Welcome to the UMDNJ
Circular Dichroism Facility
Home Page
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About The Circular Dichroism Facility
The
Data can be collected as a
function of temperature or time on up to five samples simultaneously.
Qualified personnel are available to collect spectra and thermal denaturation
experiments for researchers who do not have easy access to the center and to
help with data analysis.
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About
The Technique of Circular Dichroism
Circular Dichroism is an
excellent method for analyzing protein and nucleic acid secondary structure in
solution. It can be used to follow the changes in folding as a function of
temperature, and is also useful for measuring protein-ligand and nucleic
acid-ligand interactions.
There are several useful
introductions to CD on the web
http://www.newark.rutgers.edu/chemistry/grad/chem585/lecture1.html
http://www.enzim.hu/~szia/cddemo/edemo0.htm
http://www.ruppweb.org/cd/cdtutorial.htm
To download a pdf file with
an introduction to CD click here
For a slide show on the use of
CD to analyze protein conformation in solution click
here
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Rates for Using the Circular Dichroism Facility
The UMDNJ
Circular Dichroism facility is open to the entire scientific community.
Rates
effective
Academic
users (campus/in-house)
Instrument time (based on lamp usage)
1. $40 per hour for the first 20 hours within a
year. After 20 hours, use will be billed at $20 per hour. The Ayear@ will be calculated from the beginning
of the quarterly billing cycles.
2. The maximum charge for a 24 hour period will be
$350. Overnight users must vacate the instrument by
Operator time
Services of the Director (training, running an experiment or
data analysis etc.): $50 per hour.
Introductory training offer
All new users must receive training and be authorized by the
Director for independent use.
$500 Includes discussion of experimental
design and sample preparation, one day (up to 8 hours) of instrument time and
instruction in methods of data analysis in preparation for independent use.
Outside
academic rates: 20% higher than the academic rate
Industrial
users
Instrument time:
$200 per hour. Includes services of operator.
$100 per hour for instrument time when operated by a trained user
Operator time: $100 per hour for
off-line data analysis and creation of publication quality figures
Rates for major industrial users are negotiable.
Industrial
and outside academic users must have a purchase order prior to using the
instrument.
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Directions to the Circular Dichroism Facility
From Route 18:
Take Route 18 North to the
(Take an elevator to the
basement). Turn in the direction opposite the animal labs and continue through
all of the sets of double doors, past the stock room, until the corridor ends.
Make a left turn. The CD lab is on the left.
From the NJ. Turnpike North or
South. Take the Turnpike to Exit 9 to Route 18 North.
Follow the instructions above
from Route 18.
From Route 1, North or South.
Take Route 1 to Route 18 in
Follow directions above from
Route 18.
From Route
Take
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Free Software for the Analysis of Circular Dichroism Data
This site
contains programs for analyzing circular dichroism data by:
1. The method of
least squares (LINCOMB and MLR)
2. The
ridge regression procedure of Provencher and Glöckner (CONTIN)
3. The
Variable Selection Method of Johnson and Coworkers (VARSLC)
4. The
Self-Consistent Method of Sreerama and Woody (SELCON)
5. A neural
net analysis program of Andrade et al. (K2D)
6. The
convex constraint algorithm of Fasman and coworkers (CCA)
7.
Singular Value Decomposition (SVD).
Software is also
provided to convert output files from AVIV and JASCO CD machines to the correct
file formats needed for each program.
In addition there are
links to other sites with recent very good programs for analyzing CD data.
TABLE 1 compares the
agreement of the secondary structures calculated by each program with that
found by X-ray crystallography for 16 proteins and poly-L-glutamate.
Software Available at this Web
Site:
Two self extracting files,
which contain programs for estimating protein secondary structure from CD data,
can be downloaded from this web site. They are: CD1.EXE and CD2.EXE (right click on file names to download.) These files are DOS files. The programs
run under DOS, or in DOS windows in Windows 95, 98, XP or OS/2. Make a
directory to house the files - e.g. type "mkdir cd" copy CD1.EXE to
the directory e.g. type "copy cd1.exe cd" enter the cd directory by
typing "cd cd" Type "CD1 -d" to unzip the file. The
"-d" is necessary to keep the correct paths. The files can
also be unzipped using WinZip. Make a subdirectory to house the K2D
program. e.g. type mkdir \cd\k2d. Copy the CD2 file to the k2d subdirectory
e.g. type "copy cd2.exe \cd\k2d" Unzip the k2d program by typing CD2)
The files created by
CD1.EXE and CD2.EXE are described more fully below. Please read the instructions before using these files. Occasionally these files do not download
properly. Some web browsers download them as ASCII files. If the files do not
download properly, send email to greenfie@umdnj.edu
and she will email the files to you.
A program deconvoluting sets of
data into its components using singular value decomposition can also be
downloaded from this site. This program runs under Windows 95/98 or NT. The
file is a gift from Takashi Konno. The file is called SVD1.EXE (right click on file name to download.)
Instructions for the SVD program are in the file README.SVD (right click on the file name to download.)
Other useful files:
THERMODYNAMICS contains
useful files in SigmaPlot formats for calculating thermodynamic properties of
the folding of peptides and proteins from CD data.
BINDING CONSTANTS
contains useful files in SigmaPlot formats for calculating binding constants
from changes in CD as a function of ligand concentration.
Software Available from other
sites:
Neural Net Software:
Three useful Neural Net
programs are K2D, SOMCD and CDNN.
K2D and SOMCD are available directly on the Web.
References: K2D, Andrade et al., 1993 SOMCD Unneberg et al.,2001.
Unfortunately, the CDNN program by G. Bohm
is no longer on the web.
Selcon and Variable Selection:
The latest version of SELCON
called SELCON3 and two
additional programs, CONTINLL, a modified version of CONTIN by Provencher &
Glöckner and CDSSTR
from W.C.Johnson are provided in a package called CDPro which is available from Narasimha Sreerama.
References:
Sreerama and Woody, 2000, Provencher and Glöckner, 1981, Johnson, 1999.
Home Pages:
Link
to Provencher
Link to Johnson
CCA Algorithm
A version of the CCA
algorithm which runs under Windows 3.1 is available on the web on the CCA home
page.
Reference: Perczel et al., 1992
Instructions
for using the programs in CD1.EXE and CD2.EXE:
The computer programs created by
running CD1.EXE and CD2.EXE are compiled programs which will run on IBM
compatible computers. In addition the files create programs to convert
data collected on AVIV, JASCO and OLIS, instruments to the required format for
each program.
Instructions and references for
each program are in the files named README.1ST in each subdirectory.
In most cases the source code
is included in FORTRAN, QBASIC or C. The FORTRAN programs can be compiled
and run on UNIX based machines. The programs are all very primitive. To use the
programs one first must convert the CD data into the proper format for each
program using the programs called CDCONVRT or RAW2XXX, where XXX are the
first three letters of the name of the subdirectory with the programs of
interest. (Note at present only the CDCONVRT program can be used with OLIS
data.) The easiest method of converting the data is to enter the
subdirectory containing the analysis program of interest and run the conversion
programs from that directory. That way the files needed for each program will
be in the proper directory.
After converting the data one
runs the analysis program. Then one reads the output files with a text editor.
(Note that most of the output files have different names, e.g. output, out.out,
etc. ) In some cases, the calculated best fit curves can be viewed using
programs called PLOTXXX. Complete directions and references are in the files
called README.TXT in each subdirectory.
CD1.EXE will create the
following subdirectories: CCA, CONTIN, JOBIN, LINEAR, SELCON, USEFUL and VARSLC
LINEAR contains three programs
for fitting data using least squares regression.
MLR.EXE is a non-constrained
least squares analysis program.
LINCOMB.EXE is a constrained
least squares analysis program of Fasman.
Perczel,
A., Park, K., and Fasman, G.D. (1992) Anal. Biochem. 203, 83-93.
G&F.EXE is the original
method of
CONTIN contains the ridge
regression procedure of Provencher and Glöckner.
SELCON contains programs to
estimate protein conformation using the self-consistent method of Sreerama and
Woody.
Sreerama, N and
Woody, R.W. A self-consistent method for the analysis of protein secondary
structure from circular dichroism.
Anal
Biochem. 1993 Feb 15;209(1):32-44.
Sreerama N and Woody, R.W.
Protein secondary structure from circular dichroism spectroscopy. Combining variable
selection principle and cluster analysis with neural network, ridge regression
and self-consistent methods. J
Mol Biol. 1994 Sep 30;242(4):497-507.
Sreerama
N, Woody RW. Poly(pro)II helices in globular proteins: identification and
circular dichroic analysis. Biochemistry.
1994 Aug 23;33(33):10022-5.
VARSLC contains the variable
selection program of Manavalan and Johnson.
Manavalan, P., and Johnson,
W.C. Jr.
Variable selection
method improves the prediction of protein secondary structure from circular
dichroism spectra.
Anal
Biochem. 1987 Nov 15;167(1):76-85.
Link to Johnson
CCA contains the convex
constraint algorithm of Perczel et al.
References for the CCA program:
Perczel,
A., Holl¢si, M., Tusnady, G., and Fasman, G.D. (1991) Prot. Eng. 4, 669-679.
Perczel,
A., Park, K., and Fasman, G.D. (1992) Anal. Biochem. 203, 83-93.
CD2.EXE is a self extracting
file containing the K2D program of Andrade et al .
Andrade,
M.A., Chacon, P., Merolo, J.J., and Moran, F. (1993) Prot. Engin. 6, 383-390.
USEFUL is a subdirectory with
files containing protocols for protein determination and for estimating the
helical content of proteins from the ellipticity at 222 nm and 208 nm. JOBIN
contains programs for converting files from JOBIN spectrometers to a format
which can be used by the analysis programs (The Jobin conversion programs have
not been debugged since I did not have access to the raw data files.)
The installation disks will
also create the program called CDCONVRT.EXE that can convert any x,y file of CD
data, where x is wavelength in nm and y is ellipticity in millidegrees or mean
residue ellipticity, to the proper formats for the SELCON, VARSLC, CONTIN, K2D,
LINCOMB, MLR and G&F programs. The intervals between the data points must
be even and the data file may not have spaces between lines. Data sets must
begin and end at integer values of wavelengths, e.g. 180.0 nm, not 180.5. The x
and y values may be separated by commas, spaces or tabs but each x,y pair must
be on a separate line. The order of the wavelengths does not matter, they may
either increase or decrease. When the output is for the SELCON program, the
output file must be named or renamed test.dat before the SELCON program is run.
If you have any problems with
the conversion programs, the simplest solution will be to email me a sample
data file. I will try to figure out the problem and fix the conversion
programs.
My current email address is greenfie@umdnj.edu. After July
1, 2007 I can be reached at normajg@bellatlantic.net.
After July 1, for questions
about the CD facility contact:
Alla S. Kostyukova, Ph.D.
Department of
Neuroscience and
675
Telephone 732-235-5791
or 732-235-4528
FAX 732-235-4029
Research Articles, Notes and Reviews Related to Circular Dichroism
Review Articles:
Greenfield, N.J.
Determination of the folding of proteins as a function of denaturants,
osmolytes or ligands using circular dichroism. Nat Protoc. 1(6):2733-41. PubMed
Article
Adler, A.J., Greenfield,
N.J. and Fasman, G.D. (1973) Circular dichroism and optical rotatory dispersion
of proteins and polypeptides. Methods. Enzymol. 27 part D: 675-735. PubMed
Representative publications by users of the
CD facility:
Ackerman MS, Bhate M, Shenoy N, Beck K, Ramshaw JA, Brodsky B. 1999. Sequence dependence of the folding of collagen-like peptides. Single amino acids affect the rate of triple-helix nucleation. J Biol Chem 274(12):7668-73. PubMed10075654
Baum J,
Brodsky B. 1999. Folding of peptide models of collagen and misfolding in
disease. Curr Opin Struct Biol 9(1):122-8. PubMed10047579
Beck K, Chan
VC, Shenoy N, Kirkpatrick A, Ramshaw JA, Brodsky B. 2000. Destabilization of
osteogenesis imperfecta collagen-like model peptides correlates with the
identity of the residue replacing glycine. Proc Natl Acad Sci U S A
97(8):4273-8. PubMed10725403
Bhate M,
Wang X, Baum J, Brodsky B. 2002. Folding and conformational consequences of
glycine to alanine replacements at different positions in a collagen model
peptide. Biochemistry 41(20):6539-47. PubMed12009919
Brodsky B,
Li MH, Long CG, Apigo J, Baum J. 1992. NMR and CD studies of triple-helical
peptides. Biopolymers 32(4):447-51. PubMed1623141
Buevich AV,
Silva T, Brodsky B, Baum J. 2004. Transformation of the mechanism of
triple-helix peptide folding in the absence of a C-terminal nucleation domain
and its implications for mutations in collagen disorders. J Biol Chem
279(45):46890-5. PubMed15299012
Chan VC,
Ramshaw JA, Kirkpatrick A, Beck K, Brodsky B. 1997. Positional preferences of
ionizable residues in Gly-X-Y triplets of the collagen triple-helix. J Biol
Chem 272(50):31441-6. PubMed9395477
Chatterjee
S, Jiang W,
Chen CY,
Reese ML, Hwang PK, Ota N, Agard D, Brodsky FM. 2002. Clathrin light and heavy
chain interface: alpha-helix binding superhelix loops via critical tryptophans.
Embo J 21(22):6072-82. PubMed12426379
Dennison SM,
Deprez P,
Doss-Pepe E, Brodsky B, Inestrosa NC. 2000. Interaction of the collagen-like
tail of asymmetric acetylcholinesterase with heparin depends on triple-helical
conformation, sequence and stability. Biochem J 350 Pt 1:283-90. PubMed10926855
Doss-Pepe E,
Deprez P, Inestrosa NC, Brodsky B. 2000. Interaction of collagen-like peptide
models of asymmetric acetylcholinesterase with glycosaminoglycans:
spectroscopic studies of conformational changes and stability. Biochemistry
39(48):14884-92. PubMed11101304
Egger LA,
Inouye M. 1997. Purification and characterization of the periplasmic domain of
EnvZ osmosensor in Escherichia coli. Biochem Biophys Res Commun
231(1):68-72. PubMed9070221
Falzon L,
Patel S, Chen YJ, Inouye M. 2007. Autotomic behavior of the propeptide in
propeptide-mediated folding of prosubtilisin E. J Mol Biol
366(2):494-503. PubMed17169372
Farnsworth
PN, Frauwirth H, Groth-Vasselli B, Singh K. 1998. Refinement of 3D structure of
bovine lens alpha A-crystallin. Int J Biol Macromol 22(3-4):175-85. PubMed9650072
Farnsworth
PN, Groth-Vasselli B, Greenfield NJ, Singh K. 1997. Effects of temperature and
concentration on bovine lens alpha-crystallin secondary structure: a circular
dichroism spectroscopic study. Int J Biol Macromol 20(4):283-91. PubMed9253648
Flach CR, Brauner JW, Taylor JW, Baldwin RC, Mendelsohn R.
1994. External reflection FTIR of peptide
monolayer films in situ at the air/water interface: experimental design,
spectra-structure correlations, and effects of hydrogen-deuterium exchange.
Biophys J 67(1):402-10. PubMed7919013
Gao Y,
Gilbert SM,
Wellner N, Belton PS, Greenfield JA, Siligardi G, Shewry PR, Tatham AS. 2000.
Expression and characterisation of a highly repetitive peptide derived from a
wheat seed storage protein. Biochim Biophys Acta 1479(1-2):135-46. PubMed11004535
Golitsina N,
An Y, Greenfield NJ, Thierfelder L, Iizuka K, Seidman JG, Seidman CE, Lehrer
SS, Hitchcock-DeGregori SE. 1997. Effects of two familial hypertrophic
cardiomyopathy-causing mutations on alpha-tropomyosin structure and function.
Biochemistry 36(15):4637-42. PubMed9109674
Greenfield
NJ, Huang YJ, Palm T, Swapna GV, Monleon D, Montelione GT, Hitchcock-DeGregori
SE. 2001b. Solution NMR structure and folding dynamics of the N terminus of a
rat non-muscle alpha-tropomyosin in an engineered chimeric protein. J Mol Biol
312(4):833-47. PubMed11575936
Hitchcock-DeGregori
SE, Song Y, Greenfield NJ. 2002. Functions of tropomyosin's periodic repeats.
Biochemistry 41(50):15036-44. PubMed12475253
Hu Z, Zhu X,
Jordan F, Inouye M. 1994. A covalently trapped folding intermediate of
subtilisin E: spontaneous dimerization of a prosubtilisin
Hyde TJ,
Bryan MA, Brodsky B, Baum J. 2006. Sequence dependence of renucleation after a
Gly mutation in model collagen peptides. J Biol Chem 281(48):36937-43. PubMed16998200
Inouye M, Fu X, Shinde U. 2001. Substrate-induced activation of a trapped IMC-mediated
protein folding intermediate. Nat Struct Biol 8(4):321-5. PubMed11276251
Inouye M, Ke
H, Yashio A, Yamanaka K, Nariya H, Shimamoto T, Inouye S. 2004. Complex
formation between a putative 66-residue thumb domain of bacterial reverse
transcriptase RT-Ec86 and the primer recognition RNA. J Biol Chem
279(49):50735-42. PubMed15371452
Kapurniotu
A, Bernhagen J, Greenfield N, Al-Abed Y, Teichberg S, Frank RW, Voelter W,
Bucala R. 1998. Contribution of advanced glycosylation to the amyloidogenicity
of islet amyloid polypeptide. Eur J Biochem 251(1-2):208-16. PubMed9492286
Kapurniotu
A, Taylor JW. 1995. Structural and conformational requirements for human
calcitonin activity: design, synthesis, and study of lactam-bridged analogues.
J Med Chem 38(5):836-47. PubMed7877149
Kayed R,
Bernhagen J, Greenfield N, Sweimeh K, Brunner H, Voelter W, Kapurniotu A. 1999.
Conformational transitions of islet amyloid polypeptide (IAPP) in amyloid
formation in vitro. J Mol Biol 287(4):781-96. PubMed10191146
Li Y, Hu Z,
Jordan F, Inouye M. 1995. Functional analysis of the propeptide of subtilisin E
as an intramolecular chaperone for protein folding. Refolding and inhibitory
abilities of propeptide mutants. J Biol Chem 270(42):25127-32. PubMed7559646
Li Y, Inouye
M. 1994. Autoprocessing of prothiolsubtilisin E in which active-site serine 221
is altered to cysteine. J Biol Chem 269(6):4169-74. PubMed8307978
Long CG,
Braswell E, Zhu D, Apigo J, Baum J, Brodsky B. 1993. Characterization of
collagen-like peptides containing interruptions in the repeating Gly-X-Y
sequence. Biochemistry 32(43):11688-95. PubMed8218237
Long CG, Li
MH, Baum J, Brodsky B. 1992. Nuclear magnetic resonance and circular dichroism
studies of a triple-helical peptide with a glycine substitution. J Mol Biol
225(1):1-4. PubMed1583683
Lu B, Liang X, Scott GK, Chang CH, Baldwin MA, Thomas T,
Benz CC. 1998. Polyamine inhibition of
estrogen receptor (ER) DNA-binding and ligand-binding functions. Breast Cancer
Res Treat 48(3):243-57. PubMed9598871
Marie-Claire
C, Yabuta Y, Suefuji K, Matsuzawa H, Shinde U. 2001. Folding pathway mediated
by an intramolecular chaperone: the structural and functional characterization
of the aqualysin I propeptide. J Mol Biol 305(1):151-65. PubMed11114254
McBride DJ,
Jr., Choe V, Shapiro JR, Brodsky B. 1997. Altered collagen structure in mouse
tail tendon lacking the alpha 2(I) chain. J Mol Biol 270(2):275-84. PubMed9236128
Mielewczyk
SS, Breslauer KJ, Anachi RB, Brodsky B. 1996. Binding studies of a
triple-helical peptide model of macrophage scavenger receptor to tetraplex
nucleic acids. Biochemistry 35(35):11396-402. PubMed8784195
Mohs A, Li
Y, Doss-Pepe E, Baum J, Brodsky B. 2005. Stability junction at a common
mutation site in the collagenous domain of the mannose binding lectin.
Biochemistry 44(6):1793-9. PubMed15697204
Moraczewska
J,
Moraczewska
J, Hitchcock-DeGregori SE. 2000. Independent functions for the N- and C-termini
in the overlap region of tropomyosin. Biochemistry 39(23):6891-7. PubMed10841770
Palm T,
Graboski S, Hitchcock-DeGregori SE,
Palm T,
Persikov AV,
Ramshaw JA, Kirkpatrick A, Brodsky B. 2000. Amino acid propensities for the
collagen triple-helix. Biochemistry 39(48):14960-7. PubMed11101312
Persikov AV,
Ramshaw JA, Kirkpatrick A, Brodsky B. 2002. Peptide investigations of pairwise
interactions in the collagen triple-helix. J Mol Biol 316(2):385-94. PubMed11851346
Persikov AV,
Ramshaw JA, Kirkpatrick A, Brodsky B. 2003. Triple-helix propensity of
hydroxyproline and fluoroproline: comparison of host-guest and repeating
tripeptide collagen models. J Am Chem Soc 125(38):11500-1. PubMed13129344
Persikov AV,
Xu Y, Brodsky B. 2004. Equilibrium thermal transitions of collagen model
peptides. Protein Sci 13(4):893-902. PubMed15010541
Phadtare
S, Inouye M, Severinov K. 2002. The nucleic acid melting activity of
Escherichia coli CspE is critical for transcription antitermination and cold
acclimation of cells. J Biol Chem 277(9):7239-45. PubMed11756430
Shah NK,
Brodsky B, Kirkpatrick A, Ramshaw JA. 1999. Structural consequences of D-amino
acids in collagen triple-helical peptides. Biopolymers 49(4):297-302. PubMed10079768
Shang Z,
Isaac VE, Li H, Patel L, Catron KM, Curran T, Montelione GT, Abate C. 1994.
Design of a "minimAl" homeodomain: the N-terminal arm modulates DNA
binding affinity and stabilizes homeodomain structure. Proc Natl Acad Sci U S A
91(18):8373-7. PubMed7915838
Shinde U,
Inouye M. 1995. Folding pathway mediated by an intramolecular chaperone:
characterization of the structural changes in pro-subtilisin E coincident with
autoprocessing. J Mol Biol 252(1):25-30. PubMed7666430
Shinde U, Li
Y, Chatterjee S, Inouye M. 1993. Folding pathway mediated by an intramolecular
chaperone. Proc Natl Acad Sci U S A 90(15):6924-8. PubMed8346198
Silva T,
Kirkpatrick A, Brodsky B, Ramshaw JA. 2005. Effect of deamidation on stability
for the collagen to gelatin transition. J Agric Food Chem 53(20):7802-6. PubMed16190633
Singh A,
Hitchcock-DeGregori SE. 2003. Local destabilization of the tropomyosin coiled
coil gives the molecular flexibility required for actin binding. Biochemistry
42(48):14114-21. PubMed14640678
Singh K,
Zewge D, Groth-Vasselli B, Farnsworth PN. 1996. A comparison of structural
relationships among alpha-crystallin, human Hsp27, gamma-crystallins and beta
B2-crystallin. Int J Biol Macromol 19(4):227-33. PubMed9024897
Smith L,
Greenfield NJ, Hitchcock-DeGregori SE. 1994. The effects of deletion of the
amino-terminal helix on troponin C function and stability. J Biol Chem
269(13):9857-63. PubMed8144578
Smith L,
Greenfield NJ, Hitchcock-DeGregori SE. 1999. Mutations in the N- and D-helices
of the N-domain of troponin C affect the C-domain and regulatory function.
Biophys J 76(1 Pt 1):400-8. PubMed9876151
Sone M,
Falzon L, Inouye M. 2005. The role of tryptophan residues in the autoprocessing
of prosubtilisin E. Biochim Biophys Acta 1749(1):15-22. PubMed15848132
Suciu D,
Inouye M. 1996. The 19-residue pro-peptide of staphylococcal nuclease has a
profound secretion-enhancing ability in Escherichia coli. Mol Microbiol 21(1):181-95.
PubMed8843444
Taylor JW,
Greenfield NJ, Wu B, Privalov PL. 1999. A calorimetric study of the
folding-unfolding of an alpha-helix with covalently closed N and C-terminal
loops. J Mol Biol 291(4):965-76. PubMed10452900
Taylor JW,
Jin QK, Sbacchi M, Wang L, Belfiore P, Garnier M, Kazantzis A, Kapurniotu A,
Zaratin PF, Scheideler MA. 2002. Side-chain lactam-bridge conformational
constraints differentiate the activities of salmon and human calcitonins and
reveal a new design concept for potent calcitonin analogues. J Med Chem
45(5):1108-21. PubMed11855991
Taylor JW,
Shih IL, Lees AM, Lees RS. 1993. Surface-induced conformational switching in
amphiphilic peptide segments of apolipoproteins B and E and model peptides. Int
J Pept Protein Res 41(6):536-47. PubMed8349411
Thomas T, Gallo MA, Klinge CM, Thomas TJ. 1995. Polyamine-mediated conformational perturbations in DNA
alter the binding of estrogen receptor to poly(dG-m5dC).poly(dG-m5dC) and a
plasmid containing the estrogen response element. J Steroid Biochem Mol Biol
54(3-4):89-99. PubMed7662593
Thomas T,
Kulkarni GD, Gallo MA,
Thomas T,
Thomas TJ. 1993. Structural specificity of polyamines in modulating the binding
of estrogen receptor to potential Z-DNA forming sequences. J Recept Res
13(8):1115-33. PubMed8254578
Tongaonkar
P, Beck K, Shinde UP, Madura K. 1999. Characterization of a
temperature-sensitive mutant of a ubiquitin-conjugating enzyme and its use as a
heat-inducible degradation signal. Anal Biochem 272(2):263-9. PubMed10415098
Venugopal
MG, Ramshaw JA, Braswell E, Zhu D, Brodsky B. 1994. Electrostatic interactions
in collagen-like triple-helical peptides. Biochemistry 33(25):7948-56. PubMed8011657
Vijayanathan
V, Greenfield NJ, Thomas TJ, Ivanova MM, Tyulmenkov VV, Klinge CM, Gallo MA,
Thomas T. 2007. Effects of estradiol and 4-hydroxytamoxifen on the
conformation, thermal stability, and DNA recognition of estrogen receptor beta.
Biochem Cell Biol 85(1):1-10. PubMed17464340
Wang N,
Yamanaka K, Inouye M. 2000. Acquisition of double-stranded DNA-binding ability
in a hybrid protein between Escherichia coli CspA and the cold shock domain of
human YB-1. Mol Microbiol 38(3):526-34. PubMed11069676
Xu Y, Bhate
M, Brodsky B. 2002. Characterization of the nucleation step and folding of a
collagen triple-helix peptide. Biochemistry 41(25):8143-51. PubMed12069607
Xu Y, Hyde
T, Wang X, Bhate M, Brodsky B, Baum J. 2003. NMR and CD spectroscopy show that
imino acid restriction of the unfolded state leads to efficient folding.
Biochemistry 42(29):8696-703. PubMed12873129
Yabuta
Y, Takagi H, Inouye M,
Yu C, Taylor
JW. 1999. Synthesis and study of peptides with semirigid i and i + 7 side-chain
bridges designed for alpha-helix stabilization. Bioorg Med Chem
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Zhang M, Wu
B, Baum J, Taylor JW. 2000. Conformational characterization of a
helix-nucleated bicyclic GCN4 decapeptide by proton NMR. J Pept Res
55(5):398-408. PubMed10863936
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For Help with CD programs contact Norma J. Greenfield. mailto:greenfie@umdnj.eduor mailto:mnormajg@bellatlantic.net
- Centre for Protein and Membrane Structure and
Dynamics
The Centre for Protein and Membrane Structure and Dynamics (CPMSD) is one of only six Structural Biology Centres established by the BBSRC as part of its framework of support for structual biology in the UK. This will be a virtual centre linking
The center has a new beamline on the Synchrotron Radiation Source at CLRC Daresbury Laboratory for the collection of rapid kinetic and steady state vacuum-ultraviolet and deep-ultraviolet CD spectra. This beamline will provide many orders of magnitude more photon flux than conventional CD instruments. The advantages of Synchrotron Radiation as a light source for
CD have been demonstrated by data from the existing facilities on the SRS, and the new station will allow the full exploitation of SRCD for the first time. The center has recently added on-line CD analysis software with a friendly user interface.
Link to Center: http://www.srs.dl.ac.uk/VUV/CD/cpmsd.html
- CD
analysis programs can also be found at at the Dicroprot web site
DICROPROT (DICHROism of PROTeins) is the website of the Institute of Biology and Chemistry of Proteins. They have a computer program that runs on Windows with many of the methods designed for the estimation of protein sequence secondary structure derivation from circular dichroism experiments. The CD package was originally a part of the ANTHEPROT one (PC DOS version and IBM rs 6000). The current Windows version is a 32 bits release (Dicro_2000). The major goal in making DICROPROT is to help the user to manage the spectra acquired with Jobin-Yvon apparatus, but the package can be used with data from other instruments.
Contact the Director of the Facility
To make an appointment to use
the facility before
After
Alla S. Kostyukova
Department of
Neuroscience and
675
Telephone 732-235-5791
or 732-235-4528