臺灣博碩士論文加值系統

核磁共振是用來解蛋白質三維結構的主要實驗方法之一。該技術通常用於解析較小的蛋白質。在先前的結果，我們已由結晶所解出的蛋白質中，觀察到結構堆疊程度和序列的保留程度存有一定相關性。藉由考慮或忽略複合體中其它的subunits，我們發現該蛋白質的結構堆疊程度會相近於它的胺基酸的保留程度。這結果顯示，蛋白質可能會傾向形成有或無其他分子伴隨的構形，進而在演化過程施加約束力。 在此篇研究，由核磁共振技術解出的蛋白質所組成的資料集中，藉由比較結構堆疊程度和序列的保留程度，我們發現與先前研究一致的結果。基於蛋白質的大小，我們觀察到結構屬性的一些明顯趨勢，可能在後續研究核磁共振所解出的蛋白質其結構堆疊程度時，能作為有用的指引。雖然核磁共振所解出的蛋白質結構，在過去常被認為大部分品質低落於結晶蛋白。但在我們的結果中，兩者結構差異性似乎並不顯著。本篇論文也許對研究核磁共振解出的蛋白質，其結構和演化間的關係有所幫助。

Nuclear Magnetic Resonance (NMR) is one of primary experimental methods to determine protein three-dimensional structures. This technique is usually used for smaller protein. In our previous study, we have observed that the structural packing profile has correlated to the sequence conservation profile of a protein determined by X-ray. By considering or ignoring other subunits in a complex, we found that the degree of structural packing of a protein will become closer to its conservation of residues. The result suggests that a protein may tend to form the conformation, which exerts constraints on its evolutionary processes, by accompanied with or without other molecules. Here, we find the consistent result that conforms our previous study in a dataset composed of NMR proteins. Based on protein size, we observe some obvious tendencies of structural properties that may be a useful guide for studying the structural packing of NMR proteins. Although NMR structures were viewed as being of generally lower quality than X-ray structures, in our result, the consequences show a small difference between the two kinds of structures. Our research may contribute to people who want to study the relationship between structure and evolution of NMR proteins.

摘要............................................................................................................i
ABSTRACT..............................................................................................ii
誌謝..........................................................................................................iii
CONTENTS.............................................................................................iv
FIGURE CONTENTS.............................................................................v
TABLE CONTENTS………………………………………………….vii
INTRODUCTION………………………………………………………1
METHODS...............................................................................................8
The weighted contact number profile.…………………………….8
The sequence conservation profile...……………………………...9
Dataset……………………………………………………………10
RESULTS……………………………………………………………....11
Comparison of the weighted contact number profiles and the sequence conservation profiles…………………………………..11
The protein size affects structural properties of NMR proteins…16
Analysis of the NMR and the X-ray structure of same proteins…27
CONCLUSIONS………………………………………………………40
FUTURE WORKS…………………………………………………….41
REFERENCE………………………………………………………….42
APPENDIX…………………………………………………………….46

1. Bernstein FC, Koetzle TF. Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard 0, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol;112:535-542.
2. Berman HM. The Protein Data Bank: a historical perspective. Acta Crystallogr A 2008;64:88-95.
3. Mao B, Guan R, Montelione GT. Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure 2011;19(6):757-766.
4. Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P. Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 2012;20(2):227-236.
5. Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T. CASD-NMR: critical assessment of automated structure determination by NMR. Nature methods 2009;6(9):625-626.
6. Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, Wagner G. Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 2008;321(5893):1206-1210.
7. Hiller S, Wagner G. The role of solution NMR in the structure determinations of VDAC-1 and other membrane proteins. Current opinion in structural biology 2009;19(4):396-401.
8. Lange OF, Rossi P, Sgourakis NG, Song Y, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proceedings of the National Academy of Sciences 2012;109(27):10873-10878.
9. Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T. NMR structure determination for larger proteins using backbone-only data. Science 2010;327(5968):1014-1018.
10. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Science 1994;3(3):522-524.
11. Laskowski RA. Structural quality assurance. Structural Bioinformatics 2003;44:273-303.
12. Ratnaparkhi GS, Ramachandran S, Udgaonkar JB, Varadarajan R. Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. Biochemistry 1998;37(19):6958-6966.
13. Doreleijers JF. Validation of Biomolecular NMR Structures.
14. Doreleijers JF, Raves ML, Rullmann T, Kaptein R. Completeness of NOEs in protein structures: A statistical analysis of NMR data. Journal of biomolecular NMR 1999;14(2):123-132.
15. Doreleijers JF, Rullmann JAC, Kaptein R. Quality assessment of NMR structures: a statistical survey. Journal of molecular biology 1998;281(1):149-164.
16. Doreleijers JF, Vriend G, Raves ML, Kaptein R. Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature. Proteins: Structure, Function, and Bioinformatics 1999;37(3):404-416.
17. Nabuurs SB, Spronk C, Vuister GW, Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2006;2(2):e9.
18. Rosato A, Tejero R, Montelione GT. Quality assessment of protein NMR structures. Current opinion in structural biology 2013;23(5):715-724.
19. Vuister GW, Fogh RH, Hendrickx PMS, Doreleijers JF, Gutmanas A. An overview of tools for the validation of protein NMR structures. Journal of biomolecular NMR 2014;58(4):259-285.
20. Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D: Biological Crystallography 2009;66(1):12-21.
21. Chang CM, Huang YW, Shih CH, Hwang JK. On the relationship between the sequence conservation and the packing density profiles of the protein complexes. Proteins: Structure, Function, and Bioinformatics 2013;81(7):1192-1199.
22. Stamper CGF, Morollo AA, Ringe D. Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine. Biochemistry 1998;37(29):10438-10445.
23. Bernstein BE, Michels PAM, Hol WGJ. Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. 1997.
24. Lin CP, Huang SW, Lai YL, Yen SC, Shih CH, Lu CH, Huang CC, Hwang JK. Deriving protein dynamical properties from weighted protein contact number. Proteins: Structure, Function, and Bioinformatics 2008;72(3):929-935.
25. Halle B. Flexibility and packing in proteins. Proceedings of the National Academy of Sciences 2002;99(3):1274-1279.
26. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic acids research 2010:gkq399.
27. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A. Uniprotkb/swiss-prot. Plant bioinformatics: Springer; 2007. p 89-112.
28. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 1997;25(17):3389-3402.
29. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22(13):1658-1659.
30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 2004;32(5):1792-1797.
31. Mayrose I, Graur D, Ben-Tal N, Pupko T. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Molecular biology and evolution 2004;21(9):1781-1791.
32. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution 1987;4(4):406-425.
33. Shih CH, Chang CM, Lin YS, Lo WC, Hwang JK. Evolutionary information hidden in a single protein structure. Proteins: Structure, Function, and Bioinformatics 2012;80(6):1647-1657.
34. Huang SW, Yu SH, Shih CH, Guan HW, Huang TT, Hwang JK. On the relationship between catalytic residues and their protein contact number. Current Protein and Peptide Science 2011;12(6):574-579.
35. Yuan Z, Zhao J, Wang ZX. Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein engineering 2003;16(2):109-114.
36. Creighton TE. Disulphide bonds and protein stability. BioEssays 1988;8(2‐3):57-63.
37. Mangani S. Disruption of Protein-protein Interfaces: In Search of New Inhibitors: Springer Science &; Business Media; 2013.
38. Barb AW, Jiang L, Raetz CRH, Zhou P. Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: time-dependent inhibition and specificity in ligand binding. Proceedings of the National Academy of Sciences 2007;104(47):18433-18438.
39. Thornton JM, Sibanda BL, Edwards MS, Barlow DJ. Analysis, design and modification of loop regions in proteins. Bioessays 1988;8(2‐3):63-69.
40. Prlić A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE. Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics 2010;26(23):2983-2985.
41. Downing AK. Protein Nuclear Magnetic Resonance Techniques: Springer Science &; Business Media; 2004.
42. Hayashi F, Ishima R, Liu D, Tong KI, Kim S, Reinberg D, Bagby S, Ikura M. Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain. Biochemistry 1998;37(22):7941-7951.
43. Huang YW, Chang CM, Hwang JK. The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein. Proteins: Structure, Function, and Bioinformatics 2015.
44. Liao DI, Calabrese JC, Wawrzak Z, Viitanen PV, Jordan DB. Crystal structure of 3, 4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis. Structure 2001;9(1):11-18.
45. Bastos‐Aristizabal S, Kozlov G, Gehring K. Structural insight into the dimerization of human protein disulfide isomerase. Protein Science 2014;23(5):618-626.