135

DAFTAR PUSTAKA

Adams, M.W., Perler, F.B., dan Kelly, R.M. (1995) : Extremozymes: Expdaning the Limits of Biocatalysis, Nat Biotech, 13(7), 662-668.

Aguilar, C.F., Cronin, N.B., Badasso, M., Dreyer, T., Newman, M.P., Cooper,

J.B., Hoover, D.J., Wood, S.P., Johnson, M.S., dan Blundell, T.L. (1997) : The three dimensional structure at 2.4 Å resolution of glycosylated proteinase A from the lysosome-like vacuole of Saccharomyces cerevisiae, J. Mol. Biol. 257, 899-915.

Akhmaloka, Tika, I.N., Pramono, H., dan Sindumarta, M. (2000) : Isolation dan

characterization of DNA Polymerase from a local thermophilic microorganism, JMS, 4, 335-343.

Akhmaloka, Pramono, H., Tika, I.N., Ambarsari, L., Susanti, E., Suharto, A.,

Sutedjo, H., dan Madayanti, F. (2002) : Eksplotasi Bakteri Termofilik Isolat Loka, Studi Kasus DNA Polimerase Termostabil, Prosiding Seminar Nasional Himpunan Kimia Indonesia, Bdanung

Akhmaloka, Pramono, H., Ambarsari, L., Susanti, E., Nurbaiti, S., dan Madayanti,

F. (2007) : Cloning, Homological Analysis, dan Expression of DNA Pol I from Geobacillus thermoleovorans, IJIB, 1(3), 206-215.

Albà, M., (2001) : Replicative DNA polymerases, Genome Biology, 2(1), 3002.1-

3002.4 Alder, B.J., dan Wainwright, T.E. (1957) : Phase Transition for a Hard Sphere

System, J. Chem. Phys., 27(5), 1208-1209. Allen, M.P. dan Tildesley, D.J. (1989) : Computer Simulation of Liquids, Oxford

University Press, USA. Allen, W.J., Rothwell, P.J., dan Waksman, G. (2008) : An intramolecular FRET

system monitors fingers subdomain opening in Klentaq, Protein Sci.,17(3), 401-408.

Amadei, A., Linssen, A.B.M., dan Berendsen, H.J.C. (1993) : Essential dynamics

of proteins. Proteins, 17(4), 412–425. Ambarsari, L., Madayanti, F., Moeis M. R., dan Akhmaloka. (2006) : Pengaruh

Mutasi D802N pada Aktivitas Polimerase DNA Pol I ITB-1, Proceeding ITB on Engineering Sciences, 38B (1), 1-10.

Anderson, D.E., Becktel, W.J., dan Dahlquist, F.W. (1990) : pH-induced

denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to

136

the free energy of folding of T4 lysozyme, Biochemistry, 29(9), 2403-2408.

Andreotti, G., Cubellis, M.V., Nitti, G., Sannia, G., Mai, X., Adams, M.W., dan

Marino G. (1995) : An extremely thermostable aromatic aminotransferase from the hyperthermophilic archaeon Pyrococcus furiosus, Biochim. Biophys. Acta, 1247(1), 90-96.

Arnold, K., Bordoli, L., Kopp, J., dan Schwede, T. (2006) : The SWISS-MODEL

workspace: a web-based environment for protein structure homology modelling, Bioinformatics, 22(2), 195-201.

Aravind, L., dan Koonin, E. (1998) : Phosphoesterase domains associated with

DNA polymerases of diverse origins, Nucl. Acids Res., 26(16), 3746-3752. Argos, P., Rossman, M.G., Grau, U.M., Zuber, H., Frank, G., Tratschin, J.D.

(1979) : Thermal stability dan protein structure, Biochemistry, 18(25), 5698-5703.

Astatke, M., Grindley, N.D.F., Joyce, C.M. (1998) : A single Side Chain Prevents

Escherichia coli DNA Polymerase I (Klenow Fragment) from Incorporating Ribonucleotides, Proc. Natl. Acad. Sci. U.S.A., 95 (7), 3402-3407.

Baker, N.A. Sept, D., Joseph, S., Holst, M.J., dan McCammon, J.A. (2001)

: Electrostatics of nanosystems: Application to microtubules dan the ribosome, Proc. Natl. Acad. Sci. U.S.A., 98(18), 10037-10041.

Bambara, R.A., Murane, R.S., Henricksen, L.A. (1997) : Enzymes dan reactions

at the eukaryotic DNA replication fork, J. Biol. Chem., 272 (8), 4647-4650.

Barnes, W.M. (1994) : PCR amplification of up to 35-kb DNA with high fidelity

dan high yield from lambda bacteriophage templates, Proc. Natl. Acad. Sci. U.S.A., 91 (6), 2216–2220.

Barth, E., dan Schlick, T. (1998) : Extrapolation versus impulse in multiple-

timestepping schemes. II. Linear analysis dan applications to Newtonian dan Langevin dynamics, J. Chem. Phys., 109(5), 1633-1642.

Bartolucci, S., De Simone, G., Galdiero, S., Improta, R., Menchise, V., Pedone,

C., dan Saviano, M. (2003) : An Integrated Structural dan Computational Study of the Thermostability of Two Thioredoxin Mutants from Alicyclobacillus acidocaldarius, J. Bacteriol, 185, 4285-4289.

Bebenek, K., dan Kunkel, T.A. (1990) : Frameshift errors initiated by nucleotide

misincorporation. Proc. Natl. Acad. Sci. U.S.A., 87(13), 4946–4950.

137

Becker, O.M., MacKerrel, A.D., Roux, B., dan Watanabe, M. (2001). Computational Biochemistry dan Biophysics, Marcel Dekker, Inc., New York.

Beese, L.S., dan Steitz, T.A. (1991) : Structural basis for the 3'�5 exonuclease

Activity of Esherichia coli DNA polymerase I: a two metal ion mechanism, EMBO J., 10 (1), 25-33.

Beese, L.S., Friedman, J.M., dan Steitz, T.A. (1993) : Crystal structures of the

Klenow Fragment of DNA polymerase I complexed with deoxynucleoside triphosphate dan pyrophosphate, Biochemistry, 32(51), 14095-14101.

Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., dan

Haak, J. R. (1984) : Molecular dynamics with coupling to an external bath, J. Chem. Phys., 81(8), 3684-3690

Bonch-Osmolovskaya, E.A. Miroshnichenko, M.L., Lebedinsky, A.V., Chernyh,

N.A., Nazina, T.N., Ivoilov,V.S., Belyaev, S.S., Boulygina, E.S., Lysov, Y.P., Perov, A.N., Mirzabekov, A.D., Hippe, H., Stackebrdant, E., L'Haridon, S., dan Jeanthon, C. (2003) : Radioisotopic, Culture-Based, dan Oligonucleotide Microchip Analyses of Thermophilic Microbial Communities in a Continental High-Temperature Petroleum Reservoir, Appl. Environ. Microbiol., 69(10), 6143-6151.

Bosshard, H.R., Daniel N. M., dan Jelesarov, I. (2004) : Protein stabilization by

salt bridges: concepts, experimental approaches dan clarification of some misunderstdanings, J. Mol. Recognit., 17(1), 1-16.

Braithwaite, D.K., dan Ito, J. (1993) : Compilation, alignment, dan phylogenetic

relationships of DNA polymerases, Nucl. Acids Res., 21(4), 787–802. Brdanen, C., dan Tooze, J. (1999) : Introduction to Protein Structure,2nd Ed.,

Garldan Science Publishing, Inc., New York, 347-371. Breitung, J., Borner, G., Scholz, S., Linder, D., Stetter, K.O., dan Thauer, R.K.

(1992) : Salt dependence, kinetic properties dan catalytic mechanism of N-formylmethanofuran:tetrahydromethanopterin formyltransferase from the extreme thermophile Methanopyrus kdanleri, FEBS J., 210(3), 971-981.

Brock, T.D., dan Freeze, H. (1969) : Thermus aquaticus gen. n. dan sp. n., a

nonsporulating extreme thermophile, J. Bacteriol., 98 (1), 289-297. Brock, T.D., dan Boylen, K.L. (1973) : Presence of thermophilic bacteria in

laundry dan domestic hot-water heaters, Appl. Microbiol., 25 (1), 72-76. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S.,

dan Karplus, M. (1983) : CHARMM: A Program for Macromolecular

138

Energy, Minimization, dan Dynamics Calculations, J. Comput. Chem., 4(2),187-217.

Burgers, P.M.J., Koonin, E.V., Bruford, E., Blanco, L., Burtis, K., Christman,

M.F., Copeldan, W.C., Friedberg, E.C., Hanaoka, F., Hinkle, D.C., Lawrence, C.W., Nakanishi, M., Ohmori, H., Prakash, L., Prakash, S., Reynaud, C., Sugino, A., Todo, T., Wang, Z., Weill, J., Woodgate, R. (2001) : Eukaryotic DNA Polymerases : proposal for a revised nomenclature, J. Biol. Chem., 276, 43487-43490.

Burley, S., dan Petsko, G. (1985) : Aromatic-aromatic interaction: a mechanism of

protein structure stabilization, Science, 229(4708), 23-28. Cann, I.K., Komori, K., Toh, H., Kanai, S., dan Ishino, Y. (1998) : A

heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase, Proc. Natl. Acad. Sci. U.S.A., 95(24), 14250-14255.

Cariello, N. F., Swenberg, J. A., dan Skopek, T. R. (1991) : Fidelity of

Thermococcus litoralis DNA polymerase (Vent) in PCR determined by denaturating gradient gel electrophoresis. Nucl. Acids Res.. 19, 4193-4198.

Case, D.A., Cheatham, T.E.III., Darden, T., Gohlke, H., Luo, R., Mrez, K.M.JR.,

Onofriev, A., Simerling, C., Wang, B., dan Woods, R.J. (2005) : The Amber Biomolecular Simulation Programs. J. Comput.Chem. 26, 1668-1688.

Case, D.A., Darden, T.A., Cheatham, III, T.E., Simmerling, C.L., Wang, J., Duke,

R.E., Luo, R., Crowley, M., Walker, R.C., Zhang, W., Merz, K.M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K.F., Paesani, F., Vanicek, J., Wu, X., Brozell, S.R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D.H., Seetin, M.G., Sagui, C., Babin, V., Kollman, P.A., 2008, AMBER 10, University of California, San Francisco.

Ceska, T.A., dan Sayers, J.R. (1998) : Structure-specific DNA cleavage by 5'

nucleases, Trends in Biochem. Sci., 23(9), 331-336. Chi, Y., Martinez-Cruz, L.A., Jancarik, J., Swanson, R.V., Robertson, D.E., dan

Kim, S. (1999) : Crystal structure of the beta-glycosidase from the hyperthermophile Thermosphaera aggregans: insights into its activity dan thermostability, FEBS Lett., 445(2-3), 375-383.

Chirakkal, H., Ford, G., dan Moir, A. (2001) : Analysis of a conserved

hydrophobic pocket important for the thermostability of Bacillus pumilus chloramphenicol acetyltransferase (CAT-86), Protein Eng., 14(3), 161-166.

139

Choi, I.G., Bang, W.G., Kim, S.H., Yu, Y.G. (1999) : Extremely thermostable serine-type protease from Aquifex pyrophilus. Molecular cloning, expression, dan characterization, J. Biol. Chem., 274(2), 881-888.

Chong, Y., dan Chu, C.K. (2002) : Understdaning the unique mechanism of L-

FMAU (clevudine) against hepatitis B virus: molecular dynamics studies, Bioorg. Med. Chem. Letters, 12(23), 3459-3462.

Cline, J., Braman, J., dan Hogrefe, H. H. (1996) : PCR fidelity of Pfu DNA

polymerase dan other thermostable DNA polymerase. Nucl. Acids Res., 24, 3546-3551.

Coutsias, E.A., Seok, C., dan Dill, K.A. (2004) : Using quaternions to calculate

RMSD, J. Comput. Chem., 25(15), 1849-1857. Daniel, R. M., dan Cowan, D.A. (2000) : Biomolecular stability dan life at high

temperatures, Cell. Mol. Life Sci., 57, 250-264. Darden, T., York, D., dan Pedersen, L. (1993) : Particle mesh Ewald: An N.

log(N) method for Ewald sums in large systems, J. Chem. Phys., 98(12), 10089-10092.

Das, R., dan Gerstein, M. (2000) : The stability of thermophilic protein : a study

based on comprehensive genome comparison, Funct. Integr. Genom., 1(1), 76-88.

Day, R, Bennion, B.J., Ham, S., dan Daggett, V. (2002) : Increasing temperature

accelerates protein unfolding without changing the pathway of unfolding, J. Mol. Biol., 322 (1), 189-203.

Deift, P., dan Zhou, X. (1993) : A Steepest Descent Method for Oscillatory

Riemann-Hilbert Problems : Asymptotics for the MKdV Equation, Annals of Mathematics, 137(2), 295-368.

Delarue, M., Poch, O., Tordo, N., Moras, D., dan Argos, P. (1990) : An attempt to

unify the structure of polymerases, Protein Eng., 3 (6), 461-467. Delarue, M. Boulé, J.B., Lescar, J., Expert-Bezançon, N., Jourdan, N., Sukumar,

N., Rougeon, F., dan Papanicolaou, C. (2002) : Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase, EMBO J., 21(3), 427-439.

Dill, K.A. (1990) : Dominant forces in protein folding, Biochemistry, 29(31),

7133-7155. Dolinsky, T.J., Nielsen, J.E., McCammon, J.A., dan Baker, N.A. (2004) :

PDB2PQR, an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations, Nucl. Acids Res., 32, W665-667.

140

Domínguez, O., Ruiz, J.F., Lain de Lera, T., Garcia-Diaz, M., Gonzalez, M.A., Kirchhoff, T., Martinez, A.C., Bernard, A., Blanco, L. (2000) : DNA polymerase mu (Pol mu), homologous to TdT, could act as a DNA mutator in eukaryotic cells, EMBO J., 19(7), 1731-1742.

Doublie S., Tabor, S., Long, A.M., Richardson, C.C., Ellenberger, T. (1998) :

Crystal Structure of Bacteriophage T7 DNA Replication Complex at 2.2 Å Resolution, Nature, 391 (6664), 251-258.

Duan, Y. Wu, C., Chowudhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R.,

Cieplak, P., Luo, R., dan Lee, T. (2003) : A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem., 24(16), 1999-2012.

Echols, A.H., dan Goodman, M.F. (2003) : Fidelity Mechanisms in DNA

Replication, Annu. Rev. Biochem., 60, 477-511. Eckert, K.A., dan Kunkel, T.A. (1990) : High fidelity DNA synthesis by the

Thermus aquaticus DNA polymerase, Nucl. Acids Res., 18(13), 3739-3744.

Emond, S., Danré, I., Jaziri, K., Potocki-Véronèse, G., Mondon, P., dan Bouayadi,

K. (2008) : Combinatorial engineering to enhance thermostability of amylosucrase. Protein Sci., 17(6), 967-976.

Eom, S.H., Wang, J., dan Steitz T.A. (1996) : Structure of Taq Polymerase with

DNA at thepolymerase active site, Nature, 382 (6588), 278-281. Ermler, U., Merckel, M., Thauer, R., dan Shima, S. (1997) : Formylmethanofuran:

tetrahydromethanopterin formyltransferase from Methanopyrus kdanleri - new insights into salt-dependence dan thermostability, Structure, 5(5), 635-646.

Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., dan Pedersen,

L.G. (1995) : A smooth particle mesh Ewald method, J. Chem. Phys., 103(19), 8577-8593.

Fabry, S., dan Hensel, R. (1987) : Purification dan characterization of d-

glyceraldehyde-3-phosphate dehydrogenase from the thermophilic archaebacterium Methanothermus fervidus, Eur. J. Biochem., 165(1), 147-155.

Fan, H., dan Mark, A.E. (2004) : Refinement of homology-based protein

structures by molecular dynamics simulation techniques, Protein Sci., 13(1), 211–220.

Farias, S.T., dan Bonato, M.C.M. (2003) : Preferred amino acids dan

thermostability, Genet. Mol. Res., 2(4), 383-393.

141

Ferrara, P., Apostolakis, J., dan Caflisch, A. (2000) : Thermodynamics dan kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B104, 5000–5010.

Fiorentino, G., Cannio, R., Rossi, M., dan Bartolucci, S. (1998) : Decreasing the

stability dan changing the substrate specificity of the Bacillus strearothermophilus alcohol dehydrogenase by single amino acid replacements, Protein Eng., 11, 925-930.

Flaugh, S.L., Kosinski-Collins, M.S. dan King, J. (2005) : Interdomain side-chain

interactions in human γD crystallin influencing folding dan stability, Protein Sci., 14(8), 2030-2043.

Freemont, P.S., Friedman, J.M., Beese, L.S., Sdanerson, M.R., dan Steitz, T.A.

(1988) : Cocrystal structure of an editing complex of Klenow fragment with DNA, Proc. Natl. Acad. Sci. U.S.A., 85(23), 8924-8928.

Friedberg, E.C., Feaver, W.J., dan Gerlach, V.L. (2000) : The many faces of DNA

polymerases: Strategies for mutagenesis dan for mutational avoidance, Proc. Natl. Acad. Sci. U.S.A., 97(11), 5681-5683.

Frishman, D., dan Argos, P. (1995) : Knowledge-based protein secondary

structure assignment, Proteins, 23(4), 566-579. Fujii, T., Hata, Y., Oozeki, M., Moriyama, H., Wakagi, T., Tanaka, N.,

Oshima, T. (1997) : The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7, Biochemistry, 36(6), 1505-1513.

Fukuchi, S., dan Nishikawa, K. (2001) : Protein surface amino acid compositions

distinctively differ between thermophilic dan mesophilic bacteria, Journal of Molecular Biology, 309(4), 835-843.

Gangurde, R., Kaushik, N., Singh, K., dan Modak, M.J. (2000) : A Carboxylate

triad Is essential for the polymerase activity of Escherichia coli DNA polymerase I (Klenow Fragment) : Presence of two functional triads at the catalytic center, J. Biol. Chem, 275 (26), 19685 -19692.

Georis, J., de Lemos Esteves, F., Lamotte-Brasseur, J., Bougnet, V., Devreese,

B., Giannotta, F., Granier, B., Frere, J.M. (2000) : An additional aromatic interaction improves the thermostability dan thermophilicity of a mesophilic family 11 xylanase: structural basis dan molecular study, Protein Sci., 9(3), 466-475.

Ghoufi, A., Bonal, C., Morel, J.P., Morel-Desrosiers, N., Malfreyt, P. (2004) :

Gibbs Free Energy Perturbation Calculations, An Application to the Binding of Alkylammonium Cations by Water-Soluble Calixarene, J. Phys. Chem. B, 108, 11744-11752.

142

Gianese, G., Bossa, F., dan Pascarella, S. (2002) : Comparative structural analysis

of psychoprilic dan meso- dan thermophilic enzymes, Proteins, 47(2), 236-249.

Guenot, J., dan Kollman, P.A. (1992) : Molecular dynamics studies of a DNA-

binding protein: 2. An evaluation of implicit dan explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor, Protein Sci., 1(9), 1185–1205.

Haider, S., Parkinson, G.N., dan Neidle, S. (2008) : Molecular dynamics dan

principal components analysis of human telomeric quadruplex multimers, Biophys. J., 95(1), 296–311.

Hammond, R.A., Barnes, M.H., Mack, S.L., Mitchener, J.A., Brown, N.C.

(1991) : Bacillus subtilis DNA polymerase III: complete sequence, overexpression, dan characterization of the polC gene, Gene, 98(1), 29-36.

Haney, P.J., Badger, J.H., Buldak, G.L., Reich, C.I., Woese C.R., dan Olsen ,G.J.

(1999) : Thermal adaptation analyzed by comparison of protein sequences from mesophilic dan extremely thermophilic Methanococcus species, Proceeding of the National Academy of Sciences, 96, 3578-3583.

Hashimoto, H., Inoue, T., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T.,

Kai, Y. (1999) : Hyperthermostable protein structure maintained by intra dan inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase, J. Mol. Biol., 292(3), 707-716.

Hashimoto, H,. Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Inoue, T.,

dan Kai, Y. (2001) : Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1, J. Mol. Biol., 306(3), 469–477.

Hopfner, K.P., Eichinger, A., Engh, R.A., Laue., F., Ankenbauer, W., Huber, R.,

Angerer, B. (1999) : Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius, Proc. Natl. Acad. Sci. U.S.A., 96(7), 3600-3605.

Hubscher, U., Maga, G., Spadari, S. (2002) : Eukaryotic DNA Polymerases,

Annu. Rev. Biochem., 71, 133-163. Humphrey, W., Dalke, A., dan Schulten, K. (1996) : VMD: visual molecular

dynamics, J. Mol. Graph., 14(1), 33-38, 27-28. Indrajaya, Madayanti, F., dan Akhmaloka. (2003) : Isolation dan Identification of

Thermophilic Microorganisms from Wayang Crater. Jurnal Mikrobiologi Indonesia, 8, 53-56.

143

Ishikawa, K., Nakamura, H., Morikawa, K., dan Kanaya, S. (1993) : Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core, Biochemistry, 32(24), 6171-6178.

Ishikawa, K., Okumura, M., Katayanagi, K., Kimura, S., Kanaya, S., Nakamura,

H., dan Morikawa, K. (1993) : Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 Å resolution, J. Mol. Biol., 230(2), 529-542.

Ito, J., dan Braithwaite, D.K., 1991. Compilation dan alignment of DNA

polymerase sequences. Nucl. Acids Res., 19(15), 4045-4057. Jacobsen, H., Klenow, H. dan Overgaard-Hansen, K., 1974. The N-terminal

amino-acid sequences of DNA polymerase I from Escherichia coli dan of the large dan the small fragments obtained by a limited proteolysis, FEBS J., 45(2), 623-627.

Jaenicke, R., dan Böhm, G. (1998) : The stability of proteins in extreme

environments, Curr. Opin. Struct. Biol., 8(6), 738-748. Jaenicke, R., dan Závodszky, P. (1990) : Proteins under extreme physical

conditions, FEBS Lett., 268(2), 344-349. Johnson, R.E., Kondratick, C.M., Prakash, S., dan Prakash, L. (1999) : hRAD30

Mutations in the Variant Form of Xeroderma Pigmentosum, Science, 285(5425), 263-265.

Joyce, C.M., Kelley, W.S., dan Grindley, N.D.F. (1982) : Nucleotide Sequence of

the Escherichia coli polA gene dan primary structure of DNA Polymerase I , J.Biol. Chem., 257, 1958-1964.

Joyce, C.M., dan Steitz, T.A. (1994) : Function Dan Structure Relationships In

DNA Polymerases, Ann. Rev. Biochem., 63, 773 – 822. Joyce, C.M., dan Steitz, T.A. (1995) : Polymerase Structures dan Function:

Variations on a Theme?, J. Bacteriol., 177 (22), 6321-6329. Joyce, C.M. (1997) : Choosing the right sugar: How polymerase select a

nucleotide substrate, Proc. Natl. Acad. Sci. U.S.A., 94 (5), 1619-1622. Kaiser M.W., Lyamicheva, N.L., Ma, W., Miller, C., Neri, B., Fors, L., dan

Lyamichev, V.I. (1999) : A comparison of eubacterial dan arhaeal structure-specific 5`-exonucleases, J. Biol. Chem., 274 (30), 21387-21394.

Kaledin, A.S., Sliusarenko, A.G., dan Gorodetskii, S.I. (1982) : Isolation dan

properties of DNA polymerase from the extreme thermophilic bacterium Thermus ruber, Biokhimia, 47(11), 1785-1791.

144

Kannan, N., dan Vishveshwara, S. (2000) : Aromatic clusters: a determinant of thermal stability of thermophilic proteins, Protein Eng., 13(11), 753-761.

Karantzeni, I., Ruiz, C., Liu, C., dan Licata, V.J. (2003) : Comparative thermal

denaturation of Thermus aquaticus dan Escherichia coli type 1 DNA polymerases, Biochem. J., 374, 785–792.

Karshikoff, A., dan Ladenstein, R. (2001) : Ion pairs dan the thermotolerance of

proteins from hyperthermophiles: a "traffic rule" for hot roads, Trends Biochem. Sci., 26(9), 550-556.

Kataeva, I.A., Blum, D.L., Li, X., dan Ljungdahl, L.G. (2001) : Do domain

interactions of glycosyl hydrolases from Clostridium thermocellum contribute to protein thermostability? Protein Eng., 14(3), 167-172.

Kelman, Z., dan O'Donnell, M. (1995) : DNA polymerase III holoenzyme:

structure dan function of a chromosomal replicating machine, Ann. Rev. Biochem., 64, 171-200.

Kelman, Z., Yuzhakov, A., Danjelkovic, J., O'Donnell, M. (1998) : Devoted to the

lagging strdan-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation dan sliding clamp assembly, EMBO J., 17(8), 2436-2449.

Kermekchiev, M.B., Tzekov, A., dan Barnes, W.M. (2003) : Cold-sensitive

mutants of Taq DNA polymerase provide a hot start for PCR, Nucl. Acids Res., 31(21), 6139-6147.

Kiefer, J.R., Mao, C., Hansen, C.J., Basehore, S.L., Hogrefe, H.H., Braman, J.C.,

dan Beese, L.S. (1997) : Crystal Structure of a Thermostable Bacillus DNA Polymerase I Large Fragment at 2.1 Å Resolution, Structure, 5, 95-108.

Kim, Y., Eom, S.H., Wang, J., Lee, D., Suh, S.W., dan Steitz, T.A. (1995) :

Crystal Structure of Thermus aquaticus DNA Polymerase, Nature, 376, 612 –616.

Kirino, H., Aoki, M., Aoshima, M., Hayashi, Y., Ohba, M., Yamagishi, A.,

Wakagi, T., dan Oshima, T. (1994) : Hydrophobic interaction at the subunit interface contributes to the thermostability of 3-isopropylmalate dehydrogenase from an extreme thermophile, Thermus thermophilus, FEBS J., 220(1), 275-281.

Klapper, M.H. (1971) : On the nature of the protein interior, Biochim. Biophys.

Acta, 229(3), 557-566.

145

Klenow, H., dan Henningsen, I. (1970) : Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis, Proc. Natl. Acad. Sci. U.S.A., 65(1), 168–175.

Klingeberg, M., Galunsky, B., Sjoholm, C., Kasche, V., dan Antranikian, G.

(1995) : Purification dan Properties of a Highly Thermostable, Sodium Dodecyl Sulfate-Resistant dan Stereospecific Proteinase from the Extremely Thermophilic Archaeon Thermococcus stetteri, Appl. Environ. Microbiol., 61(8), 3098-3104.

Koch, R., Canganella, F., Hippe, H., Jahnke, K.D., Antranikian, G. (1997) :

Purification dan Properties of a Thermostable Pullulanase from a Newly Isolated Thermophilic Anaerobic Bacterium, Fervidobacterium pennavorans Ven5, Appl. Environ. Microbiol., 63(3), 1088-1094.

Kollman, P. (1993) : Free energy calculations: Applications to chemical dan

biochemical phenomena, Chem. Rev., 93(7), 2395-2417. Kornberg, A., Lieberman, I., dan Simms, E.S. (1955) : Enzymatic synthesis dan

properties of 5-phosphoribosylpyrophosphate, J. Biol. Chem., 215(1), 389-402.

Kornberg, A., dan Baker, T.A. (2005) : DNA Replication, 3rd Ed, University

Science Books. Korolev, S., Nayal, M., Barnes, W.M., di Cera, E,. Wakman, G. (1995) : Crystal

structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5 Å resolution: Structural basis for thermostability, Proc. Natl. Acad. Sci. U.S.A., 92 (20), 9264-9268.

Kroutil, L.C., Register, K., Bebenek, K., Kunkel, T.A. (1996) : Exonucleolytic

proofreading during replication of repetitive DNA, Biochemistry, 35(3), 1046-1053.

Kumar, S., Tsai, C., dan Nussinov, R. (2000a) : Factors enhancing protein

thermostability, Protein Eng., 13(3), 179-191. Kumar, S., Ma,Y. B., Tsai, C. J., dan Nussinov, R. (2000b) : Electrostatic

strengths of salt bridges in thermophilic dan mesophilic glutamate dehydrogenase monomers, Proteins, 38, 368-383.

Kumar, S., dan Nussinov, R. (2001) : How do thermophilic proteins deal with

heat? Cell. Mol. Life Sci., 58 (9), 1216-1233. Kunkel, T.A., dan Loeb, L.A. (1981) : Fidelity of mammalian DNA polymerases,

Science, 213(4509), 765–767.

146

Kunkel, T.A., Sabatino, R.D., dan Bambara, R.A. (1987) : Exonucleolytic proofreading by calf thymus DNA polymerase delta, Proc. Natl. Acad. Sci. U.S.A., 84 (14), 4865–4869.

Kunkel, T.A., Patel, S.S., dan Johnson, K.A. (1994) : Error-prone replication of

repeated DNA sequences by T7 DNA polymerase in the absence of its processivity subunit, Proc. Natl. Acad. Sci. U.S.A., 91(15), 6830–6834.

Kyte, J., dan Doolittle, R.F. (1982) : A simple method for displaying the

hydropathic character of a protein, J. Mol. Biol., 157(1), 105-132. Lancy, E.D., Lifsics, M.R., Munson, P., dan Maurer, R. (1989) : Nucleotide

sequences of dnaE, the gene for the polymerase subunit of DNA polymerase III in Salmonella typhimurium, dan a variant that facilitates growth in the absence of another polymerase subunit, J. Bacteriol., 171(10), 5581–5586.

Lawyer, F.C., Stoffel, S., Saiki, R.K., Mymbo, K., Drummond, R., dan Gelfdan,

D.H. (1989) : Isolation, Characterization dan Expresstion in E.coli of the DNA Polymerase Gene from Thermus aquaticus, J. Biol. Chem., 264, 6427- 6437.

Lebbink, J.H., Knapp, S., van der Oost, J., Rice, D., Ladenstein, R., de Vos, W.M.

(1999) : Engineering activity dan stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface, J. Mol. Biol., 289(2), 357-369.

Lee, B., dan Richards, F.M. (1971) : The interpretation of protein structures:

estimation of static accessibility, J. Mol. Biol., 55(3), 379-400. Leeuw, S.W.D., Perram, J.W., dan Smith, E.R. (1980a) : Simulation of

Electrostatic Systems in Periodic Boundary Conditions. I. Lattice Sums dan Dielectric Constants, Proceedings of the Royal Society of London, Series A, Mathematical dan Physical Sciences, 373(1752), 27-56.

Leeuw, S.W.D., Perram, J.W., dan Smith, E.R. (1980b) : Simulation of

Electrostatic Systems in Periodic Boundary Conditions. II. Equivalence of Boundary Conditions, Proc. Roy. Soc of London, Ser. A Math. Phys. Sci., 373(1752), 57-66.

Li, Y., Korolev, S., dan Waksman, G. (1998) : Crystal structures of open dan

closed forms of binary dan ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation, EMBO J., 17(24), 7514–7525.

Li, A., dan Daggett, V. (1994) : Characterization of the transition state of protein

unfolding by use of molecular dynamics: chymotrypsin inhibitor 2, Proc. Natl. Acad. Sci. U.S.A., 91(22), 10430-10434.

147

Liu, H. dan Wang, W. (2003) : Protein engineering to improve the thermostability

of glucoamylase from Aspergillus awamori based on molecular dynamics simulations, Protein Eng., 16(1), 19-25.

Lo Leggio, L., Kalogiannis, S., Bhat, M.K., Pickersgill, R.W. (1999) : High

resolution structure dan sequence of T.aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases dan enzymes with (beta)alpha-barrel architecture, Proteins, 36(3), 295-306.

Lowe, S.E., Jain, M.K., dan Zeikus, J.G. (1993) : Biology, ecology, dan

biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates, Microbiol. Mol. Biol. Rev., 57(2), 451-509.

Maki, S., dan Kornberg, A. (1988) : DNA polymerase III holoenzyme of

Escherichia coli. II. A novel complex including the gamma subunit essential for processive synthesis. J. Biol. Chem., 263(14), 6555-6560.

Mallick, P., Boutz, D.R., Eisenberg, D., Yeates, T.O. (2002) : Genomic evidence

that the intracellular proteins of archaeal microbes contain disulfide bonds, Proc. Natl. Acad. Sci. U.S.A, 99(15), 9679-9684.

Marg, G.A., dan Clark, D.S. (1990) : Activation of glucose isomerase by divalent

cations: evidence for two distinct metal-binding sites, Enzyme dan Microbial Tech., 12(5), 367-373.

Martins, A., Ribeiro, G., Marques, M.I., dan Costa, J.V. (1994) : Genetic

identification dan nucleotide sequence of the DNA polymerase gene of African swine fever virus, Nucl. Acids Res., 22(2), 208-213.

Mathews, C. K., dan van Holde, K. E. (1996) : Biochemistry, 2nd, The

Benjamin/Cummings Publishing Company, Inc. Matsumoto, Y., dan Bogenhagen, D.F. (1991) : Repair of a synthetic abasic site

involves concerted reactions of DNA synthesis followed by excision dan ligation, Mol. Cell. Biol., 11(9), 4441-4447.

Matsumura, M., Signor, G., dan Matthews, B.W. (1989) : Substantial increase of

protein stability by multiple disulphide bonds, Nature, 342(6247), 291-293.

Matthews, B.W. (1993) : Structural dan genetic analysis of protein stability, Annu.

Rev. Biochem., 62, 139-160. McCammon, J.A., Gelin, B.R., dan Karplus, M. (1977) : Dynamics of folded

proteins, Nature, 267(5612), 585-590.

148

Melchionna, S., Sinibaldi, R., dan Briganti, G. (2006) : Explanation of the

Stability of Thermophilic Proteins Based on Unique Micromorphology, Biophys. J., 90(11), 4204–4212.

Moriyama, H., Onodera, K., Sakurai, M., Tanaka, N., Kirino-Kagawa, H.,

Oshima, T., dan Katsube, Y. (1995) : The crystal structures of mutated 3-isopropylmalate dehydrogenase from Thermus thermophilus HB8 dan their relationship to the thermostability of the enzyme, J. Biochem., 117(2), 408-413.

Mrabet, N.T., van den Broeck, A., van den Brdane, I. Stanssens, P., Laroche, Y.,

Lambeir, A.M., Matthijssens, G., Jenkins, J., Chiadmi, M., dan van Tilbeurgh, H. (1992) : Arginine residues as stabilizing elements in proteins, Biochemistry, 31(8), 2239-2253.

Mullis, K., Falooma, F., Saiki, R., Horn, G., dan Ehrlich, H. (1986) : Specific

enzymatic amplification of DNA in vitro : the polymerase chain reaction, Cold Spring Harbor Symp. Quant. Biol. 247, 7116-7122.

Mueser, T.C., Nossal, N.G., dan Hyde, C.C. (1996) : Structure of bacteriophage

T4 RNase H, a 5' to 3' RNA-DNA dan DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins, Cell, 85(7), 1101-1112.

Myers, J.K., dan Pace, C.N. (1996) : Hydrogen bonding stabilizes globular

proteins, Biophys. Journal, 71(4), 2033-2039. Nakashima, H., Fukuchi, S., dan Nishikawa, K. (2003) : Compositional changes

in RNA, DNA dan proteins for bacterial adaptation to higher dan lower temperatures, J. Biochem., 133(4), 507-513.

Nesper, M., Nock, S., Sedlák, E., Antalík, M., Podhradský, D., Sprinzl, M. (1998)

: Dimers of Thermus thermophilus elongation factor Ts are required for its function as a nucleotide exchange factor of elongation factor Tu, FEBS J., 255(1), 81-86.

Nurbaiti, S. (2002) : Kloning gen 16s rRNA dari Bakteri Termofilik Isolat Kawah

Gunung Guntur, Garut. Skripsi Sarjana, Institut Teknologi Bdanung. Ollis, D.L., Brick, P., Hamlin, R., Xuong, N.G., dan Steitz, T.A. (1985) : Structure

of large fragment of Escherichia coli DNA polymerase I complexed with dTMP, Nature, 313(6005), 762–766.

Onufriev, A., Bashford, D., dan Case, D.A. (2004) : Exploring protein native

states dan large-scale conformational changes with a modified generalized born model, Proteins, 55(2), 383-394.

149

Onufriev, A., Bashford, D., dan Case, D.A. (2000) : Modification of the Generalized Born Model Suitable for Macromolecules, J. Phys. Chem. B, 104(15), 3712-3720.

Pace, C.N. (1992) : Contribution of the hydrophobic effect to globular protein

stability, J. Mol. Biol., 226(1), 29-35. Pdaney, V., Kaushik, N., dan Modak, M. (1994) : Role of lysine 758 of

Escherichia coli DNA polymerase I as assessed by site-directed mutagenesis, J. Biol. Chem., 269(18), 13259-13265.

Patel, P.H., dan Loeb, L.A. (2000) : DNA Polymerase Active Sites is Highly

Mutable: Evolutionary Consequences. Proc. Natl. Acad. Sci. U.S.A., 97(10), 5095 – 5100.

Patel, P.H., Suzuki, M., Adman, E., Shinkai, A., dan Loeb, L.A. (2001) :

Prokaryotic DNA polymerase I: Evolution, structure, dan “Base Flipping” mechanism for nucleotide selection, J. Mol. Biol., 308 (5), 823-837.

Perler, F.B., Kumar, S., Kong, H. (1996) : Thermostable DNA Polymerase, Adv.

Prot. Chem., 48, 377-435. Perutz, M. (1978) : Electrostatic effects in proteins, Science, 201(4362), 1187-

1191. Phillips, J.C. Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot,

C., Skeel, R.D., Kale, L., dan Schulten, K. (2005) : Scalable molecular dynamics with NAMD, J. Comput. Chem., 26(16), 1781-1802.

Pikkemaat, M.G., Linssen, A.B.M., Berendsen, H.C.J., dan Janssen, D.B. (2002)

: Molecular dynamics simulations as a tool for improving protein stability, Protein Eng., 15(3), 185–192.

Polesky, A.H., Steitz, T.A., Grindley, N.D.F., dan Joyce, C.M. (1990) :

Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli, J. Biol. Chem., 265(24), 14579–91.

Polesky, A.H., Dahlberg, M.E., Benkovic, S.J., Grindley, N.D., Joyce, C.M.

(1992) : Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli, J. Biol. Chem., 267(12), 8417–28.

Pramono, H. (2004) : Kloning dan Ekspresi di Escherichia coli Gen DNA

Polimerase I Bankteri Termofilik isolate Cimanggu, Disertasi Program Doktor, Institut Teknologi Bdanung.

150

Purcarea, C., Evans, D.R., dan Herve, G. (1999) : Channeling of Carbamoyl Phosphate to the Pyrimidine dan Arginine Biosynthetic Pathways in the Deep Sea Hyperthermophilic Archaeon Pyrococcus abyssi, J. Biol. Chem., 274(10), 6122-6129.

Radhakrishnan, R., dan Schlick, T. (2004) : Orchestration of cooperative events in

DNA synthesis dan repair mechanism unraveled by transition path sampling of DNA polymerase β's closing, Proc. Natl. Acad. Sci. U.S.A., 101(16), 5970–5975.

Rahman, A. (1964) : Correlations in the Motion of Atoms in Liquid Argon, Phys.

Rev., 136(2A), A405. Rahman, A., dan Stillinger, F.H. (1974) : Propagation of sound in water. A

molecular-dynamics study, Phys. Rev. A, 10(1), 368. Rahman, R.N., Fujiwara, S., Nakamura, H., Takagi, M., Imanaka, T. (1998) : Ion

pairs involved in maintaining a thermostable structure of glutamate dehydrogenase from a hyperthermophilic archaeon, Biochem. Biophys. Res. Commun., 248(3), 920-926.

Rangarajan, S., Woodgate, R., dan Goodman, M.F. (1999) : A phenotype for

enigmatic DNA polymerase II: A pivotal role for pol II in replication restart in UV-irradiated Escherichia coli, Proc. Natl. Acad. Sci. U.S.A., 96(16), 9224-9229.

Rodriguez, A.C., Park, H.W., Mao, C., Beese, L.S. (2000) : Crystal structure of a

pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7, J. Mol. Biol., 299(2), 447-462.

Rost, B., Yachdav, G., dan Liu, J. (2004) : The PredictProtein server, Nucl. Acids

Res., 32, W321–W326. Rothwell, P.J., dan Waksman, G. (2005) : Structure dan mechanism of DNA

polymerases, Adv. Prot. Chem., 71, 401-440. Rothwell, P.J., Mitaksov, V., dan Waksman, G. (2005) : Motions of the Fingers

Subdomain of Klentaq Are Fast dan Not Rate Limiting: Implications for the Molecular Basis of Fidelity in DNA Polymerases, Mol. Cell, 19(3), 345-355.

Roux, B., Allen, T., Bernèche, S., Im, W. (2004) : Theoretical dan computational

models of biological ion channels, Quart. Rev. Biophys., 37(1), 15-103. Ryckaert, J., Ciccotti, G., dan Berendsen, H. (1977) : Numerical Integration of the

Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes, J. Comput. Phys., 23, 327.

151

Sacquin-Mora, S., dan Lavery, R. (2006) : Investigating the Local Flexibility of Functional Residues in Hemoproteins, Biophys. J., 90(8), 2706-2717.

Sakasegawa, S., Takehara, H., Yoshioka, I., Takahashi, M., Kagimoto, Y., Misaki,

H., Sakuraba, H., dan Ohshima, T. (2001) : Increasing the thermostability of Flavobacterium meningosepticum glycerol kinase by changing Ser329 to Asp in the subunit interface region, Protein Eng., 14(9), 663-667.

Saunders, N.F.W., Thomas, T., Curmi, P.M., Mattick, J.S., Kuczek, E., Slade, R.,

Davis, J., Franzmann, P.D., Boone. D., Rusterholtz, K., Feldman, R., Gates, C., Bench, S., Sowers ,K., Kadner, K., Aerts, A., Dehal, P., Detter, C., Glavina, T., Lucas, S., Richardson, P., Larimer, F., Hauser, L., Ldan, M., Cavicchioli, R. (2003) : Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum dan Methanococcoides burtonii, Genome Res., 13(7), 1580-1588.

Schwede, T., Kopp, J., Guex, N., dan Peitsch, M.C. (2003) : SWISS-MODEL: an

automated protein homology-modeling server, Nucl. Acids Res., 31(13), 3381-3385.

Serrano, L., Bycroft, M., dan Fersht, A.R. (1991) : Aromatic-aromatic interactions

dan protein stability. Investigation by double-mutant cycles, J. Mol. Biol., 218(2), 465-475.

Sham, Y.Y., Ma, B., Jung, T. C., dan Nussinov, R. (2002) : Thermal unfolding

molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains dan unfolding pathway, Proteins, 46(3), 308-320.

Shirley, B.A., Stanssens, P., Hahn, U., Pace, CN. (1992) : Contribution of

hydrogen bonding to the conformational stability of ribonuclease T1, Biochemistry, 31(3), 725-732.

Soeharto, A. R. (2000) : Identifikasi Bakteri Termofilik Isolat Papdanayan dengan

Penentuan rutan dan Analisa Gen 16S rRNA, Skripsi Sarjana, Institut Teknologi Bdanung.

Sousa, R., Chung, Y.J., Rose, J.P., Wang, B.C. (1993) : Crystal structure of

bacteriophage T7 RNA polymerase at 3.3 Å resolution, Nature, 364 (6438), 593-599.

Steitz, T.A. (1993) : DNA- dan RNA-dependent DNA polymerases, Curr. Opin.

Struct. Biol., 3(1), 31-38. Steitz, T.A. (1999) : DNA Polymerase: Structural Diversity dan Common

Mechanisms, J. Biol. Chem., 274(25), 17395-17398.

152

Stickle, D.F., Presta, L.G., Dill, K.A., Rose, G.D. (1992) : Hydrogen bonding in globular proteins, J. Mol. Biol., 226(4), 1143-1159.

Suzuki, M., Yoshida, S., Adman, E.T., Blank, A., dan Loeb, L.A. (2000) :

Thermus aquaticus DNA Polymerase I Mutants with Altered Fidelity : Interacting mutations in the O-helix, J. Biol. Chem., 275 (42), 32728-32735.

Szilágyi, A., dan Závodszky, P. (2000) : Structural differences between

mesophilic, moderately thermophilic dan extremely thermophilic protein subunits: Results of a comprehensive survey, Structure, 8(5), 493-504.

Tanaka, Y., Tsumoto, K., Yasutake, Y., Umetsu, M., Yao, M., Fukada, H.,

Tanaka, I., dan Kumagai, I. (2004) : How oligomerization contributes to the thermostability of an archaeon protein. Protein L-isoaspartyl-O-methyltransferase from Sulfolobus tokodaii, J. Biol. Chem., 279(31), 32957-32967.

Tang, M., Shen, X., Frank, E.G., O'Donnell, M., Woodgate, R., dan Goodman,

M.F. (1999) : UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V, Proc. Natl. Acad. Sci. U.S.A., 96(16), 8919-8924.

Teplyakov, A.V., Kuranova, I.P., Harutyunyan, E.H., Vainshtein, B.K., Frömmel,

C., Höhne, W.E., dan Wilson, K.S. (1990) : Crystal structure of thermitase at 1.4 Å resolution, J. Mol. Biol., 214(1), 261-279.

Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., dan Higgins, D.G.

(1997) : The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucl. Acids Res., 25(24), 4876-4882.

Tolner, B., Poolman, B., dan Konings, W.N. (1997) : Adaptation of

microorganisms dan their transport systems to high temperatures, Comp. Biochem. Physiol. A, Physiology, 118(3), 423-428.

Tomazic, S.J., dan Klibanov, A.M. (1988) : Mechanisms of irreversible thermal

inactivation of Bacillus alpha-amylases, J. Biol. Chem., 263(7), 3086-3091.

Trivedi, S., Gehlot, H.S., dan Rao, S.R. (2006) : Protein thermostability in

Archaea dan Eubacteria. Genet. Mol. Res., 5(4), 816-827. Tsai, J., dan Levitt, M. (2002) : Evidence of turn dan salt bridge contributions to

beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G, Biophys. Chem., 101-102, 187-201.

153

Turchi, J.J. Huang, L., Murante , R.S., Kim, Y., dan Bambara, R.A. 1994. Enzymatic completion of mammalian lagging-strdan DNA replication. Proc. Natl. Acad. Sci. U.S.A., 91(21), 9803-9807.

Turner, S., Ford, G.C., Mountain, A., dan Moir, A. (1992) : Selection of a

thermostable variant of chloramphenicol acetyltransferase (Cat-86), Protein Eng., 5(6), 535-541.

Uemori, T., Sato, Y., Kato, H., Doi, dan Kato, I. (1997) : A Novel DNA

polymerase in hyperthermophilic qrchaeon, Pyrococcus furiosus: Gene cloning, expression, dan characterization, Genesto Cells, 2 (8) , 499-512.

Urs, U.K., Murali, R. dan Murthy, H.M.K. (1999) : Structure of Taq DNA

polymerase shows a new orientation for the structure-specific nuclease domain, Acta Cryst., Sec. D, Biol. Cryst., 55, 1971-1977.

Venkatramani, R., dan Radhakrishnan, R. (2008) : Effect of oxidatively damaged

DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus, Proteins, 71(3), 1360-1372.

Ventosa, A., Nieto, J.J., dan Oren, A. (1998) : Biology of moderately halophilic

aerobic bacteria, Microbiol. Mol. Biol. Rev., 62 (2), 504-544. Vetriani, C., Maeder, D.L., Tolliday, N., Yip, K.S., Stillman, T.J., Britton, K.L.,

Rice, D.W., Klump, H.H., dan Robb, F.T. (1998) : Protein thermostability above 100°C: A key role for ionic interactions, Proc. Natl. Acad. Sci. U.S.A., 95(21), 12300-12305.

Vieille, C., Burdette, D.S., dan Zeikus, J.G. (1996) : Thermozymes, Biotechnol.

Annu. Rev., 2, 1-83. Vieille, C., dan Zeikus, G.J. (2001) : Hyperthermophilic enzymes: sources, uses,

dan molecular mechanisms for thermostability, Microbiol. Mol. Biol. Rev., 65(1), 1-43.

Villa, A., Zecca, L., Fusi, P., Colombo, S., Tedeschi, G., dan Tortora, P. (1993) :

Structural features responsible for kinetic thermal stability of a carboxypeptidase from the archaebacterium Sulfolobus solfataricus, Biochem. J., 295, 827-831.

Villbrdant, B., Sagner, G., dan Schomburg, D. (1997) : Investigations on the

thermostability dan function of truncated Thermus aquaticus DNA polymerase fragments, Protein Eng., 10(11), 1281-1288.

Villbrdant, B., Sobek, H., dan Schomburg, D. (2000) : Domain Exchange:

Chimeras of Thermus aquatiqus DNA Polymerase, Escherichia coli DNA

154

Polymerase I dan Thermotoga neapolitana DNA Polymerase, Protein Eng., 13 (9), 645-654.

Vogt, G., Woell, S., dan Argos, P. (1997) : Protein thermal stability, Hydrogen

bonds, dan Ion pairs, J. Mol. Biol., 269, 631-643. Wampler, J.E., Bradley, E.A., Stewart, D.E., dan Adams, M.W. (1993) : Modeling

the structure of Pyrococcus furiosus rubredoxin by homology to other X-ray structures, Protein Sci., 2(4), 640–649.

Wang, J., Yu, P., Lin, T.C., Konigsberg, W.H., Steitz, T.A. (1996) : Crystal

structures of an NH2-terminal fragment of T4 DNA polymerase dan its complexes with single-strdaned DNA dan with divalent metal ions, Biochemistry, 35(25), 8110-8119.

Wang, J., Sattar, A.K., Wang, C.C., Karam, J.D., Konigsberg, W.H., Steitz, T.A.

(1997) : Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69, Cell, 89(7), 1087-1099.

Wetzel, R. et al., 1988. Disulfide bonds dan thermal stability in T4 lysozyme.

Proc. Natl. Acad. Sci. U.S.A., 85(2), 401-405. Whitlow, M., Howard, A.J., Finzel, B.C., Poulos, T.L., Winborne, E., dan

Gillildan, G.L. (1991) : A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 Å Streptomyces rubiginosus structures with xylitol dan D-xylose, Proteins, 9(3), 153-173.

Wieligmann, K., Mayr, E.M., dan Jaenicke, R. (1999) : Folding dan self-assembly

of the domains of betaB2-crystallin from rat eye lens, J. Mol. Biol., 286(4), 989-994

Wilquet, V., Gaspar, J.A., van de Ldane, M., van de Casteele, M., Legrain, C.,

Meiering, E.M., dan Glansdorff, N. (1998) : Purification dan characterization of recombinant Thermotoga maritima dihydrofolate reductase, FEBS J., 255(3), 628-637.

Wood, T.C. dan Pearson, W.R. (1999) : Evolution of protein sequences dan

structures, J. Mol. Biol., 291(4), 977-995. Xiang, T., Liu, Q., Deacon, A.M., Koshy, M., Kriksunov, I.A., Lei, X.G., Hao, Q.,

dan Thiel, D.J. (2004) : Crystal structure of a heat-resilient phytase from Aspergillus fumigatus, carrying a phosphorylated histidine, J. Mol. Biol., 339(2), 437-445.

Xiao, L. dan Honig, B. (1999) : Electrostatic contributions to the stability of

hyperthermophilic protein, J. Mol. Biol, 289, 1435-1444.

155

Yang, L., Beard, W,, Wilson, S., Roux, B., Broyde, S., Schlick, T. (2002) : Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus, J. Mol. Biol., 321(3), 459-478

Yip, K.S., Britton, K.L., Stillman, T.J., Lebbink, J., de Vos, W.M., Robb, F.T.,

Vetriani, C., Maeder, D., Rice, D.W. (1998) : Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family, FEBS J., 255(2), 336-346.

Yip, K.S., Stillman, T.J., Britton, K.L., Artymiuk, P.J., Baker, P.J., Sedelnikov,

S.E., Engel, P.C., Pasquo, A., Chiaraluce, R., dan Consalvi, V. (1995) : The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures, Structure, 3(11), 1147-1158.

Zhang, J., Zhang, L., dan Zhou, L. (2004) : Thermostability of protein studied by

molecular dynamics simulation, J. Biomol. Struct. Dyn., 21(5), 657-662. Zhang, W., Mullaney, E.J., dan Lei, X.G. (2007) : Adopting selected hydrogen

bonding dan ionic interactions from Aspergillus fumigatus phytase structure improves the thermostability of Aspergillus niger PhyA phytase, Appl. Environ. Microbiol., 73(9), 3069-3076

Ziff, R.M. (1998) : Four-tap shift-register-sequence rdanom-number generators,

Comput. Phys., 12(4), 385-392.

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RIWAYAT HIDUP

Penulis dilahirkan sebagai putri pertama dari 2 bersaudara dari pasangan Bapak

Suba'i Deswanto dan Ibu Emmy Nurmiaty pada tanggal 4 November 1978 di

Jakarta.

Gelar Sarjana Kimia diperoleh pada tahun 2002 di Jurusan Kimia Institut

Teknologi Bandung dan Magister Sains diperoleh pada tahun 2005 di Program

Pascasarjana ITB dengan bidang biokimia. Pada tahun 2005 penulis mendapat

kesempatan untuk mengikuti Program Doktor di Program Pascasarjana ITB dalam

bidang Biokomputasi di bawah bimbingan Akhmaloka, PhD sebagai ketua,

Rukman Hertadi, DSc dan Muhamad Abdulkadir Martoprawiro, PhD sebagai

anggota Tim Pembimbing.

Sejak tahun 2006 hingga sekarang penulis menjadi staf pengajar di Program Studi

Kimia, Fakultas Matematika dan Ilmu Pengetahuan Alam, Institut Teknologi

Bandung.

Penulis menikah dengan H. Deki Ersanda, MM pada tahun 2005 dan dikaruniai

dua orang anak, yaitu Fatimah Azzahra, berusia 2.5 tahun, dan Muhammad

Dzakwan Ghozizahran, berusia 1.5 tahun.

Selama mengikuti pendidikan Program Doktor di ITB, penulis telah

mengkomunikasikan sebagian hasil-hasil penelitian yang telah diperoleh dalam

sejumlah majalah ilmiah/jurnal, antara lain :

1. R. Hertadi, S. Nurbaiti and Akhmaloka. Molecular Dynamics Analysis of

Thermostable DNA Pol I ITB-1. Microbiology Indonesia. 2007, 1(3):101-

104.

2. S. Nurbaiti, R. Hertadi, Muhamad A. Martoprawiro and Akhmaloka. The

Role of Interface Domain Interactions on Thermal Stability of DNA

polymerase I ITB-1, The Open Structural Biology Journal, 2009, 3 : 16-25.

157

3. S. Nurbaiti, R. Hertadi, Muhamad A. Martoprawiro and Akhmaloka.

Interface Domain Interactions on Early Stage Unfolding of DNA

polymerase I Klenow Fragment, International Journal of Integrative

Biology, 2009, 6(1) : 46-51

4. S. Nurbaiti, H. Nagao, H. Saito, R. Hertadi, Muhamad A. Martoprawiro

and Akhmaloka. In Silico Studies of Domain Motion of DNA polymerase I

ITB-1 in the Absence of Substrate (manuscript).

Selama mengikuti pendidikan Program Doktor di ITB, penulis telah mengikuti

pula beberapa kegiatan seminar, antara lain:

1. R. Hertadi, S. Nurbaiti and Akhmaloka. Computational Study to Investigate

the Thermostability of DNA Polymerase I ITB-1, Proceeding 1st

International Conferences on Mathematics and Natural Sciences, Bandung,

2006

2. S. Nurbaiti, R. Hertadi, M. A. Martoprawiro and Akhmaloka. Study of the

unfolding mechanisms of DNA Polymerase I ITB-1 by Molecular Dynamics

Simulation, 1st International Conferences on Chemical Sciences,

Yogyakarta, 2007.

3. S.Nurbaiti, R. Hertadi, M. A. Martoprawiro and Akhmaloka. Molecular

Dynamics of Klenow Fragment DNA Pol I from E.coli and DNA Pol I from

G.thermoleovorans at 300K and 350K, Proceeding of the 1st International

Conference on Computational Sciences ITB-Kanazawa, Bandung, 2007.

4. S. Nurbaiti, R. Hertadi, M.A. Martoprawiro and Akhmaloka. Unfolding

Mechanisms of DNA Pol I ITB-1 at Various Temperature Based on

Molecular Dynamics Study, Proceeding of the Joint Seminar on Chemistry

VII ITB-UKM, Bandung, 2007.

5. Akhmaloka, S. Nurbaiti, M.A. Martoprawiro, R. Hertadi and F. Madayanti.

From Thermophiles to Thermostable Enzymes : A Case Study on Indonesia

Hot Springs, Proceeding of the Joint Seminar on Chemistry VII ITB-UKM,

Bandung, 2007

6. R. Hertadi, S. Nurbaiti and Akhmaloka. Structure and Dynamics of Klenow

Fragment of DNA Pol I Studied by Molecular Dynamics and Normal Mode

158

Analysis, Proceeding of the Joint Seminar on Chemistry VII ITB-UKM,

Bandung, 2007.

7. S. Nurbaiti, R. Hertadi, M.A. Martoprawiro and Akhmaloka. Open and

Closed Conformational Changes of DNA Pol I ITB-1 at 300K captured by

Molecular Dynamics Study, The 2nd Gruber-Soedigdo Lecture, Bandung,

2008.

8. S. Nurbaiti, R. Hertadi, M.A. Martoprawiro and Akhmaloka. Early

Unfolding of Thermostable and Thermolabile Klenow-like DNA polymerase

I based on Molecular Dynamics Simulation, The Joint Seminar on

Chemistry VIII UKM-ITB, Bangi-Malaysia, 2009.