Topology in molecular biology: [DNA and proteins]
Gespeichert in:
| Weitere Verfasser: | |
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Berlin ; Heidelberg ; New York
Springer
2007
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| Schriftenreihe: | Biological and medical physics, biomedical engineering
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| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | Literaturangaben |
| Beschreibung: | XIV, 238 S. Ill., graph. Darst. 24 cm |
| ISBN: | 9783540234074 3540234071 |
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| 245 | 1 | 0 | |a Topology in molecular biology |b [DNA and proteins] |c M. I. Monastyrsky (ed.) |
| 264 | 1 | |a Berlin ; Heidelberg ; New York |b Springer |c 2007 | |
| 300 | |a XIV, 238 S. |b Ill., graph. Darst. |c 24 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
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| 490 | 0 | |a Biological and medical physics, biomedical engineering | |
| 500 | |a Literaturangaben | ||
| 650 | 4 | |a Biologie moléculaire | |
| 650 | 2 | |a Biologie moléculaire | |
| 650 | 7 | |a Biologie moléculaire |2 ram | |
| 650 | 2 | |a Modèle génétique | |
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| 650 | 0 | 7 | |a Topologische Methode |0 (DE-588)4312758-7 |2 gnd |9 rswk-swf |
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| 700 | 1 | |a Monastyrskij, Michail I. |d 1945- |0 (DE-588)121283623 |4 edt | |
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Datensatz im Suchindex
| _version_ | 1804136293868765184 |
|---|---|
| adam_text | Contents
1 Introduction
M. Monastyrnky 1
2 Topology in Biology: From DNA Mechanics to Enzymology
S.D. Le.ve.ne. 3
2.1 Overview 3
2.1.1 Why Study DNA Topology? 4
2.1.2 Secondary and Tertiary Structure of DXA 4
2.1.3 DNA Flexibility 5
2.1.4 Topology of Circular DNA Molecules 9
2.1.5 Flexibility and Topology of DNA. and Their Relation
to Genome Organization 13
2.1.6 DNA Topology and Enzymology: Flp Site Specific
Recombination 15
2.1.7 Chromatin and Recombination Wrapping It All Up 20
References 20
3 Monte Carlo Simulation of DNA Topological Properties
A. Vologodskii 23
3.1 Introduction 23
3.2 Circular DNA and Supercoiling 24
3.3 Testing the DNA Model 2(i
3.4 DNA Model 2!)
3.5 Analysis of Topologieal State for a Particular Conformation 33
3.5.1 Knots 33
3.5.2 Links 35
3.6 Calculation of Writhe 37
3.7 Simulation Procedure 38
3.7.1 General Approach 38
3.7.2 Simulation of DNA Conformations with Low Probability
of Appearance 39
References 40
VIII Contents
4 Dynamics of DNA Supercoiling
A. Gabibov, E. Yakubovskaya, M. Lukin, P. Favorov, A. Reshetnyak,
and M. Monastyrsky 43
4.1 Introduction 43
4.2 Theory 45
4.2.1 Flow Linear Dichroisrn and Dynamics of DNA Supercoiling 47
4.2.2 Mechanisms of Biocatalytic DNA Relaxation 50
4.2.3 Interaction of scDNA with Eukaryotic DNA Topoisomerases 54
4.2.4 Dynamics of Drug Targeting 63
4.3 Conclusions 64
References 66
5 From Tangle Fractions to DNA
L.H. Kauffman, S. Lambropoulou 69
5.1 Introduction 69
5.2 Two Tangles and Rational Tangles 71
5.3 Continued Fractions and the Classification of Rational Tangles. ... 77
5.4 Alternate Definitions of the Tangle Fraction 81
5.4.1 F(T) Through the Bracket Polynomial 81
5.4.2 The Fraction Through Colouring 90
5.4.3 The Fraction Through Conductance 92
5.5 The Classification of Unoriented Rational Knots 92
5.6 Rational Knots and Their Mirror Images 97
5.7 The Oriented Case 99
5.8 Strongly Invertible Links 103
5.9 Applications to the Topology of DNA 103
References 108
6 Linear Behavior of the Writhe Versus the Number
of Crossings in Rational Knots and Links
C. Cerf, A. Stasiak Ill
6.1 Introduction Ill
6.2 Rational Tangles and Rational Links 114
6.3 Writhe of Families of Rational Links 114
6.3.1 Tangles with One Row, Denoted by (a), a Positive Integer . 114
6.3.2 Tangles with Two Rows, Denoted by (a)(b), a and b
Positive Integers 117
6.3.3 Tangles with Three Rows. Denoted by (a)(6)(c), a, b, and
c Positive Integers 120
6.3.4 Tangles with r Rows 120
6.4 Discussion 122
6.4.1 When is PWr a Linear Function of n? 122
6.4.2 PWr of Achiral Knots 123
6.4.3 Shifts Between PWr as Linear Functions of n 123
6.4.4 Knots Versus Two Component Links 124
Contents IX
6.5 Conclusion 124
References 125
7 Combinatories and Topology of the P Sandwich
and P Barrel Proteins
A.E. Kister, M. V. Kleyzit, T.I. G elf and, I.M. G elf and 127
7.1 Introduction 127
7.2 Overview of the Structures 129
7.3 Common Features in Structures and Sequences of Sandwich
Like Proteins 130
7.3.1 General Features of the Sandwich Like Proteins 130
7.3.2 Supersecondary Patterns in the Sandwich Like Proteins . . . 130
7.3.3 Structurally Based Sequence Alignment 132
7.3.4 Sequence Characteristics of the ¦/, i + 1, k. and k + 1
Strands 132
7.3.5 Structural Features of the Sequence Determinants 132
7.3.6 Method of the Sequence Determinants for Identification
of Proteins 133
7.4 Common Structural and Sequence Features of Barrel Like Proteins 135
7.4.1 Search for Sequence and Structural Invariants in Barrel
Proteins: An Outline of the Approach 135
7.4.2 Overview of the p Barrel Structures 135
7.4.3 Defining of the P Strands and Loops 136
7.4.4 Arrangement of the Strands in the p Sheet 136
7.4.5 Two Subsheets in the Barrel Structures 139
7.4.6 Four Types of Connection Between the Strands
in Two Subsheets 139
7.4.7 Classification of Barrel Based on the Strands Arrangement 140
7.4.8 Characterizing the Place of Distortion of Barrel Structures 141
7.4.9 The Rule of the Arrangement of the Edge Strands
in the Barrel Structures 141
7.4.10 Arrangement of the Barrel and Sandwich Structures
is Different 141
7.4.11 Invariant Substructure at the Place of Distortion:
A Hydrophobic Tetrahedral 142
7.4.12 The Two Hydrophobic Tetrahedrals Present the
Structural Invariant of Barrel Proteins 143
7.5 Conclusion 143
References 144
8 The Structure of Collagen
N. Rivier. J. F. Sadoc 147
8.1 Collagen: Chain. Molecule. Fibril 147
8.2 The Boerdijk Coxeter Helix and its Approximants 149
8.3 The Collagen Molecule 151
X Contents
8.4 Decurving 152
8.5 Transverse Structures (gap, overlap) on Two Orthogonal
Triangular Lattices 157
8.6 The Gap Structure 158
8.7 The Overlap Structure 158
8.8 Transverse Structure; Coincidence Lattice of Two Orthogonal,
Triangular Lattices; Approximants of /3 159
8.9 Twist Grain Boundary Overlap (Gap) Overlap 161
References 162
9 Euler Characteristic, Dehn Sommerville Characteristics,
and Their Applications
V.M. Buchstaber 163
9.1 Introduction 163
9.2 Simplicial Complexes and Maps 163
9.3 Euler Characteristic and Dehn Sommerville Characteristics 165
9.4 Homology Groups and Characteristic Classes 167
9.5 Classification of 2 Manifolds 169
9.6 Minimal and Neighbourly Triangulations 172
9.7 Smooth Manifolds 173
References 176
10 Hopf Fibration and Its Applications
M. Monastyrsky 177
10.1 Classical Hopf Fibration 177
10.1.1 Constructing the Hopf Fibrations 177
10.1.2 Linking Numbers 179
10.1.3 Intersection Number 179
10.2 Hopf Invariant 180
10.2.1 Definition of Hopf Invariant 180
10.2.2 Integral Representation of the Hopf Invariant 181
10.3 Applications of Hopf Invariant 181
10.3.1 Generalized Linking Number 182
10.3.2 Formula Calugareanu and Supercoiled DNA 184
10.3.3 Hopf Fibration and Membranes 185
10.3.4 Construction of Hopf tori 186
References 187
11 Multi Valued Functionals, One Forms and Deformed
de Rham Complex
D. V. Millionschikov 189
11.1 Introduction 189
11.2 Dirac Monopole, Multi Valued Actions
and Feynman Quantum Amplitude 190
11.3 Aharonov Bohm Field and Equivalent Quantum Systems 192
11.4 Semi Classical Motion of Electron and Critical Points of 1 Form . . 194
Contents XI
11.5 Witten s Deformation of de Rham Complex and
Morse Novikov Theory 195
11.6 Solvmanifolds and Left Invariant Forms 199
11.7 Deformed Differential and Lie Algebra Cohomology 202
References 207
12 The Spectral Geometry of Riemann Surfaces
R. Brooks 209
12.1 Introduction 209
12.2 An Opening Question 210
12.3 The Noncompact Case 211
12.4 Belyi Surfaces 214
12.5 The Basic Construction 218
12.6 The Ahlfors Schwarz Lemma 222
12.7 Large Cusps 226
12.8 The Spaghetti Model 229
12.9 An Annotated Bibliography 234
References 235
Index 237
|
| adam_txt |
Contents
1 Introduction
M. Monastyrnky 1
2 Topology in Biology: From DNA Mechanics to Enzymology
S.D. Le.ve.ne. 3
2.1 Overview 3
2.1.1 Why Study DNA Topology? 4
2.1.2 Secondary and Tertiary Structure of DXA 4
2.1.3 DNA Flexibility 5
2.1.4 Topology of Circular DNA Molecules 9
2.1.5 Flexibility and Topology of DNA. and Their Relation
to Genome Organization 13
2.1.6 DNA Topology and Enzymology: Flp Site Specific
Recombination 15
2.1.7 Chromatin and Recombination Wrapping It All Up 20
References 20
3 Monte Carlo Simulation of DNA Topological Properties
A. Vologodskii 23
3.1 Introduction 23
3.2 Circular DNA and Supercoiling 24
3.3 Testing the DNA Model 2(i
3.4 DNA Model 2!)
3.5 Analysis of Topologieal State for a Particular Conformation 33
3.5.1 Knots 33
3.5.2 Links 35
3.6 Calculation of Writhe 37
3.7 Simulation Procedure 38
3.7.1 General Approach 38
3.7.2 Simulation of DNA Conformations with Low Probability
of Appearance 39
References 40
VIII Contents
4 Dynamics of DNA Supercoiling
A. Gabibov, E. Yakubovskaya, M. Lukin, P. Favorov, A. Reshetnyak,
and M. Monastyrsky 43
4.1 Introduction 43
4.2 Theory 45
4.2.1 Flow Linear Dichroisrn and Dynamics of DNA Supercoiling 47
4.2.2 Mechanisms of Biocatalytic DNA Relaxation 50
4.2.3 Interaction of scDNA with Eukaryotic DNA Topoisomerases 54
4.2.4 Dynamics of Drug Targeting 63
4.3 Conclusions 64
References 66
5 From Tangle Fractions to DNA
L.H. Kauffman, S. Lambropoulou 69
5.1 Introduction 69
5.2 Two Tangles and Rational Tangles 71
5.3 Continued Fractions and the Classification of Rational Tangles. . 77
5.4 Alternate Definitions of the Tangle Fraction 81
5.4.1 F(T) Through the Bracket Polynomial 81
5.4.2 The Fraction Through Colouring 90
5.4.3 The Fraction Through Conductance 92
5.5 The Classification of Unoriented Rational Knots 92
5.6 Rational Knots and Their Mirror Images 97
5.7 The Oriented Case 99
5.8 Strongly Invertible Links 103
5.9 Applications to the Topology of DNA 103
References 108
6 Linear Behavior of the Writhe Versus the Number
of Crossings in Rational Knots and Links
C. Cerf, A. Stasiak Ill
6.1 Introduction Ill
6.2 Rational Tangles and Rational Links 114
6.3 Writhe of Families of Rational Links 114
6.3.1 Tangles with One Row, Denoted by (a), a Positive Integer . 114
6.3.2 Tangles with Two Rows, Denoted by (a)(b), a and b
Positive Integers 117
6.3.3 Tangles with Three Rows. Denoted by (a)(6)(c), a, b, and
c Positive Integers 120
6.3.4 Tangles with r Rows 120
6.4 Discussion 122
6.4.1 When is PWr a Linear Function of n? 122
6.4.2 PWr of Achiral Knots 123
6.4.3 Shifts Between PWr as Linear Functions of n 123
6.4.4 Knots Versus Two Component Links 124
Contents IX
6.5 Conclusion 124
References 125
7 Combinatories and Topology of the P Sandwich
and P Barrel Proteins
A.E. Kister, M. V. Kleyzit, T.I. G elf and, I.M. G elf and 127
7.1 Introduction 127
7.2 Overview of the Structures 129
7.3 Common Features in Structures and Sequences of Sandwich
Like Proteins 130
7.3.1 General Features of the Sandwich Like Proteins 130
7.3.2 Supersecondary Patterns in the Sandwich Like Proteins . . . 130
7.3.3 Structurally Based Sequence Alignment 132
7.3.4 Sequence Characteristics of the ¦/, i + 1, k. and k + 1
Strands 132
7.3.5 Structural Features of the Sequence Determinants 132
7.3.6 Method of the Sequence Determinants for Identification
of Proteins 133
7.4 Common Structural and Sequence Features of Barrel Like Proteins 135
7.4.1 Search for Sequence and Structural Invariants in Barrel
Proteins: An Outline of the Approach 135
7.4.2 Overview of the p Barrel Structures 135
7.4.3 Defining of the P Strands and Loops 136
7.4.4 Arrangement of the Strands in the p Sheet 136
7.4.5 Two Subsheets in the Barrel Structures 139
7.4.6 Four Types of Connection Between the Strands
in Two Subsheets 139
7.4.7 Classification of Barrel Based on the Strands Arrangement 140
7.4.8 Characterizing the Place of Distortion of Barrel Structures 141
7.4.9 The Rule of the Arrangement of the "Edge Strands"
in the Barrel Structures 141
7.4.10 Arrangement of the Barrel and Sandwich Structures
is Different 141
7.4.11 Invariant Substructure at the Place of Distortion:
A Hydrophobic Tetrahedral 142
7.4.12 The Two Hydrophobic Tetrahedrals Present the
Structural Invariant of Barrel Proteins 143
7.5 Conclusion 143
References 144
8 The Structure of Collagen
N. Rivier. J. F. Sadoc 147
8.1 Collagen: Chain. Molecule. Fibril 147
8.2 The Boerdijk Coxeter Helix and its Approximants 149
8.3 The Collagen Molecule 151
X Contents
8.4 Decurving 152
8.5 Transverse Structures (gap, overlap) on Two Orthogonal
Triangular Lattices 157
8.6 The Gap Structure 158
8.7 The Overlap Structure 158
8.8 Transverse Structure; Coincidence Lattice of Two Orthogonal,
Triangular Lattices; Approximants of \/3 159
8.9 Twist Grain Boundary Overlap (Gap) Overlap 161
References 162
9 Euler Characteristic, Dehn Sommerville Characteristics,
and Their Applications
V.M. Buchstaber 163
9.1 Introduction 163
9.2 Simplicial Complexes and Maps 163
9.3 Euler Characteristic and Dehn Sommerville Characteristics 165
9.4 Homology Groups and Characteristic Classes 167
9.5 Classification of 2 Manifolds 169
9.6 Minimal and Neighbourly Triangulations 172
9.7 Smooth Manifolds 173
References 176
10 Hopf Fibration and Its Applications
M. Monastyrsky 177
10.1 Classical Hopf Fibration 177
10.1.1 Constructing the Hopf Fibrations 177
10.1.2 Linking Numbers 179
10.1.3 Intersection Number 179
10.2 Hopf Invariant 180
10.2.1 Definition of Hopf Invariant 180
10.2.2 Integral Representation of the Hopf Invariant 181
10.3 Applications of Hopf Invariant 181
10.3.1 Generalized Linking Number 182
10.3.2 Formula Calugareanu and Supercoiled DNA 184
10.3.3 Hopf Fibration and Membranes 185
10.3.4 Construction of Hopf tori 186
References 187
11 Multi Valued Functionals, One Forms and Deformed
de Rham Complex
D. V. Millionschikov 189
11.1 Introduction 189
11.2 Dirac Monopole, Multi Valued Actions
and Feynman Quantum Amplitude 190
11.3 Aharonov Bohm Field and Equivalent Quantum Systems 192
11.4 Semi Classical Motion of Electron and Critical Points of 1 Form . . 194
Contents XI
11.5 Witten's Deformation of de Rham Complex and
Morse Novikov Theory 195
11.6 Solvmanifolds and Left Invariant Forms 199
11.7 Deformed Differential and Lie Algebra Cohomology 202
References 207
12 The Spectral Geometry of Riemann Surfaces
R. Brooks 209
12.1 Introduction 209
12.2 An Opening Question 210
12.3 The Noncompact Case 211
12.4 Belyi Surfaces 214
12.5 The Basic Construction 218
12.6 The Ahlfors Schwarz Lemma 222
12.7 Large Cusps 226
12.8 The Spaghetti Model 229
12.9 An Annotated Bibliography 234
References 235
Index 237 |
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV022283604 |
| illustrated | Illustrated |
| index_date | 2024-07-02T16:50:10Z |
| indexdate | 2024-07-09T20:54:06Z |
| institution | BVB |
| isbn | 9783540234074 3540234071 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-015493865 |
| oclc_num | 492840561 |
| open_access_boolean | |
| owner | DE-M49 DE-BY-TUM DE-11 |
| owner_facet | DE-M49 DE-BY-TUM DE-11 |
| physical | XIV, 238 S. Ill., graph. Darst. 24 cm |
| publishDate | 2007 |
| publishDateSearch | 2007 |
| publishDateSort | 2007 |
| publisher | Springer |
| record_format | marc |
| series2 | Biological and medical physics, biomedical engineering |
| spelling | Topology in molecular biology [DNA and proteins] M. I. Monastyrsky (ed.) Berlin ; Heidelberg ; New York Springer 2007 XIV, 238 S. Ill., graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Biological and medical physics, biomedical engineering Literaturangaben Biologie moléculaire Biologie moléculaire ram Modèle génétique Modèles biologiques Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Topologische Methode (DE-588)4312758-7 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Molekularbiologie (DE-588)4039983-7 s Topologische Methode (DE-588)4312758-7 s DE-604 Monastyrskij, Michail I. 1945- (DE-588)121283623 edt text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2668394&prov=M&dok_var=1&dok_ext=htm Inhaltstext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015493865&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Topology in molecular biology [DNA and proteins] Biologie moléculaire Biologie moléculaire ram Modèle génétique Modèles biologiques Molekularbiologie (DE-588)4039983-7 gnd Topologische Methode (DE-588)4312758-7 gnd |
| subject_GND | (DE-588)4039983-7 (DE-588)4312758-7 (DE-588)4143413-4 |
| title | Topology in molecular biology [DNA and proteins] |
| title_auth | Topology in molecular biology [DNA and proteins] |
| title_exact_search | Topology in molecular biology [DNA and proteins] |
| title_exact_search_txtP | Topology in molecular biology [DNA and proteins] |
| title_full | Topology in molecular biology [DNA and proteins] M. I. Monastyrsky (ed.) |
| title_fullStr | Topology in molecular biology [DNA and proteins] M. I. Monastyrsky (ed.) |
| title_full_unstemmed | Topology in molecular biology [DNA and proteins] M. I. Monastyrsky (ed.) |
| title_short | Topology in molecular biology |
| title_sort | topology in molecular biology dna and proteins |
| title_sub | [DNA and proteins] |
| topic | Biologie moléculaire Biologie moléculaire ram Modèle génétique Modèles biologiques Molekularbiologie (DE-588)4039983-7 gnd Topologische Methode (DE-588)4312758-7 gnd |
| topic_facet | Biologie moléculaire Modèle génétique Modèles biologiques Molekularbiologie Topologische Methode Aufsatzsammlung |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=2668394&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015493865&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT monastyrskijmichaili topologyinmolecularbiologydnaandproteins |