevered, whereupon
intramo-lecular rotation occurs.
Each residue of the chain is therefore considered
to present
essentially
two conformations : the B orhelical
conformation,
as exhibited in the(x-helix,
and the A or coiled
conformation,
whichcorresponds
to a collection of rotational isomeric
forms; p(B)
now represents the
helicity
of thechain,
which we shall call0,
as usual. With thepreceding simplified picture
theequilibrium properties
of the system can be studiedby representing
thepolypeptide
chain asa linear
Ising
lattice[7].
Schwarz’s
approach
to the kineticproblem
amountsto
assuming :
1)
that we needonly
consider the fluctuations ofhelicity ;
2)
that interactions other than those betweenadjacent neighbors
can beneglected
in the kineticsL-268 JOURNAL DE PHYSIQUE - LETTRES No 10
if
1)
is true, in which case theIsing
model can be usedfor
treating
the kinetics.Various
experimental results,
as reviewedby
Schwarz and
Engel [8],
are in favor of the correctness of1)
forlong
chains.A deviation from the behavior described
by
Schwarz
has, however,
been observed for apoly-L- glutamic
acid of molecularweight
M = 12 000[9, 10],
thereafter called PLGA 2. For this
substance,
themolecules contain about 94 monomer units and are
still
long compared
with thecooperativity length
n =
a - 112
. We recall that n is the mean number ofmonomer units in one
uninterrupted
sequence of like elements at mid-transition. If thecurrently
admitted value of a for PLGA is
used, n
is of the order of 14.The above mentionned
experimentally
observeddeviation from ideal behavior consists in a
displace-
ment of the
absorption peak
from its value 0 = 0.5 for along
chain(see
section1)
to a valueOm lying
between 0.7 and 0.85.
It has been shown in references
[2]
and[3] (and
can also be seen in
figures
1 to4)
that the fluctuations of the number v ofuninterrupted
sequences of like elements per molecule offer apossible explanation
of this
displacement
of theabsorption peak.
The,
origin
of the mean volumechange
AV thatpermits
one to account for the fluctuations of v is
discussed
in detail in reference
[3].
It wassuggested that
AV results from a redistribution of the
segments
that were apart
of a lost disordered sequence among the other disordered sequences and that forces res-ponsible
for thestability
and conformational transi- tions ofproteins
are involved. _From this scheme it follows that D Y should increase when the molecular
weight
decreases. For PLGA 2a value of
~V/bV
of several units has beenproposed
as a reasonable estimate
[3].
It must now be
emphasized
that if wereject
Schwarz’s
assumption 1),
weshould,
inprinciple,
also
reject assumption 2), i.e.,
it isquestionable
whether the
Ising
model isapplicable
to ourproblem.
There are observations
suggesting
that2)
may not beentirely
correct, even in situations in which the fluctuations ofhelicity
are theprimary factor, i.e.,
situations in whichassumption 1)
is correct. We referin
particular
to the fact that the numerical value ofkD (or kF)
asexpected by
Schwarz(i.e., 1010- 1011 S-l)
iswidely
different from those foundexperi- mentally by
Barksdale and Stuehr for PLGA[11]
(i.e.,
8x107 s-1)
andby
ourselves(see below).
One is thus led to consider
kp
as an effective kineticparameter
and this may reflect inparticular
the factthat the
elementary growth
process involves ratherlong-range
movements of the chain relative to the solvent.It should be noted here
that, according
toEggers
and Funck
[12],
at concentrations as low as those usedby
Barksdale and Stuehr(i.e.,
a few10 - 3
moleof
residue/I),
and contrary to the result of the latterauthors,
no maximum of the ultrasonicabsorption
is observable when 0 is varied. It may be that isolated PLGA molecules
collapse
to a compact cluster atrelatively high
values of thehelicity,
thusproducing departures
from the behavior describedby
Schwarz.On the other
hand,
such acollapse
may beimpos-
sible at medium concentrations such as those used
by
Michels[9, 6] (i.e.,
of the order of10-1
moleresidue/I),
at which the PLGA molecules cannot be considered isolated and presententanglements.
Theelementary
steps of the Schwarz scheme may in thiscase remain of
primary importance.
From thispoint
of
view,
thenecessity
ofusing
an effective value ofkD
when
employing
theIsing
model may reflectpartly
intermolecular and
long
range intramolecular forces.Long
range interactions are of course critical when fluctuations of the number ofuninterrupted
sequences of like elements are
considered,
as is the casehere.
Indeed,
in order that two helical sequences may linktogether they
must beproperly positioned
in space, and this is very
improbable [13].
We can,however,
take this circumstance into accountby choosing
anf B-value
that issignificantly
smallerthan
unity.
Onemight
argue that such a choice off B unduly
diminishes theprobability
of the coilnucleation,
which does notdepend
on the abovegeometrical
condition for coalescence of twoneigh- boring
helical sequences.This
objection
is of littlepractical
consequence, since we shall becompelled
to choosef A larger
thanunity
when thetheory
is confronted with the measure- ments.Thus,
coilnucleation,
for which theprobability
is
crudely approximated
in ourdescription
turnsout to be the less
probable
process. In any event, it is lessprobable
than the reverse processby
a factorSU-l
and is even less
probable
than helixnucleation,
asa consequence of the choice of
f A. Thus,
theimpor-
tant processes in
producing
fluctuations of v for PLGA 2 are the helix nucleation and its reverse,i.e.,
thedisappearance
of a helix nucleus.It is
possible
that our scheme reflects the fact that conformationalchanges
are easier at an endof the molecule.
However,
we have no way of asses-sing
whetherf A
should be smaller athigh
molecularweight since,
in the presentframework,
athigh
M-values
only
the fluctuations ofhelicity
are ofimpor-
tance.
Thus,
the values off A
andf B
are reflectedneither in the relaxation time
(time ’t’1)
nor in thecorresponding amplitude. Therefore,
when consi-dering
the results obtained for asample
ofhigher
molecular
weight. (PLGA 1;
M = 90000),
we shalluse the same values of
f A
andf B
as for PLGA 2.In addition to the use of the
Ising
model itself and to the choice of thef A
andf B-values,
the assump- tions are those of reference[3],
i.e. :1)
when the chainlength
is not less than the coope-rativity length multiplied by
a factor ofunits,
theL-269
N~ 10 KINETICS OF THE LINEAR ISING CHAIN
four rate
equations
that govern the relevantproba-
bilities for a
long
chain can beapplied.
2)
for smallerchain-lengths, however,
we must choosecorrespondingly larger
values ofAV16V,
inaccordance with the mechanism that we assume is
producing ~ V.
It will now be shown that with these
assumptions
we can understand the results obtained for both PLGA 1 and
2, including
the hitherto unnoticed fact that thedisplacement
of theabsorption peak
of relaxation 1 in the 0-scale
(or
thepH-scale)
isconcomitant with the appearance of a second relaxa- tion.
Figure
5 is a doublelogarithmic representation
of
(A 1
+A2)m (i.e.,
themaximum
ofA 1 + A2
wheno is
varied) plotted against
W7: 1M. Curve acorresponds
to the values of (1,
N, A~/5~, f A
andf B already
used. In
comparison,
curbe b is obtained for6 = 3 x
10 - 3, E-VlbV
= 10 andf A
=5, f B
= 0.2.Relaxation 2 is
displaced
tohigher frequencies
whenf A
is greater thanunity.
Curve c shows the effect ofchoosing f B
= 5 instead of 0.2. Thecomparison
with the latest measurements of Michels for PLGA 1 and 2
[6]
isgiven
infigure
6. Sinceonly
relaxation 1 contributes to the ultrasonicabsorption
for PLGA 1and since both
samples
showcomparable absorption
.
at the lower
frequencies,
relaxation 2 must contributeonly slightly
in this range for PLGA 2. ThusA~75~
must be lower than a limit of the order of 10. Curve d is similar to b of
figure 5,
except thatf B
has beenchosen
equal
to 0.5. Infigure 6,
we have also repre- sented the theoretical curve e for along chain, using
the same values of the parameters as for curve
d,
except that N = 500 and AV = 0. The maximum value ’t 1M of thelongest
time for the twosamples
lie so close
together
that wilM represents a suitable variable.FIG. 5. - The maximum values of A + A2 (reached at variable 0)
are plotted as a function of Wt 1M : Curve a : ~ = 5 x 10-3,
N = 100, _~V/bV = 15, fA = fB = 1; Curve b : 7 = 3 x 10-3,
N = 100,A~~= 10, f~ 5, fB = 0.2; Curve c : 6 = 3 x 10 - 3,
N = 100, ~Y/bV = 10, fA = fB = 5.
It is
noteworthy
that thepresently
available dataare in agreement with
theory
when the same valuesof 6V
and kD
are chosen for the twosamples :
FIG. 6. - Comparison of the theory with the experimental results
of Michels for PLGA 1 (o ; N N 700) and PLGA 2 (~ ; N N 94).
The maximum conformational contribution to the ultrasonic
absorption divided by the frequency,
2013 ,
is plotted as a functionof the frequency for solutions at 2 x 10-2 g/cc in 0.2 M NaCl.
The theoretical curves are represented as in figure 5 : Curve d :
7 = 3 x 10-’, N = 100, AF/5~ 10, fA = 5, fB = 0.5; Curve e :
y = 3 x 10-3, N = 500, AV16V = 0, fA = 5, fB = 0.5.
0.58
cc/mole
of monomer 6V 0.7cc/mole
ofmonomer
Moreover,
this value of 6V is close to those which have been obtainedby
other methods[14, 15]
andthe
kD-values
is not very different from that deducedby
Barksdale and Stuehr[11]
from their ultrasonic measurements.The results discussed here furnish for the first time an
example
which suggests an effective contri- bution of relaxation 2 of the linearIsing
chain tothe ultrasonic
absorption. Furthermore,
inspite
ofthe limitation of the
model,
it is confirmed that the fluctuations of the number ofuninterrupted
sequences of like elements offer onepossible explanation
ofthe data available for PLGA 2.
We may,
however,
note asimilarity
between the results for PLGA 2 and those obtainedby Eggers
and Funck for a molecular
weight
between that of PLGA 1 and PLGA2, i.e.,
in both series ofexperi-
ments a shift of the maximum of ultrasonic
absorp-
tion towards
high
values of thehelicity
is exhibited.On the other
hand,
atequal weight concentration,
there are less
entanglements
for the lower molecularweight. Thus,
the PLGA 2 solutions areeffectively
more dilute than those of PLGA 1.
Therefore,
itmay be that the shift of the ultrasonic
peak
for PLGA 2and the concomitant appearance of a second relaxa- tion are the result of intramolecular
interactions,
as discussed earlier in this section in connection with the results ofEggers
and Funck.We intend to carry out further measurements under conditions in which the processes are slower
(kD smaller).
In this way, wehope
to be able tostudy
the second relaxation more
effectively
and evaluate its contribution to the ultrasonicabsorption
of PLGAwith greater accuracy.
L-270 JOURNAL DE PHYSIQUE - LETTRES No 10
References [1] SCHWARZ, G., Ber. Bunsenges. Phys. Chem. 68 (1964) 843.
[2] CERF, R., J. Physique Colloq. 33 (1972) C 6-99.
[3] CERF, R., Cooperative conformational kinetics of synthetic and biological chain molecules, in Adv. Chem. Phys. ed. Pri-- gogine et Rice (Interscience, New York) 1975, vol. XXXIII,
p. 73.
[4] SCHWARZ, G., Ber. Bunsenges. Phys. Chem. 75 (1971) 40.
[5] SCHWARZ, G., J. Theoret. Biol. 36 (1972) 569.
[6] CERF, R., DORMOY, Y., MICHELS, B., 15th International
Conference on Ultrasound, Prague, July 1976.
[7] ZIMM, B. H. and BRAGG, J. K., J. Chem. Phys. 31 (1959) 526.
[8] SCHWARZ, G. and ENGEL, J., Angew. Chem. 84 (1972) 615.
[9] MICHELS, B. and CERF, R., C. R. Hebd. Séan. Acad. Sci. D 274
(1972) 1096.
[10] MICHELS, B., Thesis, Université Louis-Pasteur, Strasbourg (1972).
[11] BARKSDALE, A. B. and STUEHR, J. E., J. Am. Chem. Soc. 94
(1972) 3334.
[12] EGGERS, F. and FUNCK, Th., Studia Biophysica, to appear.
[13] DE GENNES, P. G., J. Statist. Phys. 12 (1975) 463.
[14] RIFKIND, J. and APPLEQUIST, J., J. Phys. Chem. 86 (1964) 4207.
[15] NOGUCHI, H. and JEN TSI YANG, Biopolymers 1 (1963) 379.