CRYSTALLOGRAPHY POST-DOC POSITION WANTED
Mohan Srinivasan
smohan at helix.nih.gov
Thu Mar 2 10:27:36 EST 1995
Hello!
One of friends, who is a Crystallographer, with a
background in Biophysics is seeking a post-doctoral position
in Crystallography/Protein Crystallography. His CV is attached.
Interested people may contact either him directly or me at:
smohan at helix.nih.gov
Thanks!
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CURRICULUM VITAE
1.NAME AND ADDRESS :
N.SUKUMAR
Department of Crystallography and Biophysics
University of Madras, Guindy Campus
Madras - 600 025, INDIA
Phone : 91-44-2351367
Telex : 41 6376 UNOM IN
Fax : 91-44-415856
2.DATE OF BIRTH AND AGE : June 25, 1966; 28 years
3.MARITAL STATUS : Unmarried
4.EDUCATIONAL QUALIFICATIONS :
_________________________________________________________________
Degree Institution Fields Year Class
_________________________________________________________________
Ph.D. University of Crystallography
Madras and Biophysics (Thesis submitted)
M.Phil. University of
Madras -do- 1989 FIRST
M.Sc. University of Biophysics 1988 FIRST &
Madras FIRST RANK
B.Sc. University of Physics 1986 FIRST
Madras
Title of the thesis : Structural Studies on Biologically and
Medicinally Important Molecules
________________________________________________________________
4. LANGUAGES KNOWN : Tamil (Mother Tongue)
English
5. RESEARCH / TEACHING EXPERIENCE :
_________________________________________________________________
Duration Institution Designation Nature of
work
_________________________________________________________________
Nov. 1989- School of Physics Project Research
Feb. 1990 University of Hyderabad, Assistant
Hyderabad- 500 134,
India
Feb. 1990- Department of Crystallo- University Research and
Dec. 1990 graphy and Biophysics, Research Teaching
University of Madras, Fellow (for M.Sc
Madras - 600 025 students)
India
Jan. 1991- -do- CSIR- Senior -do-
Till date Research
Fellow
_________________________________________________________________
6. AWARDS:
1. UGC SAP Merit Scholarship for the M.Sc students for the year
1986-88.
2. First Rank Holder in M.Sc degree examination conducted
by the University of Madras.
3. Senior Research Fellowship (SRF) from Council of Scientific
and Industrial Research (CSIR), New Delhi, India.
7. RESEARCH SPECIALISATION:
1. Crystal Structure Determination of Medicinally and
Biologically important molecules.
2. Data Base Analysis (Using both Cambridge Structural Data
Base (CSD) and Protein Data Bank (PDB).
8. A BRIEF OUTLINE OF RESEARCH WORK:
Since 1989, the applicant is working on the experimental and
theoretical [using Cambridge Structural Data Base (CSD) and
Protein Data Bank (PDB)] aspects of Crystallography. He has
gained good knowledge over the experimental techniques of
crystal structure determination by X-ray methods. He has
also gained knowledge of mathematics, Biostatistics and
computer programming. His research work falls under the
following categories.
(i) Peptides
(ii) Piperidines
(iii) Azabicyclononanes
(iv) Steroids
(v) Data Base Analysis
Summary of the Research work done : See Enclosure - A
9. PROGRAMS USED:
SHELXX86, SHELX76, SDP, MULTAN, PATSEE, PARST, GEOM78,
GEOM90, PLUTO, RETRIEVE, GKS SUBROUTINES
10. INSTRUMENTS USED:
Data for the all the compounds have been collected
independantly by the candidate using Enraf-Nonius CAD4
instrument available in the department. The applicant used
MicroVAX II and VAX730 computing system for the
calculations.
11. REFERENCES:
1. Dr.M.N. Ponnuswamy (Ph.D Supervisor)
Department of Crystallography and Biophysics
University of Madras
Guindy campus
Madras - 600 025, India
Phone : 91-44-2351367 (office)
Fax : 91-44-415856
2. Dr.E. Subramanian
Professor
Department of Crystallography and Biophysics
Guindy campus
University of Madras
Madras - 600 025, India
Phone : 91-44-4918512 (Residence)
Fax : 91-44-415856
3. Dr. Vasantha Pattabhi
Professor
Department of Crystallography and Biophysics
University of Madras
Guindy campus
Madras - 600 025, India
Phone : 91-44-4912081 (Residence)
Fax : 91-44-415856
12. RESEARCH PUBLICATIONS:
Please See Enclosure - B
Enclosure - A
Summary of Research Work
The work has been divided into three parts. The first
part consists of the crystal structure analysis of peptides.
The following dipeptides containing aliphatic aminoacid are
taken for structural study to find out their adopted
conformation as the statistical survey has predicted that they
are having high propensity for extended conformation. (a)
N-(t-butoxycarbonyl)-L-isoleucyl-L-alanine Benzylester, (b)
N-(t-butoxycarbonyl)- L-alanyl-(S-Benzyl)- L- cysteine Methyl
ester, (c) N-(t-butoxycarbonyl)- L-isoleucyl- L- valine Methyl
ester, (d) N-(t-butoxycarbonyl)-e-N'-benzyloxy-carbonyl-L-lysyl-
L-isoleucine and (e) N-(t-butoxycarbonyl)-L-Valine N-hydroxy
succinimide ester. In all these compounds, peptide linkage
is in trans conformation and the t-boc group is in trans-trans
conformation. In compounds (a) - (d), the molecules adopt
extended conformation. The compound (e) contains two
crystallographically independent molecules (A & B) in the
asymmetric unit. The molecules A and B adopt extended and
folded conformation respectively. In general, all the aliphatic
aminoacids containing peptides reported exhibit predominantly an
extended conformation as predicted from the data base analysis.
However, the observed (m,j) angles in cases where the side chain
adopting the less preferred conformations suggests that the sheet
forming tendencies may also depend on the side chain rotamer
conformational restrictions.
The second part consists of structural studies on
piperidine derivatives. The aim is to study the stereodynamics
of piperidine derivatives and to correlate the stereochemistry
with their cancer/anticancer properties. The following compounds
have been solved by X-ray diffraction methods:
(a) 2,6-di-(2-furyl)-3,5-dimethylpiperidin-4-one(DFMP), (b)2,6-di
-(2-furyl)-3,5-dimethyl-N-nitrosopiperidin-4-one (DFMPNO), (c)
2,6-di(2-Thioenyl)-3,5-dimethylpiperidin-4-one (DTMP), (d) 2,6-di
(o-chloro)phenyl-3,5-dimethyl-N-nitrosopiperidin-4-one (NOCDMPO),
(e) 3,5- dimethyl- N-nitroso- 4-oximino- 2,6- diphenylpiperidin-
4-one (DMNOH), (f) 5-isopropyl-N-methyl-2,6-diphenyl-1- aza-oxa
-thiaspirodecane (NMITK), (g) O-N- diacetyl-3- isopropyl-2,6
-diphenylpiperidin-4-one oxime (IODA). The piperidine ring of
compounds (a), (c) and (f) adopts chair conformation while (b),
(d) and (e) exist in distorted boat conformation. The compound
(g) is in twisted boat conformation. The detailed conformational
analysis on these piperidine derivatives indicates that the
piperidine rings normally adopt a chair conformation with the
substitutents at equatorial orientation. But, in some cases it
assumes the less favourable boat, twisted boat conformation etc.
so as to avoid steric interactions between the bulky
substitutents.
A review has been carried out to explain the uses of
X-ray Crystallography and the number of other possible ways to
design new drugs. Forces involved in the molecular interactions
which plays an important role in the mode of action of drugs also
covered. The drug-DNA interaction has also been dealt with as
many of the drugs are active at the DNA level. The principle and
techniques used in the drug design also been covered. In this
connection, the use of computer graphics and structure-activity
relationship is analysed in some details.
Another review has been made on the two classes of
anti-biotics namely anthracycline and ansamycin class of
compounds to derive the potential analogues of compounds in
both classes. These anthracycline compounds show anti-tumor
properties and used in the treatment of cancer, while the
ansamycin compounds show antiviral and antibacterial properties
and are partcularly useful in the treatment of tuberculosis.
In order to decipher the relation between their structure
and activity, biological properties of compounds such as
cellular uptake, metabolic changes, binding of DNA etc. have
been analysed.
The third part consists of Cambridge Crystallographic
Structural Data Base analysis on three important biomolecules,
namely, aminoacids, nucleotides and carbohydrates. (a) Non-
planarity of peptides and its sequence dependence, (b) Stretching
of g(N-C -C') angle in amino acids and peptides, (c) On unusual
observation of eclipsed C -NH bond in aminoacids and peptides
and (d) Molecular aggregation of nucleotides and
carbohydrates - their implication to evolution. From
the analysis of (a) and (b), we have concluded that in
general the non-planarity of peptides or stretching of
g(N-C -C') angle is evoked when there is a net gain in
energy either by reducing steric interaction or by
forming additional hydrogen bonds. In (c), a few cases of
eclipsed C -NH bond in aminoacids and peptides have been
observed, eventhough staggered conformation is known to be
energetically most favoured. An attempt to study the
cause for such occurrences and probability of observing such
eclipsed C - NH bond in any one of the naturally occurring
aminoacids, have been made. Our analysis shows that hydrogen
bonding alond is enough to cross the rotational barrier about
C -NH bond. There is correlation between hydrogen bond
geometry and the deviation frpm staggered conformation of C - N
bond is observed. A study on the head-to-tail sequence of the
solid state aggregation suggests that the presence of water
molecules do not have significant effect on the arrangement.
In (d), we have analysed hydrogen bonding pattern of
nucleotides and carbohydrates. An analysis on
ribonucleotides shows that the 3'...5' hydrogen bond mediated
aggregation to be most common alignment. The 2'...5'
alignment which occurs under special circumstances in
nature is found to be second choice. An analysis of
carbohydrates suggests that self-assembly of these molecules is
not conducive to the formation of polysaccharides of the type
which are found in present day living organisms. Further
the role of water molecules in the polymerisation of three
important biomolecules have been analysed. Implication of these
results to prebiotic polymerisation is discussed.
Enclosure - B
I. RESEARCH PUBLICATIONS
1. Crystal structure of a potential steroid intermediate -
C15H}0O}
N. Sukumar and Vasantha Pattabhi
Acta Cryst., C47 , 400, 1991.
2. Crystal Structure of LANTADENE - A, The Major Triterpenoid
of Lantana Camara, Red Variety
Vasantha Pattabhi, N. Sukumar and O.P. Sharma
Acta Cryst., C47, 810, 1991.
3. Molecular Aggregation in Nucleotides and Carbohydrates -
Their Implication to Prebiotic Polymerisation
N. Sukumar and Vasantha Pattabhi
J. Biosci., 17, 431, 1992.
4. Crystal Structure and Conformation N-(t-Butoxycarbonyl)-L-
Valine N-Hydroxysuccinimide Ester
N. Sukumar, M.N. Ponnuswamy and R. Jayakumar
Bull. Chem. Soc. Jpn., 66, 2101, 1993.
5. Crystal Structure and Conformation of N-(t-butoxycarbonyl)-
L-isoleucyl-L-alanine benzylester
N. Sukumar, M.N. Ponnuswamy and R. Jayakumar
J. Cryst. Spec. Res., 23, 769, 1993.
6. Crystal and molecular structure of 2,6-Di(o-chloro)phenyl-
3,5-dimethyl-N-nitrosopiperidin-4-one (NOCDMPO)
N. Sukumar, M.N. Ponnuswamy, J.C. Thenmozhiyal and
R. Jeyaraman
J. Cryst. Spec. Res., 23, 871, 1993.
7. Structural Investigation of 2,6-Di-2-furyl-3,5-dimethyl-4-
piperidinone and Its N-nitroso Derivative in Solution and
the Solid State - Influence of the Nitroso Moiety on the
Conformation of the Piperidine ring and Orientation of Its
Substituents
N. Sukumar, M.N. Ponnuswamy, J.C. Thenmozhiyal and
R. Jeyaraman
Bull. Chem. Soc. Jpn. 67, 1069, 1994.
8. Crystal Structure and Conformation of N-(t-Butoxycarbonyl)-
L-alanyl-S-benzyl-L-Cysteine Methyl ester
N. Sukumar, M.N. Ponnuswamy and R. Jayakumar
Bull. Chem. Soc. Jpn., 67, (in press).
9. Crystal and Molecular Structure of 3,5-Dimethyl-N-nitroso-4-
Oximino-2,6-DiphenylPiperidin-4-one (DMNOH)
N.Sukumar, M.N.Ponnuswamy, R.Vijayalashmi and R.Jeyaraman
Z. fur Kristallographie (in press).
10. Crystal Structure of 5-isopropyl-N-methyl-2,6-Diphenyl-1-Aza
-Oxa-Thiaspirodecane (NMITK)
N. Sukumar, M.N. Ponnuswamy, M. Sujatha and R. Jeyaraman
Communicated to J. Chem. Cryst.
11. Structural Characterization of 2,6-Di(2-Thioenyl)- 3,5-
Dimethyl piperidin-4-one in Solution and Solid State (DTMP)
N.Sukumar, M.N.Ponnuswamy, J.C.Thenmozhiyal and R.Jayaraman
Communicated to J. Chem. Cryst.
12. Sequence Dependence of Non-planarity of peptides and Its
Effect on Secondary Structures
N.Sukumar and Vasantha Pattabhi.
Communicated to J. Theor. Biol.
13. Stretching of g(N-C -C') Angle in Amino Acids and Peptides
N.Sukumar, D.Kumaran and M.N.Ponnuswamy (Under preparation)
14. Crystal Structure and Conformation of N-(t-butoxycarbonyl)
-L-Isoleucyl-L-Valine methyl ester
N.Sukumar, M.N.Ponnuswamy and R.Jayakumar(Under Preparation)
15. Crystal Structure and Conformation of N-(t-butoxycarbonyl)-
e-N'-benzyloxycarbonyl-L-lysyl-L-isoleucine
N.Sukumar, M.N.Ponnuswamy and R.Jayakumar
(Under Preparation).
16. Crystal Structure of O-N-Diacetyl-3-isopropyl-2,6-diphenyl
piperidin-4-one Oxime (IODA)
N.Sukumar, M.N.Ponnuswamy, R.Vijayalashmi and R.Jeyaraman
(Under Preparation)
II. PAPERS PRESENTED/ATTENDED IN INTERNATIONAL CONFERENCES
1. Presented in Asian Crystallographic Association (AsCA'92)
held during Nov. 13-16, 1992 at Singapore.
Crystal Structure of 2,6-di(2-furyl)-3,5-dimethylpiperidin-
4-one
N.Sukumar, M.N.Ponnuswamy, J.C.Thenmozhiyal and R.Jayaraman
2. Presented in the "XVI International Congress and General
Assembly", International Union of Crystallography held
during 21-29, August, 1993 at Beijing, China.
(i) Crystal Structure Studies on N-piperidin-4-ones
N.Sukumar, M.N.Ponnuswamy, R.Jeyarman and
J.C.Thenmozhiyal
(ii) Crystal Structure and Conformation of N-(t-Butoxy-
carbonyl-e- N'-Benzyloxycarbonyl- L-Lysyl- L-Isoleucyl-
Methyl ester
N. Sukumar, M.N. Ponnuswamy and R. Jayakumar
(iii) Sequence Dependence of Non-planarity of Peptides and
its Effects on Secondary Structures
N. Sukumar and Vasantha Pattabhi
3. Participated in the "Asian Region Seminar on Crystallography
in Molecular Biology" held during December 9-14, 1993 at
Madras.
4. Presented in the "4th Naples Workshop on Bioactive Peptides,
Conformation Activity in Peptides: Relationships And
Interactions" held during May 22-25, 1994 at Naples, Italy.
Conformational Studies on Hydrophobic Aminoacids Containing
Peptides
M.N.Ponnuswamy and N.Sukumar.
5. Presented in the 21 Crystallographic Course:
Crystallography of Molecular Biology, held during May 27 -
June 5, 1994 at Erice, Italy, sponsored by International
Union of Crystallography.
Peptide Models For a-Sheet Conformation
M.N.Ponnuswamy and N.Sukumar
III. PAPERS PRESENTED/ATTENDED IN NATIONAL CONFERENCES
1. Presented in the "XXI National Seminar on Crystallography"
held during Dec. 27 - 29, 1989 at Bombay.
(i) Occurrence of Eclipsed C - NH Bond in Amino acids and
Peptides.
N. Sukumar and Vasantha Pattabhi
(ii) Crystal Structure of a Potential Steroid Intermediate
N. Sukumar and Vasantha Pattabhi
2. Presented in "XXII National Seminar on Crystallography" held
during Dec. 26 - 28, 1990 at Calcutta.
Conformational Studies on Azabicyclononanes
N. Sukumar and M.N. Ponnuswamy
3. Presented in the " National Symposium on Biophysics with
special reference to Biomacromolecules", held during Feb.
7 - 9, 1991 at Madras.
Crystallographic evidences for molecular aggregation and
their implication to Evolution
N. Sukumar and Vasantha Pattabhi
4. Participated in the "Seminar on NMR Applications in
Structural Chemistry and Structural Biology" held during
January 27-28, 1992 at Madras.
5. Presented in the National Symposium on "Recent Trends in
Molecular & Medical Biophysics", held during Feb. 7 - 9,
1992 at Pune.
Non-Planarity of Peptides and its Sequence Dependence
N. Sukumar and Vasantha Pattabhi
6. Presented in "XXIII National Seminar on Crystallography",
held during March, 23-25, 1992 at Jaipur.
Structure and Conformation of N-(t-boc)-L-Ile-L-Ala-Bzlc
N. Sukumar, M.N. Ponnuswamy and R. Jayakumar
7. Attended workshop/Training on single crystal X-ray
Diffractometer held at the Department of Biophysics, AIIMS,
New Delhi from April 6-11, 1992.
8. Presented in the "XXIV National Seminar on Crystallography
and Microsymposium on the Crystallography of Superconducting
Materials" held during Oct. 20-22, 1992 at Jammu.
Crystal structure of N- (t-butoxycarbonyl)- L-alanyl -
(s-benzyl)-L-cysteine Methyl ester
N. Sukumar, M.N. Ponnuswamy and R. Jayakumar
9. Presented in the "IBS XVIII National Symposium on Molecular
and Cellular Biophysics" held during Jan. 7-9, 1993 at
Anantapur.
Stretching of g(N-C -C') angle in Amino acids and Peptides
N. Sukumar, D. Kumaran and M.N. Ponnuswamy
10. Presented in the "Discussion Meeting on Biomolecular
Structure, Function and Interaction" held during September,
8-10, 1993 at Bangalore.
Conformational Studies on Aliphatic Amino acid Containing
Peptides
N. Sukumar, D. Kumaran and M.N. Ponnuswamy
11. Presented in the XXV National Seminar on Crystallography
held during Dec. 15-17, 1993 at Madras.
(i) Crystal Structure of 3,5-Dimethyl-N-Nitroso-4-Oximino-
2,6-Diphenylpiperidin-4-one.
D.Kumaran, N.Sukumar and M.N.Ponnuswamy.
(ii) Conformational Studies on piperidin-4-ones.
N.Sukumar and M.N.Ponnuswamy.
--
Mohan Srinivasan Ph.D | email: smohan at helix.nih.gov
DCBDC/NCI/Bldg 37 Rm 2B10,NIH,9000 Rockville Pike| phone: 301 496 2202
Bethesda, MD 20892, USA | fax : 301 402 1031
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