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Introduction to Protein Structure 2nd Revised edition [Kietas viršelis]

  • Formatas: Hardback, 410 pages, aukštis x plotis: 275x214 mm, weight: 453 g, Illustrations (chiefly col.)
  • Išleidimo metai: 01-Dec-1998
  • Leidėjas: Garland Publishing Inc
  • ISBN-10: 0815323042
  • ISBN-13: 9780815323044
Kitos knygos pagal šią temą:
  • Formatas: Hardback, 410 pages, aukštis x plotis: 275x214 mm, weight: 453 g, Illustrations (chiefly col.)
  • Išleidimo metai: 01-Dec-1998
  • Leidėjas: Garland Publishing Inc
  • ISBN-10: 0815323042
  • ISBN-13: 9780815323044
Kitos knygos pagal šią temą:
Introduction to Protein Structure provides an account of the principles of protein structure, with examples of key proteins in their biological context generously illustrated in full-color to illuminate the structural principles described in the text. The first few chapters introduce the general principles of protein structure both for novices and for non-specialists needing a primer. Subsequent chapters use specific examples of proteins to show how they fulfill a wide variety of biological functions. The book ends with chapters on the experimental approach to determining and predicting protein structure, as well as engineering new proteins to modify their functions.
Part 1 Basic Structural Principles 1(126)
1. The Building Blocks
3(10)
Proteins are polypeptide chains
4(1)
The genetic code specifies 20 different amino acid side chains
4(1)
Cysteines can form disulfide bridges
5(3)
Peptide units are building blocks of protein structures
8(1)
Glycine residues can adopt many different conformations
9(1)
Certain side-chain conformations are energetically favorable
10(1)
Many proteins contain intrinsic metal atoms
11(1)
Conclusion
12(1)
Selected readings
12(1)
2. Motifs of Protein Structure
13(22)
The interior of proteins is hydrophobic
14(1)
The alpha (Alpha) helix is an important element of secondary structure
14(2)
The Alpha helix has a dipole moment
16(1)
Some amino acids are preferred in Alpha helices
16(3)
Beta (Beta) sheets usually have their Beta strands either parallel of antiparallel
19(2)
Loop regions are at the surface of protein molecules
21(1)
Schematic pictures of proteins highlight secondary structure
22(1)
Topology diagrams are useful for classification of protein structures
23(1)
Secondary structure elements are connected to form simple motifs
24(2)
The hairpin Beta motif occurs frequently in protein structures
26(1)
The Greek key motif is found in antiparallel Beta sheets
27(1)
The Beta-Alpha-Beta motif contains two parallel Beta strands
27(1)
Protein molecules are organized in a structural hierarchy
28(1)
Large polypeptide chains fold into several domains
29(1)
Domains are built from structural motifs
30(1)
Simple motifs combine to form complex motifs
30(1)
Protein structures can be divided into three main classes
31(1)
Conclusion
32(1)
Selected readings
33(2)
3. Alpha-Domain Structures
35(12)
Coiled-coil Alpha helices contain a repetitive heptad amino acid sequence pattern
35(2)
The four-helix bundle is a common domain structure in Alpha proteins
37(2)
Alpha-helical domains are sometimes large and complex
39(1)
The globin fold is present in myoglobin and hemoglobin
40(1)
Geometric considerations determine Alpha-helix packing
40(1)
Ridges of one Alpha helix fit into grooves of an adjacent helix
40(1)
The globin fold has been preserved during evolution
41(1)
The hydrophobic interior is preserved
42(1)
Helix movements accommodate interior side-chain mutations
43(1)
Sickle-cell hemoglobin confers resistance to malaria
43(2)
Conclusion
45(1)
Selected readings
45(2)
4. Alpha/Beta Structures
47(20)
Parallel Beta strands are arranged in barrels or sheets
47(1)
Alpha/beta barrels occur in many different enzymes
48(1)
Branched hydrophobic side chains dominate the core of Alpha/Beta barrels
49(2)
Pyruvate kinase contains several domains, one of which is an Alpha/Beta barrel
51(1)
Double barrels have occurred by gene fusion
52(1)
The active site is formed by loops at one end of the Alpha/Beta barrel
53(1)
Alpha/beta barrels provide examples of evolution of new enzyme activities
54(1)
Leucine-rich motifs form an Alpha/Beta-horseshoe fold
55(1)
Alpha/beta twisted open-sheet structures contain Alpha helices on both sides of the Beta sheet
56(1)
Open Beta-sheet structures have a variety of topologies
57(1)
The positions of active sites can be predicted in Alpha/Beta structures
57(2)
Tyrosyl-tRNA synthetase has two different domains (Alpha/Beta+Alpha)
59(1)
Carboxypeptidase is an Alpha/Beta protein with a mixed Beta sheet
60(2)
Arabinose-binding protein has two similar Alpha/Beta domains
62(1)
Conclusion
63(1)
Selected readings
64(3)
5. Beta Structures
67(22)
Up-and-down barrels have a simple topology
68(1)
The retinol-binding protein binds retinol inside an up-and-down Beta barrel
68(1)
Amino acid sequence reflects Beta Structure
69(1)
The retinol-binding protein belongs to a superfamily of protein structures
70(1)
Neuraminidase folds into up-and-town Beta sheets
70(1)
Folding motifs form a propeller-like structure in neuraminidase
71(1)
The active site is in the middle of one side of the propeller
72(1)
Greek key motifs occur frequently in antiparallel Beta structures
72(2)
The Gamma-crystallin molecule has two domains
74(1)
The domain structure has a simple topology
74(1)
Two Greek key motifs form the domain
74(1)
The two domains have identical topology
75(1)
The two domains have similar structures
76(1)
The Greek key motifs in Gamma crystallin are evolutionarily related
76(1)
The Greek key motifs can form jelly roll barrles
77(1)
The jelly roll motif is wrapped around a barrel
77(1)
The jelly roll barrel is usually divided into two sheets
78(1)
The functional hemagglutining subunit has two polypeptide chains
79(1)
The subunit structure is divided into a stem and a tip
79(1)
The receptor binding site is formed by the jelly roll domain
80(1)
Hemaggluthining acts as a membrane fusogen
80(1)
The structure of hemagglutinin is affected by pH changes
81(3)
Parallel Beta-helix domains have a novel fold
84(1)
Conclusion
85(2)
Selected readings
87(2)
6. Folding and Flexibility
89(32)
Globular proteins are only marginally stable
90(1)
Kinetic factors are important for folding
91(1)
Molten globules are intermediates in folding
92(1)
Burying hydrophobic side chains is a key event
93(1)
Both single and multiple folding pathways have been observed
93(3)
Enzymes assist formation of proper disulfide bonds during folding
96(2)
Isomerization of proline residues can be a rate-limiting step in protein folding
98(1)
Proteins can fold or unfold inside chaperonins
99(1)
GroEL is a cylindrical structure with a central channel in which newly synthesized polypeptides bind
100(2)
GroES closes off one end of the GroEL cylinder
102(1)
The GroEL-GroES complex binds and releases newly synthesized polypeptides in an ATP-dependent cycle
102(2)
The folded state has a flexible structure
104(1)
Conformational changes in a protein kinase are important for cell cycle regulation
105(4)
Peptide binding to calmodulin induces a large interdomain movement
109(1)
Serpins inhibit serine proteinases with a spring-loaded safety catch mechanism
110(3)
Effector molecules switch allosteric proteins between R and T states
113(1)
X-ray structures explain the allosteric properties of phosphofructokinase
114(3)
Conclusion
117(2)
Selected readings
119(2)
7. DNA Structures
121(6)
The DNA double helix is different in A- and B-DNA
121(1)
The DNA helix has major and minor grooves
122(1)
Z-DNA forms a zigzag pattern
123(1)
B-DNA is the preferred conformation in vivo
124(1)
Specific base sequences can be recognized in B-DNA
124(1)
Conclusion
125(1)
Selected readings
126(1)
Part 2 Structure, Function, and Engineering 127(266)
8. DNA Recognition in Procaryotes by Helix-Turn-Helix Motifs
129(22)
A molecular mechanism for gene control
129(1)
Repressor and Cro proteins operate a procaryotic genetic switch region
130(1)
The x-ray structure of the complete lambda Cro protein is known
131(1)
The x-ray structure of the DNA-binding domain of the lambda repressor is known
132(1)
Both lambda Cro and repressor proteins have a specific DNA-binding motif
133(1)
Model building predicts Cro-DNA interactions
134(1)
Genetic studies agree with the structural model
135(1)
The x-ray structure of DNA complexes with 434 Cro and repressor revealed novel features of protein-DNA interactions
136(1)
The structures of 434 Cro and the 434 repressor DNA-binding domain the very similar
137(1)
The proteins impose precise distortions on the B-DNA in the complexes
138(1)
Sequence-specific protein-DNA interactions recognize operator regions
138(1)
Protein-DNA backbone interactions determine DNA conformation
139(1)
Conformational changes of DNA are important for differential binding of repressor and Cro to different operator sites
140(1)
The essence of phage repressor and Cro
141(1)
DNA binding is regulated by allosteric control
142(1)
The trp repressor forms a helix-turn-helix motif
142(1)
A conformational change operates a functional switch
142(1)
Lac repressor binds to both the major and minor grooves inducing a sharp bend in the DNA
143(3)
CAP-induced DNA binding could activate transcription
146(1)
Conclusion
147(1)
Selected readings
148(3)
9. DNA Recognition by Eucaryotic Transcription Factors
151(24)
Transcription is activated by protein-protein interactions
152(1)
The TATA box-binding protein is ubiquitous
153(1)
The three-dimensional structures of TBP-TATA box complexes are known
154(1)
A Beta sheet in TBP forms the DNA-binding site
154(1)
TBP binds in the minor groove and induces large structural changes in DNA
155(2)
The interaction area between TBP and the TATA box is mainly hydrophobic
157(1)
Functional implications of the distortion of DNA by TBP
158(1)
TFIIA and TFIIB bind to both TBP and DNA
159(1)
Homeodomain proteins are involved in the development of many eucaryotic organisms
159(1)
Monomers of homeodomain proteins bind to DNA through a helix-turn-helix motif
160(2)
In vivo specificity of homeodomain transcription factors depends on interactions with other proteins
162(2)
POU regions bind to DNA by two tandemly oriented helix-turn-helix motifs
164(2)
Much remains to be learnt about the function of homeodomains in vivo
166(1)
Understanding tumorigenic mutations
166(1)
The monomeric p53 polypeptide chain is divided in three domains
167(1)
The oligomerization domain forms tetramers
167(1)
The DNA-binding domain of p53 is an antiparallel Beta barrel
168(1)
Two loop regions and one Alpha helix of p53 bind to DNA
169(1)
Tumorigenic mutations occur mainly in three regions involved in DNA binding
170(2)
Conclusions
172(1)
Selected readings
172(3)
10. Specific Transcription Factors Belong to a Few Families
175(30)
Several different groups of zinc-containing motifs have been observed
176(1)
The classic zinc fingers bind to DNA in tandem along the major groove
177(1)
The finger region of the classic zinc finger motif interacts with DNA
178(3)
Two zinc-containing motifs in the glucocorticoid receptor form one DNA-binding domain
181(2)
A dimer of the glucocorticoid receptor binds to DNA
183(1)
An Alpha helix in the first zinc motif provides the specific protein-DNA interactions
184(1)
Three residues in the recognition helix provide the sequence-specific interactions with DNA
184(1)
The retinoid X receptor forms heterodimers that recognize tandem repeats with variable spacings
185(2)
Yeast transcription factor GAL4 contains a binuclear zinc cluster in its DNA-binding domain
187(1)
The zinc cluster regions of GAL4 bind at the two ends of the enhancer element
188(1)
The linker region also contributes to DNA binding
189(1)
DNA-binding site specificity among the C(6)-zinc cluster family of transcription factors is achieved by the linker regions
190(1)
Families of zinc-containing transcription factors bind to DNA in several different ways
191(1)
Leucine zippers provide dimerization interactions for some eucaryotic transcription factors
191(2)
The GCN4 basic region leucine zipper binds DNA as a dimer of two uninterrupted Alpha helices
193(1)
GCN4 binds to DNA with both specific and nonspecific contacts
194(2)
The HLH motif is involved in homodimer and heterodimer associations
196(2)
The Alpha-helical basic region of the b/HLH motif binds in the major groove of DNA
198(1)
The b/HLH/zip family of transcription factors have both HLH and leucine zipper dimerization motifs
199(2)
Max and MyoD recognize the DNA HLH consensus sequence by different specific protein-DNA interactions
201(1)
Conclusion
201(2)
Selected readings
203(2)
11. An Example of Enzyme Catalysis: Serine Proteinases
205(18)
Proteinases form four functional families
205(1)
The catalytic properties of enzymes are reflected in K(m) and k(cat) values
206(1)
Enzymes decrease the activation energy of chemical reactions
206(2)
Serine proteinases cleave peptide bonds by forming tetrahedral transition states
208(1)
Four important structural features are required for the catalytic action of serine proteinases
209(1)
Convergent evolution has produced two different serine proteinases with similar catalytic mechanisms
210(1)
The chymotrypsin structure has two antiparallel Beta-barrel domains
210(1)
The active site is formed by two loop regions from each domain
211(1)
Did the chymotrypsin molecule evolve by gene duplication?
212(1)
Different side chains in the substrate specificity pocket confer preferential cleavage
212(1)
Engineered mutations in the substrate specificity pocket change the rate of catalysis
213(2)
The Asp 189-Lys mutation in trypsin causes unexpected changes in substrate specificity
215(1)
The structure of the serine proteinase subtilisin is of the Alpha/Beta type
215(1)
The active sites of subtilism and chymotrypsin are similar
216(1)
A structural anomaly in subtilisin has functional consequences
217(1)
Transition-state stabilization in subtilisin is dissected by protein engineering
217(1)
Catalysis occurs without a catalytic triad
217(1)
Substrate molecules provide catalytic groups in substrate-assisted catalysis
218(1)
Conclusion
219(1)
Selected readings
220(3)
12. Membrane Proteins
223(28)
Membrane proteins are difficult to crystallize
224(1)
Novel crystallization methods are being developed
224(1)
Two-dimensional crystals of membrane proteins can be studied by electron microscopy
225(1)
Bacteriorhodopsin contains seven transmembrane Alpha helices
226(1)
Bacteriorhodopsin is a light-driven proton pump
227(1)
Porins form transmembrane channels by Beta strands
228(1)
Porins channels are made by up and down Beta barrels
229(1)
Each porin molecule has three channels
230(2)
Ion channels combine ion selectivity with high levels of ion conductance
232(1)
The K^(+) channel is a tetrameric molecule with one ion pore in the interface between the four subunits
232(1)
The ion pore has a narrow ion selectivity filter
233(1)
The bacterial photosynthetic reaction center is built up from four different polypetide chains and many pigments
234(2)
The L, M, and H subunits have transmembrane Alpha helices
236(1)
The photosynthetic pigments are bound to the L and M subunits
237(2)
Reaction centers convert light energy into electrical energy by electron flow through the membrane
239(1)
Antenna pigment proteins assemble into multimeric light-harvesting particles
240(1)
Chlorophyll molecules form circular rings in the light-harvesting complex LH2
241(1)
The reaction center is surrounded by a ring of 16 antenna proteins of the light-harvesting complex LH1
242(2)
Transmembrane Alpha helices can be predicted from amino acid sequences
244(1)
Hydrophobicity scales measure the degree of hydrophobicity of different amino acid side chains
245(1)
Hydropathy plots identify transmembrane helices
245(1)
Reaction center hydropathy plots agree with crystal structural data
246(1)
Membrane lipids have no specific interaction with protein transmembrane Alpha helices
246(1)
Conclusion
247(1)
Selected readings
248(3)
13. Signal Transduction
251(32)
G proteins are molecular amplifiers
252(2)
Ras proteins and the catalytic domain of G(Alpha) have similar three-dimensional structures
254(3)
G(Alpha) is activated by conformational changes of three switch regions
257(2)
GTPases hydrolyze GTP through nucleophilic attack by a water molecule
259(2)
The G(Beta) subunit has a seven-blade propeller fold, build up from seven WD repeat units
261(2)
The GTPase domain of G(Alpha) binds to G(Beta) in the heterotrimeric G(AlphaBetaGamma) complex
263(2)
Phosducin regulates light adaptation in retinal rods
265(1)
Phosducin binding to G(BetaGamma) blocks binding of G(Alpha)
265(2)
The human growth hornmone induces dimerization of its cognate receptor
267(1)
Dimerization of the growth hormone receptor is a sequential process
268(1)
The growth hormone also binds to the prolactin receptor
269(1)
Tyrosine kinase receptors are important enzyme-linked receptors
270(2)
Small protein modules form adaptors for a signaling network
272(1)
SH2 domains bind to phosphotyrosine-containing regions of target molecules
273(1)
SH3 domains bind to proline-rich regions of target molecules
274(1)
Src tyrosine kinases comprise SH2 and SH3 domains in addition to a tyrosine kinase
275(2)
The two domains of the kinase in the inactive state are held in a closed conformation by assembly of the regulatory domains
277(1)
Conclusion
278(2)
Selected readings
280(3)
14. Fibrous Proteins
283(16)
Collagen is a superhelix formed by three parallel, very extended left-handed helices
284(2)
Coiled coils are frequently used to form oligomers of fibrous and globular proteins
286(2)
Amyloid fibrils are suggested to be built up from continuous Beta sheet helices
288(1)
Spider silk is nature's high-performance fiber
289(1)
Muscle fibers contain myosin and actin which slide against each other during muscle contraction
290(1)
Myosin heads form cross-bridges between the actin and myosin filaments
291(1)
Time-resolved x-ray diffraction of frog muscle confirmed movement of the cross-bridges
292(1)
Structures of actin and myosin have been determined
293(2)
The structure of myosin supports the swinging cross-bridge hypothesis
295(1)
The role of ATP in muscular contraction has parallels to the role of GTP in G-protein activation
296(1)
Conclusion
297(1)
Selected readings
298(1)
15. Recognition of Foreign Molecular by the Immune System
299(26)
The polypeptide chains of antibodies are divided into domains
300(2)
Antibody diversity is generated by several different mechanisms
302(1)
All immunoglobulin domains have similar three-dimensional structures
303(1)
The immunoglobulin fold is best described as two antiparallel Beta sheets packed tightly against each other
304(1)
The hypervariable regions are clustered in loop regions at one end of the variable domain
305(1)
The antigen-binding site is formed by close association of the hypervariable regions from both heavy and light chains
306(2)
The antigen-binding site binds haptens in crevices and protein antigens on large flat surfaces
308(3)
The CDR loops assume only a limited range of conformations, except for the heavy chain CDR3
311(1)
An IgG molecule has several degrees of conformational flexibility
312(1)
Structures of MHC molecules have provided insights into the molecular mechanisms of T-cell activation
312(1)
MHC molecules are composed of antigen-binding and immunoglobulin-like domains
313(1)
Recognition of antigen is different in MHC molecules compared with immunoglobulins
314(1)
Peptides are bound differently by class I and class II MHC molecules
315(1)
T-cell receptors have variable and constant immunoglobulin domains and hypervariable regions
316(2)
MHC-peptide complexes are the ligands for T-cell receptors
318(1)
Many cell-surface receptors contain immunoglobulin-like domains
318(2)
Conclusions
320(1)
Selected readings
321(4)
16. The Structure of Spherical Viruses
325(22)
The protein shells of spherical viruses have icosahedral symmetry
327(1)
The icosahedron has high symmetry
327(1)
The simplest virus has a shell of 60 protein subunits
328(1)
Complex spherical viruses have more than one polypeptide chain in the asymmetric unit
329(2)
Structural versatility gives quasi-equivalent packing in T = 3 plant viruses
331(1)
The protein subunits recognize specific parts of the RNA inside the shell
332(1)
The protein capsid of picornaviruses contains four polypeptide chains
333(1)
There are four different structural proteins in picornaviruses
334(1)
The arrangement of subunits in the shell of picornaviruses is similar to that of T = 3 plant viruses
334(1)
The coat proteins of many different spherical plant and animal viruses have similar jelly roll barrel structures, indicating an evolutionary relationship
335(2)
Drugs against the common cold may be designed from the structure of rhinovirus
337(2)
Bacteriophage MS2 has a different subunit structure
339(1)
A dimer of MS2 subunits recognizes an RNA packaging signal
339(1)
The core protein of alphavirus has a chymotrypsin-like fold
340(1)
SV40 and polyomavirus shells are constructed from pentamers of the major coat protein with nonequivalent packing but largely equivalent interactions
341(2)
Conclusion
343(1)
Selected readings
344(3)
17. Prediction, Engineering, and Design of Protein Structures
347(26)
Homologous proteins have similar structure and function
348(1)
Homologous proteins have conserved structural cores and variable loop regions
349(1)
Knowledge of secondary structure is necessary for prediction of tertiary structure
350(1)
Prediction methods for secondary structure benefit from multiple alignment of homologous proteins
351(1)
Many different amino acid sequences give similar three-dimensional structures
352(1)
Prediction of protein structure from sequence is an unsolved problem
352(1)
Threading methods can assign amino acid sequences to known three-dimensional folds
353(1)
Proteins can be made more stable by engineering
354(1)
Disulfide bridges increase protein stability
355(1)
Glycine and proline have opposite effects on stability
356(1)
Stabilizing the dipoles of Alpha helices increases stability
357(1)
Mutants that fill cavities in hydrophobic cores do not stabilize T4 lysozyme
358(1)
Proteins can be engineered by combinatorial methods
358(1)
Phage display links the protein library to DNA
359(2)
Affinity and specificity of proteinase inhibitors can be optimized by phage display
361(2)
Structural scaffolds can be reduced in size while function is retained
363(1)
Phage display of random peptide libraries identified agonists of erythropoetin receptor
364(1)
DNA shuffling allows accelerated evolution of genes
365(2)
Protein structures can be designed from first principles
367(1)
A Beta structure has been converted to an Alpha structure by changing only half of the sequence
368(2)
Conclusion
370(1)
Selected readings
371(2)
18. Determination of Protein Structures
373(20)
Several different techniques are used to study the structure of protein molecules
373(1)
Protein crystals are difficult to grow
374(2)
X-ray sources are either monochromatic or polychromatic
376(1)
X-ray data are recorded either on image plates or by electronic detectors
377(1)
The rules for diffraction are given by Bragg's law
378(1)
Phase determination is the major crystallographic problem
379(2)
Phase information can also be obtained by Multiwavelength Anomalous Diffraction experiments
381(1)
Building a model involves subjective interpretation of the data
381(2)
Errors in the initial model are removed by refinement
383(1)
Recent technological advances have greatly influenced protein crystallography
383(1)
X-ray diffraction can be used to study the structure of fibers as well as crystals
384(2)
The structure of biopolymers can be studied using fiber diffraction
386(1)
NMR methods use the magnetic properties of atomic nuclei
387(2)
Two-dimensional NMR spectra of proteins are interpreted by the method of sequential assignment
389(1)
Distance constraints are used to derive possible structures of a protein molecule
390(1)
Biochemical studies and molecular structure give complementary functional information
391(1)
Conclusion
391(1)
Selected readings
392(1)
Protein Structure on the World Wide Web 393
Carl Branden was educated at Uppsala University (Ph.D.) and the MRC Laboratory for Molecular Biology, Cambridge, where he was a postdoctoral fellow in the laboratory of J.C. Kendrew. He has pursued a career in basic research, science administration (as science advisor to the Swedish Government), and biotechnology. Formerly Research Director of the European Synchrotron Radiation Facility in Grenoble, France, he is now at the Microbiology and Tumor Biology Center at the Karolinska Institute in Stockholm. A protein crystallographer with a distinguished academic career in research and teaching, he has made major contributions to the understanding of many biological structures, and is an editor of Structure. John Tooze was educated at Cambridge University (M.A.), London University (Ph.D.) and Harvard University (where he was a postdoctoral fellow in the laboratory of J.D. Watson). After several years in basic research, he moved principally into science administration and science publishing, notably as the executive secretary of the European Molecular Biology Organisation, Heidelberg, Germany. He is currently Director of Support Services at the Imperial Cancer Research Fund Laboratories, London, and editor of EMBO Journal. A molecular biologist, his previous books include Molecular Biology of Tumor Viruses, The DNA Story (with J.D. Watson) and the very successful first edition of Recombinant DNA: A Short Course (with J.D. Watson and D.T. Kurtz).