Modeling and simulation of protein folding:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
Göttingen
Cuvillier
2011
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | XV, 194 S. Ill., graph. Darst. |
| ISBN: | 9783869557984 |
Internformat
MARC
| LEADER | 00000nam a2200000 c 4500 | ||
|---|---|---|---|
| 001 | BV040965257 | ||
| 003 | DE-604 | ||
| 005 | 20130510 | ||
| 007 | t | ||
| 008 | 130424s2011 ad|| m||| 00||| eng d | ||
| 015 | |a 11N27 |2 dnb | ||
| 016 | 7 | |a 1013142853 |2 DE-101 | |
| 020 | |a 9783869557984 |c Kart. : EUR 36.25 (DE) |9 978-3-86955-798-4 | ||
| 035 | |a (OCoLC)837904264 | ||
| 035 | |a (DE-599)DNB1013142853 | ||
| 040 | |a DE-604 |b ger |e rakddb | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-83 | ||
| 082 | 0 | |a 510 | |
| 082 | 0 | |a 572.633015197 |2 22/ger | |
| 084 | |a 35.06 |2 bkl | ||
| 084 | |a 31.48 |2 bkl | ||
| 084 | |a 92Cxx |2 msc | ||
| 084 | |a 35.62 |2 bkl | ||
| 084 | |a 31.25 |2 bkl | ||
| 100 | 1 | |a Shumilina, Anna |d 1977- |e Verfasser |0 (DE-588)1014259177 |4 aut | |
| 245 | 1 | 0 | |a Modeling and simulation of protein folding |c vorgel. von Anna Shumilina |
| 264 | 1 | |a Göttingen |b Cuvillier |c 2011 | |
| 300 | |a XV, 194 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 502 | |a Zugl.: Kaiserslautern, Univ., Diss., 2011 | ||
| 650 | 0 | 7 | |a Mehrkriterielle Optimierung |0 (DE-588)4610682-0 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Proteinfaltung |0 (DE-588)4324567-5 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4113937-9 |a Hochschulschrift |2 gnd-content | |
| 689 | 0 | 0 | |a Proteinfaltung |0 (DE-588)4324567-5 |D s |
| 689 | 0 | 1 | |a Mehrkriterielle Optimierung |0 (DE-588)4610682-0 |D s |
| 689 | 0 | |5 DE-604 | |
| 856 | 4 | |q text/html |u http://deposit.dnb.de/cgi-bin/dokserv?id=3847032&prov=M&dok_var=1&dok_ext=htm |3 Inhaltstext | |
| 856 | 4 | 2 | |m DNB Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025943557&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-025943557 | |
Datensatz im Suchindex
| _version_ | 1809404296129675264 |
|---|---|
| adam_text |
IMAGE 1
CONTENTS
PREFACE IX
OUTLINE OF THE WORK BE
REMARKS ABOUT NOTATIONS XIII
ACKNOWLEDGMENT XIV
1 BIOLOGICAL, CHEMICAL, AND PHYSICAL BACKGROUND 1
1.1 INTRODUCTION 1
1.2 CHEMICAL STRUCTURE OF PROTEINS 3
1.3 CHIRALITY OF AMINO ACIDS 6
1.4 IONIZATION OF AMINO ACID RESIDUES 8
1.5 INTRAMOLECULAR INTERACTIONS 12
1.5.1 PRINCIPLES OF QUANTUM MECHANICS AND ATOMIC ORBITALS 13
1.5.2 COVALENT BONDING 28
1.5.3 ELECTROSTATIC INTERACTIONS 30
1.5.4 VAN DER WAALS FORCES 32
1.5.5 HYDROGEN BONDING 34
1.6 THREE-DIMENSIONAL STRUCTURE OF PROTEINS 36
1.6.1 DIHEDRAL ANGLES 36
1.6.2 ELEMENTS OF SECONDARY STRUCTURE 47
1.6.3 TERTIARY AND QUATERNARY STRUCTURE OF PROTEINS 50
BIBLIOGRAFISCHE INFORMATIONEN HTTP://D-NB.INFO/1013142853
DIGITALISIERT DURCH
IMAGE 2
VI CONTENTS
1.7 INFLUENCE OF ENVIRONMENT 51
1.7.1 THE HYDROPHOBIC EFFECT 52
1.7.2 INTERACTION OF CHARGED GROUPS WITH SOLVENT 54
1.7.3 CHAPERONES AND ASSISTED PROTEIN FOLDING 56
1.7.4 PRIONS 57
1.8 PROTEIN SYNTHESIS 58
1.8.1 RIBOSOMES 59
1.8.2 MECHANISM OF TRANSLATION 61
1.8.3 COTRANSLATIONAL PROTEIN FOLDING 63
1.8.4 POSTTRANSLATIONAL MODIFICATIONS 67
1.9 EXPERIMENTAL PROTEIN STRUCTURE DETERMINATION 68
1.9.1 X-RAY CRYSTALLOGRAPHY 68
1.9.2 NUCLEAR MAGNETIC RESONANCE (NMR) SPECTROSCOPY 69
1.10 STRUCTURE DATABASES 71
2 APPROACHES FOR PROTEIN STRUCTURE PREDICTION 73
2.1 FROM AB INITIO TO KNOWLEDGE-BASED APPROACHES 73
2.1.1 AB INITIO PROTEIN FOLDING 73
2.1.2 KNOWLEDGE-BASED STRUCTURE PREDICTION 76
2.2 EMPIRICAL FORCE FIELDS 79
2.2.1 HARMONIC APPROXIMATION FOR BOND LENGTHS AND ANGLES . . . 80
2.2.2 TORSION ANGLES AND OUT-OF-PLANE BENDING 81
2.2.3 NON-BONDED INTERACTIONS AND ASSIGNMENT OF ATOM CHARGES . . 83
2.2.4 MODELS FOR HYDROGEN BONDING 87
2.3 SOLVATION MODELS 88
2.3.1 ESTIMATION OF SOLVENT-EXPOSED AREA 88
2.3.2 POISSON-BOLTZMANN EQUATION 89
IMAGE 3
C O N T E N TS VUE
3 MODELING INTRACELLULAR PROTEIN FOLDING 91
3.1 THE GENERAL IDEA OF THE NEW APPROACH 91
3.2 INTERATOMIC DISTANCES VERSUS DIHEDRAL ANGLES 92
3.3 ENERGY AS A FUNCTION OF TORSION ANGLES 109
3.4 MODELING HYDRATION 112
3.4.1 RATIONALE 113
3.4.2 GRID GENERATION 116
3.4.3 ACCESSIBILITY CHECK 118
3.5 MODELING COTRANSLATIONAL FOLDING 120
3.5.1 OPERATIONS FOR COORDINATE TRANSFORMATIONS 122
3.5.2 APPENDING A NEW AMINO ACID RESIDUE 126
3.6 TWISTING FORCES 130
3.7 DYNAMICS IN DIHEDRAL ANGLE SPACE 137
4 SIVIPROF SOFTWARE 141
4.1 S I V I P R OF - A NEW SIMULATION SOFTWARE 141
4.2 IMPLEMENTATION OF THE MODEL 145
4.2.1 LISTING DEGREES OF FREEDOM 145
4.2.2 GENERATION OF INITIAL COORDINATES 148
4.2.3 CHIRALITY CORRECTION 153
4.2.4 OVERALL ORGANIZATION 155
4.2.5 ENHANCEMENT OF COMPUTATIONAL EFFICIENCY 157
4.3 SIMULATIONS 158
4.3.1 CONTRIBUTIONS OF DIFFERENT INTERACTION TYPES 158
4.3.2 MINIMIZATION OF ENERGY 163
4.4 CONCLUSIONS AND OUTLOOK 166
IMAGE 4
VIII CONTENTS
A IMPLEMENTATION DETAILS 169
A.I VISUAL REPRESENTATION OF MOLECULAR ELEMENTS 169
A.2 ATOM NUMERATION IN AMINO ACIDS 170
A.3 S I V I P R OF INPUT FORMAT 173
B PHYSICAL QUANTITIES, CONSTANTS AND UNITS 175
C MATHEMATICAL NOTATIONS 177
C.I GENERAL NOTATIONS 177
C.2 GENERAL EXPRESSIONS 177
C.3 PROBLEM-SPECIFIC NOTATIONS 178
C.4 INTRODUCED OPERATIONS 178
C.5 CONVENTIONAL NOTATIONS 179
D PARAMETERS 181
REFERENCES 185 |
| any_adam_object | 1 |
| author | Shumilina, Anna 1977- |
| author_GND | (DE-588)1014259177 |
| author_facet | Shumilina, Anna 1977- |
| author_role | aut |
| author_sort | Shumilina, Anna 1977- |
| author_variant | a s as |
| building | Verbundindex |
| bvnumber | BV040965257 |
| ctrlnum | (OCoLC)837904264 (DE-599)DNB1013142853 |
| dewey-full | 510 572.633015197 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 510 - Mathematics 572 - Biochemistry |
| dewey-raw | 510 572.633015197 |
| dewey-search | 510 572.633015197 |
| dewey-sort | 3510 |
| dewey-tens | 510 - Mathematics 570 - Biology |
| discipline | Biologie Mathematik |
| format | Thesis Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>00000nam a2200000 c 4500</leader><controlfield tag="001">BV040965257</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20130510</controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">130424s2011 ad|| m||| 00||| eng d</controlfield><datafield tag="015" ind1=" " ind2=" "><subfield code="a">11N27</subfield><subfield code="2">dnb</subfield></datafield><datafield tag="016" ind1="7" ind2=" "><subfield code="a">1013142853</subfield><subfield code="2">DE-101</subfield></datafield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">9783869557984</subfield><subfield code="c">Kart. : EUR 36.25 (DE)</subfield><subfield code="9">978-3-86955-798-4</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)837904264</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)DNB1013142853</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rakddb</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-83</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">510</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">572.633015197</subfield><subfield code="2">22/ger</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">35.06</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">31.48</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">92Cxx</subfield><subfield code="2">msc</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">35.62</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">31.25</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Shumilina, Anna</subfield><subfield code="d">1977-</subfield><subfield code="e">Verfasser</subfield><subfield code="0">(DE-588)1014259177</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Modeling and simulation of protein folding</subfield><subfield code="c">vorgel. von Anna Shumilina</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="a">Göttingen</subfield><subfield code="b">Cuvillier</subfield><subfield code="c">2011</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">XV, 194 S.</subfield><subfield code="b">Ill., graph. Darst.</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="502" ind1=" " ind2=" "><subfield code="a">Zugl.: Kaiserslautern, Univ., Diss., 2011</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Mehrkriterielle Optimierung</subfield><subfield code="0">(DE-588)4610682-0</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Proteinfaltung</subfield><subfield code="0">(DE-588)4324567-5</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="655" ind1=" " ind2="7"><subfield code="0">(DE-588)4113937-9</subfield><subfield code="a">Hochschulschrift</subfield><subfield code="2">gnd-content</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">Proteinfaltung</subfield><subfield code="0">(DE-588)4324567-5</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2="1"><subfield code="a">Mehrkriterielle Optimierung</subfield><subfield code="0">(DE-588)4610682-0</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="856" ind1="4" ind2=" "><subfield code="q">text/html</subfield><subfield code="u">http://deposit.dnb.de/cgi-bin/dokserv?id=3847032&prov=M&dok_var=1&dok_ext=htm</subfield><subfield code="3">Inhaltstext</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">DNB Datenaustausch</subfield><subfield code="q">application/pdf</subfield><subfield code="u">http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025943557&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="943" ind1="1" ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-025943557</subfield></datafield></record></collection> |
| genre | (DE-588)4113937-9 Hochschulschrift gnd-content |
| genre_facet | Hochschulschrift |
| id | DE-604.BV040965257 |
| illustrated | Illustrated |
| indexdate | 2024-09-06T00:26:44Z |
| institution | BVB |
| isbn | 9783869557984 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-025943557 |
| oclc_num | 837904264 |
| open_access_boolean | |
| owner | DE-83 |
| owner_facet | DE-83 |
| physical | XV, 194 S. Ill., graph. Darst. |
| publishDate | 2011 |
| publishDateSearch | 2011 |
| publishDateSort | 2011 |
| publisher | Cuvillier |
| record_format | marc |
| spelling | Shumilina, Anna 1977- Verfasser (DE-588)1014259177 aut Modeling and simulation of protein folding vorgel. von Anna Shumilina Göttingen Cuvillier 2011 XV, 194 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Zugl.: Kaiserslautern, Univ., Diss., 2011 Mehrkriterielle Optimierung (DE-588)4610682-0 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Proteinfaltung (DE-588)4324567-5 s Mehrkriterielle Optimierung (DE-588)4610682-0 s DE-604 text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3847032&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025943557&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Shumilina, Anna 1977- Modeling and simulation of protein folding Mehrkriterielle Optimierung (DE-588)4610682-0 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| subject_GND | (DE-588)4610682-0 (DE-588)4324567-5 (DE-588)4113937-9 |
| title | Modeling and simulation of protein folding |
| title_auth | Modeling and simulation of protein folding |
| title_exact_search | Modeling and simulation of protein folding |
| title_full | Modeling and simulation of protein folding vorgel. von Anna Shumilina |
| title_fullStr | Modeling and simulation of protein folding vorgel. von Anna Shumilina |
| title_full_unstemmed | Modeling and simulation of protein folding vorgel. von Anna Shumilina |
| title_short | Modeling and simulation of protein folding |
| title_sort | modeling and simulation of protein folding |
| topic | Mehrkriterielle Optimierung (DE-588)4610682-0 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| topic_facet | Mehrkriterielle Optimierung Proteinfaltung Hochschulschrift |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=3847032&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=025943557&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT shumilinaanna modelingandsimulationofproteinfolding |