Kural பெற்றாற பெறின்பெறுவர் பெண்டிர் பெருஞ்சிறப்புப் புத்தேளிர் வாழும் உலகு.       In English: Women who win their husbands' heart Shall flourish where the gods resort.

Department of Crystallography and Biophysics

Faculty Profiles

Employee No:
Name:
Dr. P. Karthe , M. Phil., Ph.D
Designation:
Professor and Head
Specialization:
Structural Biology (Crystal structure studies on protein molecules)

Contacts

Address:

Office: Centre of Advanced Study in Crystallography and Biophysics University of Madras Guindy Campus, Chennai - 600 025

Residence:

Phone:

Off: +91 44 2220 2775, +91 44 2220 2776

Res: 044 2243 2045

Mobile: 9841560496

Email:

Achievements

  • US patent application number : 20040101919 Title : Bioinformatic method for identifying surface-anchored proteins from gram-positive bacteria and proteins obtained thereby Inventors : Hook, Magnus; (Houston, TX) ; Xu, Yi; (Houston, TX) ; Sillanpaa, Jouko V.; (Houston, TX) ; Sthanam, Narayana; (Birmingham, AL) ; Ponnuraj, Karthe; (Birmingham, AL) ; Patti, Joseph M.; (Cumming, GA) ; Hutchins, Jeff T.; (Cumming, GA) ; Hall, Andrea; (Acworth, GA) ; Bowden, Maria G.; (Sugarland, TX)
  • DBT - National Bioscience Award (2010)
  • Elected member (2010) - Executive Council of Indian Biophysical Society
  • Elected to the executive council of the International Union of Pure and Applied Biophysics (IUPAB) -  INSA. (2016-2019).
  • Elected to the executive council of the Indian Crystallographic Association (ICA) – (2016-2018).

Membership

National

  • Indian Crystallographic Association
  • Indian Biophysical Society

Projects (Total Projects : 11)

  • Title : X-ray Crystallographic Studies On Some Plant Ureases
    Duration : 2007-2010
    Funding Agency : DST
    Amount Sanctioned (in Lakhs.) : 20
  • Title : Structural studies on surface proteins of Streptococcus agalactiae and their interaction with extracellular matrix molecules
    Duration : 2007-2010
    Funding Agency : DBT
    Amount Sanctioned (in Lakhs.) : 29
  • Title : Structural studies of Erysipelothrix rhusiopathiae surface protein RspB and its interaction with collagen
    Duration : 2010-2014
    Funding Agency : DST
    Amount Sanctioned (in Lakhs.) : 18
  • Title : Structure-function analysis of laminin-binding adhesin (Lmb) of Streptococcus agalactiae and its mutants
    Duration : 2010-2013
    Funding Agency : DBT (Indo-German Project)
    Amount Sanctioned (in Lakhs.) : 35
  • Title : Structural and functional studies on laminin and keratin binding proteins of Streptococcus agalactiae
    Duration : 2010-2014
    Funding Agency : DBT
    Amount Sanctioned (in Lakhs.) : 42
  • Title : X-ray crystallographic structure elucidation of key drug target enzymes of Leishmania donovani
    Duration : 2012-2015
    Funding Agency : DBT – NE twinning
    Amount Sanctioned (in Lakhs.) : 73
  • Title : Structural studies of Staphylococcus aureus surface protein FnBPA and its interaction with nanoparticles
    Duration : 2012-2015
    Funding Agency : MHRD / NCNSNT, University of M
    Amount Sanctioned (in Lakhs.) :
  • Title : Structural and functional studies on PfbA, a surface adhesin and invasin of Streptococcus pneumonia
    Duration : 2013-2016
    Funding Agency : DST
    Amount Sanctioned (in Lakhs.) :
  • Title : Structural and functional characterization of HtrA protease from Listeria monocytogenes
    Duration : 2015-2017
    Funding Agency : DST (Indo-Austria)
    Amount Sanctioned (in Lakhs.) :
  • Title : Unraveling the rationale behind solvent stability of proteins
    Duration : 2014-2017
    Funding Agency : DBT
    Amount Sanctioned (in Lakhs.) :
  • Title : Crystallographic and functional characterization of the multi-ligand binding mechanism of PfbA, a surface adhesin and invasin of Streptococcus pneumonia
    Duration : 2016-2019
    Funding Agency : DST
    Amount Sanctioned (in Lakhs.) :

Publications

Articles (Total Articles: 55)

  • Karthe, P., Sadasivan, C. & Gautham, N. (1993). Packing interactions of crystallographically independent molecules in organic crystals. Acta Cryst.  B49, 1069-1071., 
  • Gautham, N. & Karthe, P. (1994). Beyond the double helix: New discoveries in the DNA structure. Biology Education, 11, 135-142., 
  • Sadasivan, C., Karthe, P. & Gautham, N. (1994). Space group degeneracy in the packing of Z-DNA hexamer. Acta Cryst.  D50, 192-196. , 
  • Karthe, P., Anil Kumar, Katti, S. B. & Gautham, N. (1997). The crystal and molecular structure of 3'deoxyadenosine. Acta Cryst.  C53, 1694-1696. , 
  • Karthe, P., Anil Kumar, Katti, S. B. & Gautham, N. (1997). The three-dimensional structure of 3'-deoxycytidine. Nucleosides & Nucleotides.  16, 1-10., 
  • Karthe, P. & Gautham, N. (1998). The structure of d(CACGCG).d(CGCGTG): Crystals grown in the presence of Ruthenium(II) hexammine chloride. Acta Cryst.  D54, 502-509. , 
  • Ponnuraj Karthe, Kelly, S., Nessi, C., Setlow, P. & Jedrzejas, M. J. (1999). Structural Studies of a novel germination protease from spores of Bacillus megaterium.  J. Struct. Biol. 125, 19-24., 
  • Ponnuraj, K., Kelly, S., Nessi, C., Setlow, P. & Jedrzejas, M. J. (2000).  Crystallization and preliminary diffraction studies of a truncated form of a novel protease from spores of Bacillus megaterium. Acta Cryst.  D56, 70-72., 
  • Ponnuraj Karthe, Rowland, S., Nessi C., Setlow, P. & Jedrzejas, M. J. (2000).  Crystal structure of novel germination protease from spores of Bacillus megaterium: Structural rearrangement and zymogen activation.  J. Mol. Biol. 300, 1-10., 
  • Ponnuraj Karthe & Jedrzejas, M. J. (2000).  Mechanism of hyaluronan binding and degradation: Structure of Streptococcus pneumoniae hyaluronate lyase in complex with hyaluronic acid disaccharide at 1.7 Å resolution. J. Mol. Biol. 299, 885-895., 
  • Thiyagarajan, S., Karthe, P., Rajan, S. S., Gautham, N., Kumar, A. & Katti, S. B. (2001). Crystal and molecular structure of 3'-deoxyguanosine- N(2)-isobutyryl dihydrate. Cryst. Res. Technol. 36, 485-492., 
  • Ponnuraj, K., Xu, Y., Moore, D., Deivanayagam, C. C. S., Boque, L., Hook, M. & Narayana, S. V. L. (2001). Crystallization and preliminary X-ray crystallographic analysis of Ace: A Collagen-binding MSCRAMM from Enterococcus faecalis. Biochim. Biophys. Acta, 1596, 173-176., 
  • Ponnuraj Karthe, Bowden, G., Davis, S. L., Gurusiddappa, S., Moore, Choe, D., Xu, Y., Hook, M. & Narayana, S. V. L. (2003). A "dock, lock and latch" structural model for a staphylococcal adhesin binding to fibrinogen. Cell 115, 217-228., 
  • Ponnuraj Karthe, Xu, Y., Macon, K., Moore, D., Volanakis, J. E. & Narayana, S. V. L. (2004). Structure analysis of engineered Bb fragment of complement factor B: Insights into the activation mechanism of the alternative pathway C3-convertase. Mol. Cell. 14, 17-28., 
  • Kumarevel T, Fujimoto Z, Karthe P, Oda M, Mizuno H, Kumar PK. (2004).  Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis. Structure, 12, 1269-1280., 
  • Ponnuraj Karthe, Narayana SV. (2007). Crystal structure of ACE19, the collagen binding subdomain of Enterococus faecalis surface protein ACE. Proteins. 69,199-203., 
  • Liu Q, Ponnuraj Karthe, Xu Y, Ganesh VK, Sillanpää J, Murray BE, Narayana SV, Höök M. (2007). The Enterococcus faecalis MSCRAMM ACE binds its ligand by the Collagen Hug model. J. Biol. Chem. 282, 19629-19637. (First two authors have equal contribution)., 
  • M. Gabriela Bowden, Alejandro P. Heuck, Karthe Ponnuraj, Elena Kolosova, Damon Choe, S. Gurusiddappa, S. V. L. Narayana, Arthur E. Johnson and Magnus Höök.  (2008). Evidence for the “Dock, Lock and Latch” ligand Binding Mechanism of the Staphylococcal MSCRAMM SDRG. J. Biol. Chem. 283, 638-647., 
  • Anuradha, B. and Karthe Ponnuraj. (2008). Purification, crystallization and preliminary X-ray analysis of urease from pigeon pea (Cajanus cajan). Acta Cryst. F64, 662-664., 
  • Kumarevel, T., Nakano, N., Ponnuraj, Karthe, Gopinath, S., Sakamoto, K., Shinkai, A., Kumar, P. K. R. and Yokoyama, S. (2008). Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding. Nucl. Acids Res. 36, 4808-4820., 
  • Preethi Ragunathan, Thirumananseri Kumarevel, Yoshihiro Agari, Akeo Shinkai, Seiki Kuramitsu, Shigeyuki Yokoyama and Karthe Ponnuraj. (2008). Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodai. Biochem. Biophys. Res. Commun. 375, 124-128., 
  • Krishnan, V., Karthe Ponnuraj, Xu, Y., Macon, M., Volanakis, J. E. and Narayana, S. V. L. (2009).  The crystal structure of cobra venom factor, a cofactor for C3- and C5-convertase CVFBb.  Structure. 17, 1-9., 
  • Preethi Ragunathan, Barbara Spellerberg and Karthe Ponnuraj. (2009). Expression, purification, crystallization and preliminary crystallographic analysis of laminin-binding protein (Lmb) from Streptococcus agalactiae. Acta Cryst. F65, 492-494., 
  • Anuradha, B. and Karthe Ponnuraj. (2009). Purification, crystallization and preliminary X-ray analysis of urease from jack bean (Canavalia ensiformis). Acta Cryst. F65, 949-951., 
  • Preethi Ragunathan, Barbara Spellerberg and Karthe Ponnuraj. (2009). Crystal structure of laminin-binding adhesin (Lmb) of Streptococcus agalactiae. Acta Cryst. D65, 1262-1269., 
  • Devi AS, Ogawa Y, Shimoji Y and Ponnuraj K. (2010). Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the collagen-binding region of RspB from Erysipelothrix rhusiopathiae. Acta Cryst. F66, 156-159., 
  • Anuradha Balasubramanian and Karthe Ponnuraj. (2010). Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure. J. Mol. Biol. 400, 274-283., 
  • Aribam Swarmistha Devi and Karthe Ponnuraj. (2010). Cloning, expression, purification and ligand binding studies of novel fibrinogen-binding protein FbsB of Streptococcus agalactiae. Protein Expr Purif. 74, 148-155., 
  • Preethi Ragunathan and Karthe Ponnuraj. (2011). Expression, purification and structural analysis of a fibrinogen receptor FbsA from Streptococcus agalactiae. Protein J. 30, 159-166., 
  • Sundaresan, R., Samen, U., Ponnuraj, Karthe (2011).  Expression, purification, crystallization and preliminary X-ray diffraction studies of the human keratin 4-binding domain of serine-rich repeat protein 1 from Streptococcus agalactiae. Acta Cryst. F67, 1582-1585., 
  • Dileep KV, Tintu I, Mandal PK, Karthe P, Haridas M, Sadasivan C. (2012). Binding to PLA2 may contribute to the anti-inflammatory activity of catechol. Chem Biol Drug Des. 79,143-147., 
  • Sundaresan R, Ragunathan P, Kuramitsu S, Yokoyama S, Kumarevel T, Ponnuraj, Karthe. (2012). The structure of putative N-acetyl glutamate kinase from Thermus thermophilus reveals an intermediate active site conformation of the enzyme. Biochem Biophys Res Commun. 420, 692-627., 
  • K.V. Dileep, I. Tintu, P.K. Mandal, P. Karthe, M. Haridas and C. Sadasivan (2012).  Crystal structure of porcine pancreatic phospholipase A2 in complex with 2-methoxycyclohexa-2-5-diene-1,4-dione. Frontiers in Life Science, iFirst, 2012, 1–5., 
  • Devi AS, Ogawa Y, Shimoji Y, Balakumar S, Ponnuraj, Karthe. (2012). Collagen adhesin-nanoparticle interaction impairs adhesin's ligand binding mechanism. Biochim Biophys Acta - General subjects, 1820, 819-828., 
  • Aparna V, Dileep KV, Mandal PK, Karthe P, Sadasivan C, Haridas M. (2012). Anti-Inflammatory Property of n-Hexadecanoic Acid: Structural Evidence and Kinetic Assessment.  Chem Biol Drug Des. 80, 434-439., 
  • Anuradha Balasubramanian, Nagarajan Balaji, Namasivayam Gautham and Karthe Ponnuraj (2012). Molecular dynamics simulation and molecular modeling studies on the insecticidal domain from jack bean urease Molecular Simulation, iFirst article, 2012, 1–10., 
  • Preethi Ragunathan, Gokul Raghunath, Seiki Kuramitsu, Shigeyuki Yokoyama, Thirumananseri Kumarevel and Karthe Ponnuraj (2013). Crystallization, characterization and preliminary X-raycrystallographic analysis of GK2848, a putative carbonic anhydrase of Geobacillus kaustophilus Acta Cryst. F69, 162-164., 
  • Aribam Swarmistha Devi, Akio Ebihara, Seiki Kuramitsu, Shigeyuki Yokoyama, Thirumananseri Kumarevel and Karthe Ponnuraj (2013).  Crystal structure of type I 3-Dehydroquinate dehydratase of Aquifex aeolicus suggests closing of active site flap is not essential for enzyme action.  Biochem Biophys Res Commun. 432, 350-354., 
  • Revathi Nagarajan, Antoni P. A. Hendrickx and Karthe Ponnuraj (2013). Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the N-terminal domain of Serine glutamate repeat A (SgrA) protein from Enterococcus faecium. Acta Cryst. F69, 441–444., 
  • Anuradha Balasubramanian, Vishnuprabu Durairajpandian, Sagadevan Elumalai, Narayanasamy Mathivanan, Arasambattu Kannan Munirajan and Karthe Ponnuraj (2013). Structural and functional studies on urease from pigeon pea (Cajanus cajan). Int. J. Biol. Macromol. 58, 301-309., 
  • Preethi Ragunathan, Divya Sridaran, Anja Weigel, Sarah Shabayek, Barbara Spellerberg and Karthe Ponnuraj  (2013).  Metal binding is critical for the folding and function of laminin binding protein, Lmb of  Streptococcus agalactiae – PLoS ONE 8(6): e67517. doi:10.1371/journal.pone.0067517, 
  • Beulin DS, Yamaguchi M, Kawabata S and Karthe Ponnuraj. (2014). Crystal structure of PfbA, a surface adhesin of Streptococcus pneumoniae, provides hints into its interaction with fibronectin. Int J Biol Macromol. 64,168-173., 
  • Sridharan U, Ebihara A, Kuramitsu S, Yokoyama S, Kumarevel T, Karthe Ponnuraj. (2014). Crystal structure and in silico studies of dihydrodipicolinate synthase (DHDPS) from Aquifex aeolicus. Extremophiles. 18, 973-985., 
  • Nagarajan, R and Karthe Ponnuraj. (2014). Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae NEM316. Acta Crystallogr. F70, 938-941., 
  • Sundaresan R, Samen U, Ponnuraj K  (2015). Structure of KRT4 binding domain of Srr-1 from Streptococcus agalactiae reveals a novel β-sheet complementation. Int J Biol Macromol. 75,97-105., 
  • Sundaresan R, Ebihara A, Kuramitsu S, Yokoyama S, Kumarevel T, Ponnuraj K. (2015). Crystal structure analysis of Ornithine Transcarbamylase from Thermus thermophilus - HB8 provides insights on the plasticity of the active site. Biochem Biophys Res Commun. 465, 174-179., 
  • Shobana ponnuvel, Balakumar Subramanian and Karthe Ponnuraj (2015). Conformational change results in loss of enzymatic activity of Jack bean urease on its interaction with silver nanoparticle. Protein J. 34, 329-337., 
  • Upasana, S. and Karthe Ponnuraj (2016). Isopeptide bond in Collagen and Fibrinogen binding MSCRAMMS. Biophysical Reviews. DOI 10.1007/s12551-015-0191-5., 
  • Beulin D.S. and Karthe Ponnuraj. (2016). Steered molecular dynamics study reveals insights into the function of the repetitive B region of collagen and fibrinogen binding MSCRAMMs. J Biomol Struct Dyn. Feb 9:1-45., 
  • Revathi Nagarajan, Antoni P. A. Hendrickx and Karthe Ponnuraj. (2016). The crystal structure of the ligand binding region of Serine-glutamate repeat protein A (SgrA) of Enterococcus faecium reveals a new protein fold: functional characterization and insights into its adhesion function. FEBS J. Jun 23. doi: 10.1111/febs.13792. [Epub ahead of print], 
  • Carmen M. Abfalter1, Esther Schönauer, Karthe Ponnuraj, Markus Huemer1, Gabriele Gadermaier, Peter Briza, Hans Brandstetter, Fatima Ferreira, Gernot Posselt, Silja Wessler. (2016). Cloning, purification and characterization of the Bacillus cereus collagenase ColA reveal a highly active and self-processing collagenolytic protease. PLoS One. Sep 2;11(9):e0162433. doi: 10.1371/journal.pone.0162433., 
  • Shobana Ponnuvel, Dhanalakshmi Bandaru, Preethi Ragunathan and Karthe Ponnuraj (2016). Functional Characterization and Molecular Modelling of FnFgBP, a Surface Protein from Streptococcus agalactiae. RSC Adv. 6, 91824–91835., 
  • Thiruselvam V, Kumarevel T, Karthe P, Kuramitsu S, Yokoyama S, Ponnuswamy MN. (2017). Crystal structure analysis of a hypothetical protein (MJ0366) from Methanocaldococcus jannaschii revealed a novel topological arrangement of the knot fold. Biochem Biophys Res Commun. 482, 264-269., 
  • Ponnuraj, Karthe and Saravanan KM. (2017). Dihedral angle preferences of DNA and RNA binding amino acid residues in proteins. Int J Biol Macromol. 97, 434-439., 
  • Sridharan U, Kuramitsu S, Yokoyama S, Kumarevel T, Ponnuraj, Karthe. (2017). Crystal structure of Aquifex aeolicus gene product Aq1627: a putative phosphoglucosamine mutase reveals a unique C-terminal end-to-end disulfide linkage. Mol Biosyst. 2017 May 26. doi: 10.1039/c7mb00182g. [Epub ahead of print], 

Research Guidance

  • Ph.D Awarded 6
    Ph.D Students 3
    M.Phil Awarded 3
    M.Phil Students

Invited book chapters

1.   The effect of non-alternating sequence on the structure of left-handed Z-DNA. (1999). In 'Perspectives in Structural Biology'.  N. Gautham, P. Karthe and S.Krishnaswamy. (Eds.) M. Vijayan, N. Yathindra and A. S. Kolaskar. Indian Academy of Sciences and Universities Press (India) Limited. P 593-601.

 

2.    Factors D and B: Substrate-inducible serine proteases of the alternative pathway of complement activation. (2005). 'Structural Biology of the Complement Systems'.  Xu,Y., Ponnuraj, K., Narayana, S. V. L.  & Volanakis, J. E.  (Eds.) Lambris, J. D. and Morikis, D. Marcel Dekker Inc. P 91-110.

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