I= COMPUTATIONAL STUDIES ON THE STUCTURE OF β-CHITIN AND OTHER POLYSACCHARIDES
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Title of Thesis
COMPUTATIONAL STUDIES ON THE STUCTURE OF β-CHITIN AND OTHER POLYSACCHARIDES

Author(s)
Aliya Zafer
Institute/University/Department Details
University of Karachi/ Department of Biochemistry
Session
2001
Subject
Biochemistry
Number of Pages
147
Keywords (Extracted from title, table of contents and abstract of thesis)
β-chitin, polysaccharides, cellulose

Abstract
The purpose of the present work is to study the structure of β-chitin and cellulose 1 by using modern computer facilities now available. The unit cell for β-chitin is monoclinic with dimensions a =4.85Ǻ, b = 10.38 Ǻ (fiber axis), c = 9.26 Ǻ and β = 97.5 the space group is P21

The location of water molecule in the β-chitin structure is varied along with other parameters (P1, P3, P4, P5, P6, P7, P8). The R-value was found to be 0.268. The structure was then refined using following parameters P1=236.628, P3 = 2.296, P4 = 3.9, P5 = -4, P6 = 0.087, P7 = 2.484, P8 = 0.1198532 and the position of water molecule (Xw, Yw, Zw). The R-value is reduced to 0.246 from 0.246. The Ǿ-value was found to be 38.491

The values of the parameters after refinement were found to be P1 = 236.628, P3 = 2.296, P4 = 3.90, P5 = -4, P6 = 0.087, P7 = 2.484, P8 = 0.1198532. The co-ordinates of water molecule, after refinement by least squares method are found to be Xw = 2.832, Yw = 4.790, Zw = 2.511

Difference fourier synthesis map for the model of β-chitin with water, after refinement by least squares method indicates the improvement of structure

The chains possess three H-bonds; O3 (II residue)-H…Ow has distance 2.41Ǻ;O5 (III resideue)-H…Ow has distance about 2.91Ǻ and O3 (IV residue)-H…Ow has distance about 3.02Ǻ. Total potential energy by Kitaigorodsky (1961) function was then computed. The minimum potential energy was found to be at Ǿ = 220 for (K1) and 240 for (K2). This value is very close to the value obtained by least squares refinement (Ǿ = 236.62). The above calculations suggest that O6 atom in the structure of β-chitin does not lie in gt conformation (Gardner and Blackwell, 1975)

The structure of cellulose 1 has been determined using the intensity data from alga Valonia ventricosa and rigid body least squares method. The unit cell is monoclinic with dimensions a = 817Ǻ and β = 97. The space group is P21. Four geometrical parameters )P1 = 130.190, P2 = 80.00, P3 = -6.328, P4 = -7.504 and temperature factor (P5 = -1.243) and scaling factor (P6 = 0.457) were used to refine the structure by least squares method. R-values were reduced from 0.334 to 0.271 and Ǿ-value wasd found to be 1625.020 respectively

The chains posses two intra-chain hydrogen bonds O5 (1 chain)-H…O3 (II chain) (2.64Ǻ), O6 (II chain)-H…O2 (I chain) (2.53Ǻ) and one inter-chain hydrogen bond O6 (I chain)-H…O3 (III chain) (3.08Ǻ)

Potential energy calculations involving orientation of O6 atom indicate that O6 atom can adopt different conformations in different chains in the monoclinic unit cell which are related to the symmetry. Different orientations of the O6 atom might give statistical model for cellulose 1

By the help of least squares method, the best position of O6 atom was redetermined, and values are found to be Ǿ = 130.19 (first chain) and Ǿ = 80 (Center chain). At this position, R and Ǿ-values are found to be 0.271 and 1625.020 respectively. The present calculations suggest parallel down model for cellulose 1 (1β)

Download Full Thesis
2316.45 KB
S. No. Chapter Title of the Chapters Page Size (KB)
1 0 Contents 0
119.39 KB
2 1 Part-1: Studies On The Structure Of Β-Chitin/Historical Introduction 1
299.09 KB
  1.1 Earlier Structure Of Β-Chitin 2
  1.2 Comparison Of A And Β-Chitin 9
  1.3 Water Mediated Structure Of Β-Chitin 9
  1.4 Polysaceharide Conformation And Position Of O6 Atom 12
  1.5 Other Polysaccharide 13
  1.6 Derivative Of Chitin; Chitosan 16
  1.7 Chitin Protein Complex 18
3 2 Comparision Of Structures Factor Calculations For Earlier Models 21
93 KB
  2.1 Computer Method For The Determination Of Structure Factors 21
  2.2 Calculation Of R-Value 24
  2.3 Ǿ-Value 25
  2.4 Calculations Of Intensities Of Composite Reflections 25
  2.5 Comparison Of The Above Structures 26
  2.6 Conclusion 28
4 3 Calulatiions Of Structure Factors, R And Ǿ-Values For Modified Model Of Β-Chitin 29
503.52 KB
  3.1 Rotation Of O6 Atom C5-C6 Axis 29
  3.2 Shift Of Molecular Chain Along Its Length 32
  3.3 Rotation Of Peptide Group About An Axis Through C2 Parallel To Ox 32
  3.4 Rotation Of C5-C6-O6 Group About An Axis Through C5 Parallel To Ox 33
  3.5 Rotation Of C5-C6-O6 Group About An Axis Through C5 Parallel To Py 33
  3.6 Rotation Of Molecular Chain About Screw Axis 34
  3.7 Isotropic Factor 33
  3.8 Results Of The Modified Model Of Β-Chitin After Trail And Error Method 35
  3.9 Determination Of New Position Of Water Molecule In The Structure Of Β-Chitin 35
  3.10 Results Of The Modified Model Of Β-Chitin With Water (Before Refinement) 38
  3.11 Conclusion 33
5 4 Difference Fourier Synthesis Maps For Β-Chitin 40
93.28 KB
  4.1 Expressions For Difference Fourier Synthesis 40
  4.2 Computation Of Difference Fourier Synthesis For 010 Projection 42
  4.3 Difference Synthesis Map For Gardner And Balckwell (1975) Model 43
  4.4 Difference Synthesis Map For Akhtar And Haleem (1990) Model 43
  4.5 Difference Synthesis Map For Model Of Β-Chitin (This Work) 43
  4.6 Conclusion 44
6 5 Refinement Of The Structure By Least Squares Method 45
202.52 KB
  5.1 Mathematical Analysis Of The Least Squares Refinement Method 46
  5.2 Rate Of Change Of Structure Factors With Respect To Parameters 50
  5.3 Calculation Of A/X1, A/X1, A/X1 And B/X1, B/X1, B/X1 For The Space Group P21 50
  5.4 Calculations Of Rate Of Change Of Structure Factors With Respect To Parameters 51
  5.5 Calculation Of Δu 57
  5.6 Correction Of Parameters 57
  5.7 Initial Stage Of Refinement And Development Of Programs 57
  5.8 Results For The Refined Model Of Β-Chitin By The Least Squares Method 58
  5.9 Difference Synthesis Map For The Refined Model Of Β-Chitin With Water 58
  5.10 Conclusion 59
7 6 Confromational Analysis Of Side Chains In The Structure Of Β-Chitin On The Basis Of Potential Energy Caculations 61
149.67 KB
  6.1 Method Of Calculations 62
  6.2 Contribution Of Potential Energy Function 62
  6.3 Total Conformational Energy 63
  6.4 Conformation Of The O6 Atom For The Model Of Β-Chitin 70
  6.5 Conforamtion Of The O6 Atom For The Model Of Β-Chitin With Water (After Refinement) 71
  6.6 Conclusion 72
8 7 Discussion 73
198.14 KB
9 8 Part-2: Studies On The Structure Of Cellulose 1 (1β)/Introduction 79
213.22 KB
  8.1 Crystal Structures Of Cellulose 1 81
  8.2 Hydrogen Bonding Network (In Cellulose 1 And Cellulose Ii) 85
  8.3 Conformation Of Side Chain 88
  8.4 Packing Analysis Of Cellulose Sheet In Cellulose 1 89
  8.5 Cellulose Ii 90
10 9 Refinement Of The Structure By Least Squares Method 93
206.08 KB
  9.1 Refinement Of The Structure Of Cellulose 1 By Least Squares Method 94
  9.2 Rifinement By Least Squares Method 95
  9.3 Retational Conformation Of –Ch2oh In The Structure Of Cellulose 1 (Refined Model This Work) On The Basis Of Potential Energy Calculations 95
11 10 Discussion 99
566.74 KB
  10.1 Future Prospects 103
  10.2 Appendix-A 104
  10.3 Appendix-B 127
  10.3 References 142