Protein folding protocols:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Totowa, NJ
Humana Press
2007
|
| Series: | Methods in molecular biology
350 |
| Subjects: | |
| Online Access: | Table of contents Klappentext Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | XIII, 327 S. Ill., graph. Darst. |
| ISBN: | 1588296229 |
Staff View
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| 650 | 4 | |a Protéines - Conformation | |
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Record in the Search Index
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| adam_text | Protein
Edited by
Yawen
Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, MD
Ruth Nussinov
Center for Cancer Research Nanobiology Program SAIC, National Cancer Institute-Frederick, Frederick, MD
and Department of Human Genetics, Sackler School ot Medicine, Tel Aviv University, Tel Aviv, Israel
Protein Folding Protocols presents protocols for studying and characterizing protein folding from the
unfolded to the folded state. Covering experiment and theory, bioinformatics approaches, and state-of-the-
art simulation protocols for better sampling oftheconformational space, this volume describes a broad range
of techniques to study, predict, and analyze the protein folding process.
Protein Folding Protocols
starting from the
have tremendous implications, ranging from drug design, functional assignment, comprehension of the
nature of regulation, understanding molecular machines, viral entry into cells, and putting together cellular
pathways and their dynamics.
The protocols follow the successful Methods in Molecular Biology™ser es format, each one offering
step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of
equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
FEATURES
Cutting-edge techniques for studying and character¬
izing protein folding from the unfolded to the
folded state.
Specific approaches toward the prediction of
protein structures
Step-by-step instructions that ensure successful
results
Tricks of the trade and notes on troubleshooting and
avoiding known pitfalls
CONTENTS
Infrared Temperature-jump Study of the Folding Dynamics of
a-Helices and
Magnetic Resonance to Study Protein Folding. Characteriza¬
tion of Denatured Proteins Using Residual Dipolar Couplings.
Characterizing Residual Structure in Disordered Protein
States Using Nuclear Magnetic Resonance. Population and
Structure Determination of Hidden Folding Intermediates by
Native-State Hydrogen Exchange-Directed Protein Engineer¬
ing and Nuclear Magnetic Resonance. Characterizing Protein
Folding Transition States Using ^-Analysis. Advances in the
Analysis of Conformational Transitions in Peptides Using
Differential Scanning Calorimetry. Application of Single Mol¬
ecule
Single Molecule Studies of Protein Folding Using Atomic
Force Microscopy. Using Triplet-Triplet Energy Transfer to
Measure Conformational Dynamics in Polypeptide Chains. A
Hierarchical Protein Folding Scheme Based on the Building
Block Folding Model. Replica Exchange Molecular Dynamics
Method for Protein Folding Simulation. Estimation of Folding
Probabilities and
lations of Reversible
Biological Structures Relate to Their Dynamics. Intermediates
and Transition States in Protein Folding. Thinking the Impos¬
sible: How to Solve the Protein Folding Problem With and
Without Homologous Structures and More. Index.
IMAGE 1
CONTENTS
PREFACE V
CONTRIBUTORS XI
1. INFRARED TEMPERATURE-JUMP STUDY OF THE FOLDING DYNAMICS OF EX-HELICES
AND SS-HAIRPINS FENG GEI, DEGUO DU, AND YAO XU 1
2. THE USE OF HIGH-PRESSURE NUCLEAR MAGNETIC RESONANCE TO STUDY PROTEIN
FOLDING MICHAEL W. LASSALLE AND KAZUYUKIAKASAKA 21
3. CHARACTERIZATION OF DENATURED PROTEINS USING RESIDUAL DIPOLAR
COUPLINGS ERIKA B. GEBEL AND DAVID SHORTLE 39
4. CHARACTERIZING RESIDUAL STRUCTURE IN DISORDERED PROTEI N STATES USING
NUCLEAR MAGNETIC RESONANCE DAVID ELIEZER 49
5. POPULATION AND STRUCTURE DETERMINATION OF HIDDEN FOLDING
INTERMEDIATES BY NATIVE-STATE HYDROGEN EXCHANGE-DIRECTED PROTEIN
ENGINEERING AND NUCLEAR MAGNETIC RESONANCE YAWEN BAI, HANQIAO FENG,AND
ZHENG ZHOU 69
6. CHARACTERIZING PROTEIN FOLDING TRANSITION STATES USING QS-ANALYSIS
ADARSH D. PANDIT, BRYAN A. KRANTZ, ROBIN S. DOTHAGER, AND TOBIN R ..
SOSNICK
................................................**....................
83
7. ADVANCES IN THE ANALYSIS OF CONFORMATIONAL TRANSITIONS IN PEPTIDES
USING DIFFERENTIAL SCANNING CALORIMETRY WERNER W. STREICHER AND GEORGE
I. MAKHATADZE.......**.................... 105
8. APPLICATION OF SINGLE MOLECULE FOERSTER RESONANCE ENERGY TRANSFER TO
PROTEI N FOLD ING BENJAMIN SCHULER , 115
9. SINGLE MOLECULE STUDIES OF PROTEIN FOLDING USING ATOMIC FORCE
MICROSCOPY SEAN P. NG, LUCY G. RANDLES, AND LSNE CLARKE
...........*..................... 139
10. USING TRIPLET-TRIPLET ENERGY TRANSFER TO MEASURE CONFORMATIONAL
DYNAMICS IN POLYPEPTIDE CHAINS BEAT FIERZ, KARIN [ODER, FLORIAN KRIEGER,
AND THOMAS KIEFHABER 169
IX
IMAGE 2
...
X
-------- .-
CONTENTS
11. A HIERARCHICAL PROTEIN FO/DING SCHEME BASED ON THE BUILDING B/OCK
FO/DING MODEL
NURIT HASPEL, GILAD WAINREB, YUVALLNBAR, HUI-HSU (GAVIN) TSAI,
CHUNG-JUNG TSAI, HAIM L. WOLFSON, AND RUTH NUSSINOV 189
12. REP/ICA EXCHANGEMOLECULAR DYNAMICS METHOD FOR PROTEIN FO/DING
SIMULATION
RUHONG ZHOU 205
13. ESTIMATION OF FALDING PROBABILITIES AND CI VALUES FROM MOLECULAR
DYNAMICS SIMULATIONS OF REVERSIBLE PEPTIDE FOLDING FRANCESCO REO,
GIOVANNISETTANNI, AND AMEDEO CAFLISCH 225
14. PACKING REGULARITIES IN BIALOGICAL STRUCTURES RELATE TO THEIR
DYNAMICS
ROBERT L. JERNIGAN ANDANDRZEJ KLOCZKOWSKI 251
15. INTERMEDIATES AND TRANSITION STATES IN PROTEIN FO/DING
D. THIRUMALAIAND DMITRI K. KLIMOV 277
16. THINKING THE IMPOSSIBLE: HOW TO SOLVE THE PROTEIN FOLDING PROBLEM
WITH AND WITHOUT HOMOLOGOUS STRUCTURES AND MORE RITA CASADIO, PIERO
FARISELLI, PIER LUIGIMARTELLI, AND GIANLUCA TASCO 305
INDEX 321
|
| adam_txt |
Protein
Edited by
Yawen
Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, MD
Ruth Nussinov
Center for Cancer Research Nanobiology Program SAIC, National Cancer Institute-Frederick, Frederick, MD
and Department of Human Genetics, Sackler School ot Medicine, Tel Aviv University, Tel Aviv, Israel
Protein Folding Protocols presents protocols for studying and characterizing protein folding from the
unfolded to the folded state. Covering experiment and theory, bioinformatics approaches, and state-of-the-
art simulation protocols for better sampling oftheconformational space, this volume describes a broad range
of techniques to study, predict, and analyze the protein folding process.
Protein Folding Protocols
starting from the
have tremendous implications, ranging from drug design, functional assignment, comprehension of the
nature of regulation, understanding molecular machines, viral entry into cells, and putting together cellular
pathways and their dynamics.
The protocols follow the successful Methods in Molecular Biology™ser\es format, each one offering
step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of
equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
FEATURES
Cutting-edge techniques for studying and character¬
izing protein folding from the unfolded to the
folded state.
Specific approaches toward the prediction of
protein structures
Step-by-step instructions that ensure successful
results
Tricks of the trade and notes on troubleshooting and
avoiding known pitfalls
CONTENTS
Infrared Temperature-jump Study of the Folding Dynamics of
a-Helices and
Magnetic Resonance to Study Protein Folding. Characteriza¬
tion of Denatured Proteins Using Residual Dipolar Couplings.
Characterizing Residual Structure in Disordered Protein
States Using Nuclear Magnetic Resonance. Population and
Structure Determination of Hidden Folding Intermediates by
Native-State Hydrogen Exchange-Directed Protein Engineer¬
ing and Nuclear Magnetic Resonance. Characterizing Protein
Folding Transition States Using ^-Analysis. Advances in the
Analysis of Conformational Transitions in Peptides Using
Differential Scanning Calorimetry. Application of Single Mol¬
ecule
Single Molecule Studies of Protein Folding Using Atomic
Force Microscopy. Using Triplet-Triplet Energy Transfer to
Measure Conformational Dynamics in Polypeptide Chains. A
Hierarchical Protein Folding Scheme Based on the Building
Block Folding Model. Replica Exchange Molecular Dynamics
Method for Protein Folding Simulation. Estimation of Folding
Probabilities and
lations of Reversible
Biological Structures Relate to Their Dynamics. Intermediates
and Transition States in Protein Folding. Thinking the Impos¬
sible: How to Solve the Protein Folding Problem With and
Without Homologous Structures and More. Index.
IMAGE 1
CONTENTS
PREFACE V
CONTRIBUTORS XI
1. INFRARED TEMPERATURE-JUMP STUDY OF THE FOLDING DYNAMICS OF EX-HELICES
AND SS-HAIRPINS FENG GEI, DEGUO DU, AND YAO XU 1
2. THE USE OF HIGH-PRESSURE NUCLEAR MAGNETIC RESONANCE TO STUDY PROTEIN
FOLDING MICHAEL W. LASSALLE AND KAZUYUKIAKASAKA 21
3. CHARACTERIZATION OF DENATURED PROTEINS USING RESIDUAL DIPOLAR
COUPLINGS ERIKA B. GEBEL AND DAVID SHORTLE 39
4. CHARACTERIZING RESIDUAL STRUCTURE IN DISORDERED PROTEI N STATES USING
NUCLEAR MAGNETIC RESONANCE DAVID ELIEZER 49
5. POPULATION AND STRUCTURE DETERMINATION OF HIDDEN FOLDING
INTERMEDIATES BY NATIVE-STATE HYDROGEN EXCHANGE-DIRECTED PROTEIN
ENGINEERING AND NUCLEAR MAGNETIC RESONANCE YAWEN BAI, HANQIAO FENG,AND
ZHENG ZHOU 69
6. CHARACTERIZING PROTEIN FOLDING TRANSITION STATES USING QS-ANALYSIS
ADARSH D. PANDIT, BRYAN A. KRANTZ, ROBIN S. DOTHAGER, AND TOBIN R .
SOSNICK
.**.
83
7. ADVANCES IN THE ANALYSIS OF CONFORMATIONAL TRANSITIONS IN PEPTIDES
USING DIFFERENTIAL SCANNING CALORIMETRY WERNER W. STREICHER AND GEORGE
I. MAKHATADZE.**. 105
8. APPLICATION OF SINGLE MOLECULE FOERSTER RESONANCE ENERGY TRANSFER TO
PROTEI N FOLD ING BENJAMIN SCHULER , 115
9. SINGLE MOLECULE STUDIES OF PROTEIN FOLDING USING ATOMIC FORCE
MICROSCOPY SEAN P. NG, LUCY G. RANDLES, AND LSNE CLARKE
.*. 139
10. USING TRIPLET-TRIPLET ENERGY TRANSFER TO MEASURE CONFORMATIONAL
DYNAMICS IN POLYPEPTIDE CHAINS BEAT FIERZ, KARIN [ODER, FLORIAN KRIEGER,
AND THOMAS KIEFHABER 169
IX
IMAGE 2
.
X
-------- .-
CONTENTS
11. A HIERARCHICAL PROTEIN FO/DING SCHEME BASED ON THE BUILDING B/OCK
FO/DING MODEL
NURIT HASPEL, GILAD WAINREB, YUVALLNBAR, HUI-HSU (GAVIN) TSAI,
CHUNG-JUNG TSAI, HAIM L. WOLFSON, AND RUTH NUSSINOV 189
12. REP/ICA EXCHANGEMOLECULAR DYNAMICS METHOD FOR PROTEIN FO/DING
SIMULATION
RUHONG ZHOU 205
13. ESTIMATION OF FALDING PROBABILITIES AND CI VALUES FROM MOLECULAR
DYNAMICS SIMULATIONS OF REVERSIBLE PEPTIDE FOLDING FRANCESCO REO,
GIOVANNISETTANNI, AND AMEDEO CAFLISCH 225
14. PACKING REGULARITIES IN BIALOGICAL STRUCTURES RELATE TO THEIR
DYNAMICS
ROBERT L. JERNIGAN ANDANDRZEJ KLOCZKOWSKI 251
15. INTERMEDIATES AND TRANSITION STATES IN PROTEIN FO/DING
D. THIRUMALAIAND DMITRI K. KLIMOV 277
16. THINKING THE IMPOSSIBLE: HOW TO SOLVE THE PROTEIN FOLDING PROBLEM
WITH AND WITHOUT HOMOLOGOUS STRUCTURES AND MORE RITA CASADIO, PIERO
FARISELLI, PIER LUIGIMARTELLI, AND GIANLUCA TASCO 305
INDEX 321 |
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| illustrated | Illustrated |
| index_date | 2024-07-02T14:55:01Z |
| indexdate | 2024-07-09T20:40:13Z |
| institution | BVB |
| isbn | 1588296229 |
| language | English |
| lccn | 2006002791 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-014840396 |
| oclc_num | 63279474 |
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| physical | XIII, 327 S. Ill., graph. Darst. |
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| publisher | Humana Press |
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| series | Methods in molecular biology |
| series2 | Methods in molecular biology |
| spelling | Protein folding protocols ed. by Yawen Bai ... Totowa, NJ Humana Press 2007 XIII, 327 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in molecular biology 350 Includes bibliographical references and index Protéines - Analyse Protéines - Conformation Protéines - Repliement Protein folding Proteins Conformation Proteins Analysis Protein Folding Protein Conformation Proteins analysis Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Untersuchungsmethode (DE-588)4324907-3 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 s Untersuchungsmethode (DE-588)4324907-3 s b DE-604 Bai, Yawen Sonstige oth Methods in molecular biology 350 (DE-604)BV035362695 350 http://www.loc.gov/catdir/toc/ecip067/2006002791.html Table of contents Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014840396&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Klappentext OEBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014840396&sequence=000003&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Protein folding protocols Methods in molecular biology Protéines - Analyse Protéines - Conformation Protéines - Repliement Protein folding Proteins Conformation Proteins Analysis Protein Folding Protein Conformation Proteins analysis Proteinfaltung (DE-588)4324567-5 gnd Untersuchungsmethode (DE-588)4324907-3 gnd |
| subject_GND | (DE-588)4324567-5 (DE-588)4324907-3 |
| title | Protein folding protocols |
| title_auth | Protein folding protocols |
| title_exact_search | Protein folding protocols |
| title_exact_search_txtP | Protein folding protocols |
| title_full | Protein folding protocols ed. by Yawen Bai ... |
| title_fullStr | Protein folding protocols ed. by Yawen Bai ... |
| title_full_unstemmed | Protein folding protocols ed. by Yawen Bai ... |
| title_short | Protein folding protocols |
| title_sort | protein folding protocols |
| topic | Protéines - Analyse Protéines - Conformation Protéines - Repliement Protein folding Proteins Conformation Proteins Analysis Protein Folding Protein Conformation Proteins analysis Proteinfaltung (DE-588)4324567-5 gnd Untersuchungsmethode (DE-588)4324907-3 gnd |
| topic_facet | Protéines - Analyse Protéines - Conformation Protéines - Repliement Protein folding Proteins Conformation Proteins Analysis Protein Folding Protein Conformation Proteins analysis Proteinfaltung Untersuchungsmethode |
| url | http://www.loc.gov/catdir/toc/ecip067/2006002791.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014840396&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014840396&sequence=000003&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035362695 |
| work_keys_str_mv | AT baiyawen proteinfoldingprotocols |