Judith Klein-Seetharaman Assistant Professor
Department of Structural Biology
University of Pittsburgh School of Medicine
Room 2051, Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261, USA
Tel. 412 383 7325
Fax. 412 648 8998
Email. jks33@pitt.edu

 

 

Other Affiliations:

·         Institute for Structural Biology IBI-2, Research Center Juelich, Germany

·         Department of Pharmacology, Univ. of Pittsburgh School of Medicine

·         Department of Computational Biology, Univ. of Pittsburgh School of Medicine

·         Language Technologies Institute, Carnegie Mellon University

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PUBLICATIONS

Judith Klein-Seetharaman

1.      Nechushtai, R., Eden, A., Cohen, Y. and Klein, J. (1994) Introduction to Photosystem I Reaction Center Function, Composition and Structure. In: D. J. Ort and C. F. Yocum. (eds.) Oxygenic Photosynthesis: The Light Reactions.

2.      Klein, J., De Las Rivas, J. and Barber, J. (1995) Indirect Reduction of Cytochrome b559 in Isolated Reaction Centers of Photosystem II by Exogenous Flavins. Bioelectrochem. and Bioenergetics 38, 9-14.

3.      De Las Rivas, J., Klein, J. and Barber, J. (1995) pH Sensitivity of the Redox State of Cytochrome b559 May Regulate Its Function As a Protectant Against Donor and Acceptor Side Photoinhibition. Photosynth. Res. 46, 193-202.

4.      Hwa, J., Reeves, P.J., Klein-Seetharaman, J., Davidson, F. and Khorana, H.G. (1999) Structure and Function in Rhodopsin: Further Elucidation of the Role of the Intradiscal Cysteines, Cys-110, -185, and -187, in Rhodopsin Folding and Function. Proc. Natl. Acad. Sci. USA 96, 1932-1935. [pdf]

5.      Cai, K., Klein-Seetharaman, J., Farrens, D., Zhang, C., Altenbach, C., Hubbell, W.L. and Khorana, H.G. (1999) Single Cysteine Substitution Mutants at Amino Acid Positions 306-312 in Rhodopsin, the Sequence between the Cytoplasmic End of Helix VII and the Palmitoylation Sites: Sulfhydryl Reactivity and Transducin Activation Reveal a Tertiary Structure. Biochemistry 38, 7925-7930. [pdf]

6.      Klein-Seetharaman, J., Hwa, J., Cai, K., Altenbach, C., Hubbell, W.L. and Khorana, H.G. (1999) Single Cysteine Substitution Mutants at Amino Acid Positions 55-75, the Sequence Connecting the Cytoplasmic Ends of Helix I and II in Rhodopsin: Reactivity of the Sulfhydryl Groups and their Derivatives Identifies a Tertiary Structure that Changes Upon Light-Activation. Biochemistry 38, 7938-7944. [pdf]

7.      Altenbach, C., Klein-Seetharaman, J., Hwa, J., Khorana, H.G. and Hubbell, W.L. (1999) Structural Features and Light-Dependent Changes in the Sequence 59-75 Connecting Helices I and II in Rhodopsin: A Site-Directed Spin Labeling Study. Biochemistry 38, 7945-7949. [pdf]

8.      Cai, K., Klein-Seetharaman, J., Hwa, J., Hubbell, W.L. and Khorana, H.G. (1999) Structure and Function in Rhodopsin. Effects of Disulfide Cross-Links in the Cytoplasmic Face of Rhodopsin on Transducin Activation and Phosphorylation by Rhodopsin Kinase. Biochemistry 38, 12893-12898. [pdf]

9.      Klein-Seetharaman, J., Getmanova, E.V., Loewen, M.C., Reeves, P.J. and Khorana, H.G. (1999) NMR Spectroscopy in Studies of Light-Induced Structural Changes in Mammalian Rhodopsin: Applicability of Solution 19F NMR. Proc. Natl. Acad. Sci. USA 96, 13744-13749. [pdf]

10.  Reeves, P.J., Klein-Seetharaman, J., Getmanova, E.V., Eilers, M., Loewen, M.C., Smith, S.O. and Khorana, H.G. (1999) Expression and Purification of Rhodopsin and Its Mutants from Stable Mammalian Cell Lines: Application to NMR Studies. Biochem. Soc. Trans. 27, 950-955.

11.  Loewen, M.C., Klein-Seetharaman, J., Getmanova, E.V., Reeves, P.J., Schwalbe, H. and Khorana, H.G. (2001) Solution 19F Nuclear Overhauser Effects in Structural Studies of the Cytoplasmic Domain of Mammalian Rhodopsin Proc. Natl. Acad. Sci. USA 98, 4888-4892. [pdf]

12.  Hwa, J., Klein-Seetharaman, J. and Khorana, H.G. (2001)  Structure and Function in Rhodopsin: Mass Spectrometric Identification of the Abnormal Intradiscal Disulfide Bond in Misfolded Retinitis Pigmentosa Mutants. Proc. Natl. Acad. Sci. 98: 4872-4876. [pdf]

13.  Klein-Seetharaman, J., Hwa, J., Cai, K., Altenbach, C., Hubbell, W.L. and Khorana, H.G. (2001) Probing the Dark State Tertiary Structure in the Cytoplasmic Domain of Rhodopsin: Proximities Between Amino Acids Deduced from Spontaneous Disulfide Bond Formation between Cys316 and Engineered Cysteines in Cytoplasmic Loop 1. Biochemistry 40, 12472-12478. [pdf]

14.  Cai, K., Klein-Seetharaman, J., Altenbach, C., Hubbell, W.L. and Khorana, H.G. (2001) Probing the Dark State Tertiary Structure in the Cytoplasmic Domain of Rhodopsin:  Proximities between Amino Acids Deduced from Spontaneous Disulfide Bond Formation between Cysteine Pairs Engineered in Cytoplasmic Loops 1, 3 and 4. Biochemistry 40, 12479-12485. [pdf]

15.  Altenbach, C., Klein-Seetharaman, J., Cai, K., Khorana, H.G. and Hubbell, W.L. (2001) Structure and Function in Rhodopsin: Mapping Light-Dependent Changes in Distance between Residue 316 in Helix 8 and Residues in the Sequence 60-75, Covering the Cytoplasmic End of Helices TM1 and TM2 and their Connection Loop CL1. Biochemistry 40, 15493-15500. [pdf]

16.  Altenbach, C., Cai, K., Klein-Seetharaman, J., Khorana, H.G. and Hubbell, W.L. (2001) Structure and Function in Rhodopsin: Mapping Light-Dependent Changes in Distance between Residue 65 in Helix TM1 and Residues in the Sequence 306-319 at the Cytoplasmic End of Helix TM7 and Helix H8. Biochemistry 40, 15483-15492. [pdf]

17.  Klein-Seetharaman,J., Reeves, P.J., Loewen, M.C., Getmanova, E.V., Chung, J., Schwalbe, H., Wright, P.E. and Khorana, H.G. (2002) Solution NMR Spectroscopy of a- 15N-Lysine Labeled Rhodopsin: The Single Peak Observed in both Conventional and TROSY-type HSQC Spectra Originates from Lys339 in the Carboxyl Terminal Peptide Sequence. Proc. Natl. Acad. Sci. USA 99, 3452-3457. [pdf]

18.  Klein-Seetharaman, J., Oikawa, M.,Wirmer, J., Duchardt, E., Ueda, T., Imoto, T., Smith, L.J., Dobson, C. and Schwalbe, H. (2002) Long-Range Interactions within a Non-Native Protein. Science 295, 1719-1722.  [pdf] Also see Perspective Article: Baldwin, R. (2002) Making a Network of Hydrophobic Clusters. Science 295, 1657-1658. [pdf]

19.  Ganpathiraju, M., Weisser, D., Rosenfeld, R., Carbonell, J., Reddy, R. and Klein-Seetharaman, J. (2002) Comparative n-gram anaylsis of whole-genome protein sequences. In: Proceedings of the Human Language Technologies Conference, San Diego 2002.

20.  Cai, Y., Snel, I., Bharathi, B.S., Klein, C. and Klein-Seetharaman, J.(2003) Towards Biomedical Problem Solving in a Game Environment. In: Lecture Notes in Computer Science 2659, 1005-1014.[pdf]

21.  Klein-Seetharaman, J. and Reddy, R. (2002) Biological Language Modeling: Convergence of Computational Linguistics and Biological Chemistry. In: Report on the NSF   Workshop "Converging Technolgoy (NBIC) for Improving Human Performance".

22.  Klein-Seetharaman, J. (2002) Dynamics in Rhodopsin. ChemBioChem 3, 981-986. [pdf]

23.  Getmanova, E., Patel, A.B., Klein-Seetharaman, J., Loewen, M.C., Reeves, P.J., Smith, S.O. and Khorana, H.G. (2004) NMR spectroscopy of phosphorylated wild-type rhodopsin: mobility of the phosphorylated C-terminus of rhodopsin in the dark and upon light-activation. Biochemistry, 43, 1126-1133 [pdf].

24.  Ganapathiraju, M., Klein-Seetharaman, J., Balakrishnan, B. and Reddy, R. (2004) Characterization of Secondary Structure using Latent Semantic Analysis. IEEE Signal Processing Magazine. 21(3), 78-87 [pdf].

25.  Klein-Seetharaman,J., Yanamala, N.V.K., Javeed, F., Reeves, P.J., Getmanova, E.V., Loewen, M.C., Schwalbe, H. and Khorana, H.G. (2004) Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR. Proc. Natl. Acad. Sci.,101(10), 3409–3413. [pdf]

26.  Rader, A.J., Anderson, G., Isin, B., Khorana H.G., Bahar, I. and Klein-Seetharaman, J. (2004) Identification of core amino acids stabilizing rhodopsin. Proc. Natl. Acad. Sci., 101(19), 7246–7251  [pdf]

27.  Weisser, D., and Klein-Seetharaman, J. (2004) Automatic identification of segment boundaries in protein sequences using mutual information. ACM Symposium on Applied Computing (SAC) 2004, 154-161.  [pdf]

28.  Liu, Y., Carbonell, J., Klein-Seetharaman, J. and Gopalakrishnan, V. (2004) Context Sensitive Vocabulary And its Application in Protein Secondary Structure Prediction. ACM SIGIR Conference [pdf]

29.  Hoberman, R, Klein-Seetharaman, J and Rosenfeld, R. (2004) Inferring Property Selection Pressure from Positional Residue Conservation. Appl. Bioinformatics 3(2-3) 167-180 [pdf].

30.  Ganapathiraju, M., Manoharan, V. and Klein-Seetharaman, J. (2004) BLMT-Statistical Sequence Analysis Using N-Grams.  Appl. Bioinformatics 3(2-3) 193-200 [pdf]

31.  Miao, J., Klein-Seetharaman, J. and Meirovitch, H. (2004) The Optimal Fraction of Hydrophobic Residues Required to Ensure Protein Collapse.  J. Mol. Biol. 344(3),  797-811. [pdf]

32.  Wirmer, J., SchlÖrb, C., Klein-Seetharaman, J.,  Hirano, R., Ueda, T., Imoto, T. and Schwalbe, H. (2004) Modulation of Compactness and Long-Range Interactions of Unfolded Lysozyme by Single Point Mutations.  Angew. Chem. Int. Ed. 43(143), 5780 –5785.  [pdf]

33.  Vries, J., Munshi, R., Tobi, D., Klein-Seetharaman, J., Benos, P.V. and Bahar, I. (2004) A Sequence Alignment-Independent Method for Protein Classification. Appl. Bioinformatics 3(2-3), 137-148.  [pdf]

34.  Klein-Seetharaman, J. (2005) The Use of Analogies for Interdisciplinary Research in the Convergence of Nano-, Bio- and Information Technology. In: NSF Report on Societal Implications of Nanoscience and Nanotechnology. 128-133. [pdf]

35.  Klein-Seetharaman, J. (2005) Interactive, Entertaining, Virtual Learning Environments. In: NSF Report on Societal Implications of Nanoscience and Nanotechnology. 258-262. [pdf]

36.  Klein-Seetharaman, J. and Loewen, M. (2005) Structures and dynamics of G protein coupled receptors. In: G protein coupled receptors. Editors: Kenneth Lundstrom, Mark Chiu, pp 230-271. Taylor & Francis Books, Boca Raton, Florida, USA.  [pdf]

37.  Ganapathiraju, M., Weisser, D., and Klein-Seetharaman, J. (2004) Yule Value Tables from Protein Datasets. In: Eighth World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, Florida, USA, July 18-21, 2004. [pdf]

38.  Ganapathiraju, M., Balakrishnan, N., Reddy, R. and Klein-Seetharaman, J., (2005) Computational Biology and Language. In:  Y. Cai (Ed.): Ambient Intelligence for Scientific Discovery, Lecture Notes in Artificial Intelligence (LNAI) 3345, 25-47. [pdf]

39.  Qi, Y., Klein-Seetharaman, J. and Joseph, Z.(2005) Random forest similarity for protein-protein interaction prediction from multiple sources. Pacific Symposium on Biocomputing 10, 531-542. [pdf]

40.  Liu, Y., Carbonell, J., Klein-Seetharaman, J. and Gopalakrishnan, V. (2004) Comparison of probabilistic combination methods for protein secondary structure prediction. Bioinformatics 20(17), 3099–3107. [pdf]

41.  Cheng, B., Carbonell, J. and Klein-Seetharaman, J. (2004) A Machine Text-Inspired Machine Learning Approach for Identification of Transmembrane Helix Boundaries. Proc. ISMIS, 15th International Symposium on Methodologies for Intelligent Systems, Saratoga Springs, New York, May 25-28, 2005. [pdf]

42.  Cheng, B., Carbonell, J. and Klein-Seetharman, J. (2005) Protein Classification based on Text Document Classification Techniques. Proteins - Structure, Function and Bioinformatics 58(4), 955-70. [pdf]

43.  Klein-Seetharaman, J. (2005) Dual role of interactions between membranous and soluble portions of helical membrane receptors for folding and signaling. Trends in Pharmacological Science 26(4), 183-189  [pdf]

44.  Cai, Y., Snel, I., Cheng, B., Bharathi, S., Klein, C. and Klein-Seetharman, J. (2005) BioSim--a biomedical character-based problem solving environment. Future Generation Computer Systems 21(7), 1145-1156 [pdf]

45.  Qi, Y., Klein-Seetharaman, J. and Bar-Joseph, Z. (2005) A mixture of experts approach for protein-protein interaction predictionIn: Proceedings of the Neural Information Processing Systems (NIPS) Workshop on Computational Biology and the Analysis of Heterogeneous Data. Whistler (B.C.) December 9-10, 2005 [pdf]

46.  Batra-Safferling R, Abarca Heidemann K, Korschen HG, Tziatzios C, Stoldt M, Budyak I, Willbold D, Schwalbe H, Klein-Seetharaman J, Kaupp UB.(2005) Glutamic acid-rich proteins of rod photoreceptors are natively unfolded. Journal of Biological Chemistry, in press.[pdf]

47.  Qi, Y., Bar-Joseph, Z. and Klein-Seetharaman, J. (2006) Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins - Structure, Function and Bioinformatics, 63, 490-500. [pdf] [Supplement]

48.  Ganapathiraju, M., Manoharan, V. Reddy, R. and Klein-Seetharaman, J. (2006) Collaborative Discovery Through Biological Language Modeling Interface. In: Y. Cai and J. Abascal (Eds.): Ambient Intelligence in Everyday Life, Lecture Notes in Artificial Intelligence, LNAI 3864, 300-321. [pdf] 

49.  Isin, B., Rader, A.J., Dhiman, H., Klein-Seetharaman, J. and Bahar, I. (2006) Predispostion of the Dark State of Rhodopsin To Functional Changes in Structure. Proteins - Structure, Function and Bioinformatics, 65(4), 970-983. [pdf] [Supplement]

50.  Alessandro Iannaccone, David Man, Naushin Waseemc, Barbara J. Jennings, Madhavi Ganapathiraju, Kevin Gallaher, Elisheva Reese, Shomi S. Bhattacharya, Judith Klein-Seetharaman. (2006) Retinitis pigmentosa associated with rhodopsin mutations: Correlation between phenotypic variability and molecular effects. Vision Research 46(27), 4556-67.[ pdf]

51. Haber-Pohlmeier, S., Körschen, H.G., Abarca-Heidemann, K., Kaur Dhiman, H., Heberle, J., Schwalbe, H., Klein-Seetharaman, J., Kaupp, U.B. and Pohlmeier, A. (2007) Binding of Ca2+ to glutamic acid-rich polypeptides from the rod outer segment. Biophys. J. 92(9), 3207-14. [pdf]

52. Budyak, I., Pipich, V., Mironova, O., Schlesinger, R., Zaccai, G. & Klein-Seetharaman, J.  (2006) Shape and oligomerization state of the cytoplasmic domain of the phototaxis transducer II from Natronobacterium pharaonis. Proc. Natl. Acad. Sci. USA 103(42), 15428-33. [pdf]

53. Tastan, O., Yu, E., Ganapathiraju, M., Aref, A., Rader, A.J. and Klein-Seetharaman, J. (2007) Comparison of stability predictions and simulated unfolding of rhodopsin structures. Photochemistry and Photobiology 83(2), 251-362. [pdf]

54. Karla Werner, Ines Lehner, Harpreet Kaur Dhiman, Christian Richter, Clemens Glaubitz, Harald Schwalbe, Judith Klein-Seetharaman and H. Gobind Khorana (2007) Combined solid state and solution NMR studies of a,e-15N labeled bovine rhodopsin. J. Biomol. NMR 37(4), 303-312. [pdf]

55. Ganapathiraju, M., Balakrishnan, N., Reddy, R. and Klein-Seetharaman, J. (2007) Transmembrane helix prediction using latent semantic analysis, Incob Proceedings http://srs1.bic.nus.edu.sg/ocs/viewabstract.php?id=46

56. Yanamala, N., Tirupula, K. and Klein-Seetharaman, J. (2007) Preferential Binding of Allosteric Modulators to Active and Inactive Conformational States of Metabotropic Glutamate Receptors, Incob Proceedings http://srs1.bic.nus.edu.sg/ocs/viewabstract.php?id=73

57. Qi, Y., Klein-Seetharaman, J. and Bar-Joseph, Z. (2007) A mixture of experts approach for protein-protein interaction prediction. BMC Bioinformatics, in press. [pdf]

58. Ganapathiraju, M., Jursa, C.J., Karimi, H.A.  & Klein-Seetharaman, J. (2007) TMpro web server and web service: Transmembrane helix prediction through amino acid property analysis, Bioinformatics, in press. [pdf]

59. Poddar, A., Chandra, N., Ganpathiraju, M., Sekar, K., Klein-Seetharaman, J., Reddy, R. & Balakrishnan, N. (2007) Evolutionary insights from suffix array based genome sequence analysis. J. Biosci. 32(5), 871-881. [pdf]

 

Theses

1.      Klein, J. (1995) Studies on a Functional Role of Cytochrome b559. Diploma Thesis at the University of Cologne, Cologne, Germany.

2.      Klein, J. (2000) Visual Signal Transduction: Studies of Light-Induced Conformational Changes in the Cytoplasmic Face of Rhodopsin. Ph.D. Thesis at the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.