Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy

Journal of Molecular Recognition

Volumn 13, Issue 6, 2000, Pages 325-351

  Jung, Christiane ^a  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

Cytochrome P450; Fourier transform infrared spectroscopy; Heme proteins; Protein ligand recognition; Proteins

Indexed keywords

ANALYTICAL PROCEDURES AND TECHNIQUES; CYTOCHROME P450; HEMOPROTEIN; INFRARED SPECTROSCOPY; ISOTOPE LABELING; PROTEIN LIGAND RECOGNITION; PROTEIN STRUCTURE; TARGETED MUTAGENESIS;

CYTOCHROME P-450 ENZYME SYSTEM; HEME; LIGANDS; PROTEIN BINDING; PROTEIN CONFORMATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 0033667559     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/1099-1352(200011/12)13:6<325::AID-JMR507>3.0.CO;2-C     Document Type: Review

References (195)

1. Ligand binding to heme proteins. V. Light-induced relaxation in proximal mutants L89I and H97F of carbonmonoxymyoglobin
2. Infrared spectroscopy of porphyrins
3. An infrared study of bound carbon monoxide in the human red blood cell, isolated hemoglobin, and heme carbonyls
4. Infrared studies of azide bound to myoglobin and hemoglobin. Temperature dependence of ionicity
5. A chemometric analysis of the resonance Raman spectra of mutant carbonmonoxy-myoglobin reveals the effect of polarity
6. Ultrafast detection and control of molecular dynamics
7. Rebinding and relaxation in the myoglobin pocket
8. Structure and dynamics of membrane proteins as studied by infrared spectroscopy
9. Temperature-jump-induced refolding of ribonuclease A: A time-resolved FTIR spectroscopic study
10. Vibrational circular dichroism spectra of proteins in the amide III region: Measurements and correlations of bandshape to secondary structure
11. Infrared studies on the interaction of carbon monoxide with divalent nickel in hydrogenase from Chromatium vinosum
12. 2 stretching vibrations in oxygen adducts of cobalt porphyrins. The importance of vibronic coupling
13. Resonance Raman detection of bound dioxygen in cytochrome P-450cam
14. Infrared spectroscopic studies of carbonyl horseradish peroxidases
15. 13C labeling
16. Stereo-chemistry of the Fe(II)- and Fe(III)-cyanide complexes of the homodimeric Scapharca inaequivalvis hemoglobin. A resonance Raman and FTIR study
17. FTIR analysis of the interaction of azide with horse heart myoglobin variants
18. Eine infrarot-untersuchung der CO-komplexe yon zytochrom P-450 und P-420
19. Infrared spectral studies of carbon monoxide complexes of microsomal cytochromes P-450 and P-448
20. X-ray structural characterization of a thiolate salt displaying a very strong S-H...S hydrogen bond
21. A mechanism essential to life
22. -1)
23. Time-resolved Fourier transform infrared spectroscopy of the bacteriorhodopsin mutant Tyr-185 → Phe: Asp-96 reprotonates during O formation; Asp-85 and Asp-212 deprotonate during O decay
24. Ligand binding to heme proteins: III. FTIR studies of His-E7 and Val-E11 mutants of carbonmonoxymyoglobin
25. Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry
26. The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin
27. Examination of the secondary structure of proteins by deconvoluted FTIR spectra
28. 68(E11) mutant investigated by X-ray crystallography and infrared spectroscopy
29. Fourier transform infrared photolysis studies of caged compounds
30. Time-resolved FTIR studies of the GTPase reaction of H-Ras P21 reveal a key role for the β-phosphate
31. Carbon monoxide binding to pentacoordinate mercaptide-heme complexes: Kinetic study on models for cytochrome P-450
32. Estimation of amino acid residue side-chain absorption in the infrared spectra of protein solutions in heavy water
33. Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin
34. Synthetic models for the oxygen-binding hemoproteins
35. Time-resolved Fourier-transform infrared studies of the cytochrome P-450cam carbonmonoxide complex bound with (1R)-camphor and (1S)-camphor
36. Step-scan time-resolved FTIR spectroscopy of cytochrome P-450cam carbon monoxide complex: A salt link involved in the ligand rebinding process
37. Changes in secondary structure and salt links of cytochrome P-450cam induced by photoreduction: A Fourier transform infrared spectroscopic study
38. The ferrous dioxygen complex of the oxygenase domain of neuronal nitric-oxide synthase
39. N-terminal domain swapping and metal ion binding in nitric oxide synthase dimerization
40. Cytochrome P-450 and chloroperoxidase: Thiolate-ligated heme enzymes. Spectroscopic determination of their active site structure and mechanistic implications of thiolate ligation
41. Modulation of protein function by exogenous ligands in protein cavities: CO binding to a myoglobin cavity mutant containing unnatural proximal ligands
42. Vibrational frequency shifts as a probe of hydrogen bonds: Thermal expansion and glass transition of myoglobin in mixed solvents
43. Bacteriorhodopsin: Fourier transform infrared methods for studies of protonation of carboxyl groups
44. Protein secondary structures in water from second-derivative amide I infrared spectra
45. On the function and mechanism of action of peroxidases
46. Fourier-transform infrared spectroscopy study of the pressure-induced changes in the structure of the bovine α-lactalbumin: The stabilizing role of the calcium ion
47. Active sites of transition-metal enzymes with a focus on nickel
48. Structure of metal nitrosyls
49. 3Fe and Cu(B) in cytochrome c oxidase in beef heart mitochondria studied by Fourier transform infrared spectroscopy at low temperatures
50. Binding of buried structural water increases the flexibility of proteins
51. Structural characterization of nitric oxide synthase isoforms reveals striking active-site conservation
52. The complexity of proteins
53. Proteins and pressure
54. Crystal structure of horseradish peroxidase C at 2.15 Å resolution
55. Cytochrome c oxidase: One enzyme, two mechanisms?
56. Factor analysis for separation of pure component spectra from mixture spectra
57. 2 analogue metalloporphyrins and metalloproteins
58. FT-IR difference spectroscopy of hemoglobins A and Kempsey: Evidence that a key quarternary interaction induces protonation of Aspβ99
59. Lyophilization-induced reversible changes in the secondary structure of proteins
60. Ligand-linked changes at the subunit interfaces in scapharca hemoglobins probed through the sulhydryl infrared absorption
61. Biological activation of hydrogen
62. X-ray structure determination of a metastable state of carbonmonoxy myoglobin after photodissociation
63. The binding of carbon monoxide and nitric oxide to leghemoglobin in comparison with other hemoglobins
64. Structure and function of cytochromes P450: A comparative analysis of three crystal structures
65. FTIR-spectroscopy of multistranded coiled coil proteins
66. Similarities and dissimilarities in the structure-function relation between the cytochrome c oxidase from bovine heart and from Paracoccus denitrificans as revealed by FT-IR difference spectroscopy
67. Biomolecules under extreme conditions
68. 2 transition
69. Spectroscopic and functional studies of a novel quadrupole myoglobin variant with increased peroxidase activity
70. Heme active-site structural characterization of chloroperoxidase by resonance Raman spectroscopy
71. 2)
72. Nanosecond step-scan FTIR spectroscopy of hemoglobin: Ligand recombination and protein conformational changes
73. Aspartic proteinases -Fourier transform IR studies of the aspartic carboxylic group in the active site of pepsin
74. Aggregation of chymotrypsinogen: Portrait by infrared spectroscopy
75. Determination of CO orientation in myoglobin by single-crystal infrared linear dichroism
76. Infrared evidences for Cu(B) ligation of photodissociated CO of cytochrome c oxidase at ambient temperatures and accompanied deprotonation of a carboxyl side chain of protein
77. 2+-binding proteins
78. The proximal residue largely determines the CO distortion in carbonmonoxy globin proteins. An ab initio study of a heme prosthetic unit
79. Dynamic behavior of the active site structure in bacterial cytochrome P-450
80. Structural multiplicity in the active center of cytochrome P-450
81. Substrate analogue induced changes of the CO-stretching mode in cytochrome P-450(cam) carbon monoxide complex
82. Compressibility of the heme pocket of substrate analogue complexes of cytochrome P450cam-CO: The effect of hydrostatic pressure on the Soret band
83. The CO stretching mode infrared spectrum of substrate-free cytochrome P450cam-CO: The effect of solvent conditions, temperature, and pressure
84. The role of the polarity of the heme environment for the CO stretch modes in cytochrome P-450cam
85. FT-infrared spectroscopic studies of the iron ligand CO stretch mode of iNOS oxygenase domain: Effect of arginine and tetrahydrobiopterin
86. Horseradish peroxidase monitored by infrared spectroscopy: Effect of temperature, substrate and calcium
87. Protein structural studies using vibrational circular dichroism spectroscopy
88. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins
89. Theoretical studies of the distalside steric and electrostatic effects on the vibrational characteristics of the FeCO unit of the carbonylheme proteins and their models
90. 17O isotropic chemical shifts, and nuclear quadrupole coupling constants
91. -
92. Determination of protein secondary structure using factor analysis of infrared spectra
93. Substrate interactions in cytochrome P-450: Correlation between carbon-13 nuclear magnetic resonance chemical shift and C-O vibrational frequencies
94. Crystal structures of zink-free and -bound heme domain of human inducible nitric-oxide synthase
95. Structural determinants of the stretching frequency of CO bound to myoglobin
96. Is bound CO linear or bent in heme proteins? Evidence from resonance Raman and infrared spectroscopic data
97. Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe - C - O
98. Mid-infrared vibrational spectrum of CO after photodissociation from heme: Evidence for a ligand docking site in the heme pocket of hemoglobin and myoglobin
99. Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin
100. 3
101. Identification of the Fe - O - O bending mode in oxycytochrome P450cam by resonance Raman spectroscopy
102. 15N shift
103. Water structural changes in lumirhodopsin, metarhodopsin I, and metarhodopsin II upon photolysis of bovine rhodopsin: Analysis by Fourier transform infrared spectroscopy
104. Intramembrane signalling mediated by hydrogen-bonding of water and carboxyl groups in bacteriorhodopsin and rhodopsin
105. 'Freezing-in' of carbonylhemoglobin's CO conformer population by hyperquenching of its aqueous solutions into the glassy state: An FTIR spectroscopic study of the limits of cryofixation
106. FTIR spectroscopic study of the dynamics of conformational substates in hydrated carbonyl-myoglobin films via temperature dependence of the CO stretching band parameters
107. Infrared studies of azido, cyano and other derivatives of metmyoglobin, methemoglobin, and hemins
108. Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of the B states
109. Secondary structure of sea anemone cytolysins in soluble and membrane bound form by infrared spectroscopy
110. Cytochrome c oxidase: Structure and spectroscopy
111. Probing conformational changes upon photolysis: FTIR studies of the low temperature liganded and photoproduct states of oxy- and carbonmonoxymyoglobin
112. 2.2 Å structure of oxyperoxidase as a model for the transient enzyme: Peroxide complex
113. Identification of conformational substates in nitric oxide binding to ferric and ferrous myoglobin through Fourier transform infrared spectroscopy (FTIR)
114. Anion complexes of ferrous porphyrins
115. A pH-dependent polarity change at the binuclear center of reduced cytochrome c oxidase detected by FTIR difference spectroscopy of the CO adduct
116. 2+ in equine lysozyme
117. A new method for picosecond time-resolved infrared spectroscopy: Application to CO photodissociation from iron porphyrins
118. Ligand binding to heme proteins: II. Transitions in the heme pocket of myoglobin
119. Comparative Fourier transform infrared studies of the secondary structure and the CO heme ligand environment in cytochrome P-450cam and cytochrome P-420cam
120. Connection between the taxonomic substates and protonation of histidines 64 and 97 in carbonmonoxy myoglobin
121. Two-dimensional FT-IR spectroscopy: A powerful method to study the secondary structure of proteins using H-D exchange
122. 2+-binding proteins. Marker bands for identifying the types of coordination of the side-chain COO-group to metal ions in pike parvalbumin (pl = 4.10)
123. Ligand binding to heme proteins: The effect of light on ligand binding in myoglobin
124. Structure of a histidine ligand in the photosynthetic oxygen-evolving complex as studied by light-induced Fourier transform infrared difference spectroscopy
125. Unique binding of nitric oxide to ferric nitric oxide reductase from Fusarium oxysporum elucidated with infrared, resonance Raman, and X-ray absorption spectroscopies
126. The structure and mechanism of the family of retinal proteins from halophilic archaea
127. An Infrared spectroscopic study of carbon monoxide bonding to ferrous cytochrome P-450
128. 2, NO, and CO by electrostatic interactions with the bound ligand
129. Orientation of carbon monoxide and structure-function relationship in carbonmonoxymyoglobin
130. Investigation of time-dependent phenomena by use of step-scan FT-IR
131. Differences between the pressure- and temperature-induced denaturation and aggregation of β-lactoglobulin A. B and AB monitored by FT-IR spectroscopy and small-angle X-ray scattering
132. Ultrafast thermally induced unfolding of RNase A
133. Time-resolved step-scan FT-IR spectroscopy of the photodynamics of carbonmonoxymyoglobin
134. 2 structures
135. Infrared spectra of carbonyl hemoglobins: Characterization of dynamic heme pocket conformers
136. High-resolution crystal structure of cytochrome P40(cam)
137. 3 from Escherichia coli
138. Crystal structure of the carbon monoxide-substrate-cytochrome P-450(CAM) ternary complex
139. Crystal structures of cytochrome P450CAM complexed with camphane, thiocamphor, and adamantane: Factors controlling P-450 substrate hydroxylation
140. Infrared spectroscopy in aqueous solution: Difficulties and accuracy of water substraction
141. Molecular reaction mechanisms of proteins monitored by nanosecond step-scan FT-IR difference spectroscopy
142. How far can proteins bend the FeCO unit? Distal polar and steric effects in heme proteins and models
143. Mutant and wild-type myoglobin-CO protein dynamics: Vibrational echo experiments
144. Infrared spectroscopy of the cyanide complex of iron(II) myoglobin and comparison with complexes of microperoxidase and hemoglobin
145. Distortion of the L → M transition in the photocycle of the bacteriorhodopsin mutant D96N: A timeresolved step-scan FTIR investigation
146. Tyrosine and Carboxyl protonation changes in the bacteriorhodopsin photocycle. 1. M412 and L550 intermediates
147. Vibrational spectroscopy of bacteriorhodopsin mutants. Evidence that Thr-46 and Thr-89 form part of a transient network of hydrogen bonds
148. Structural characterization of the myoglobin active site using infrared crystallography
149. Nitrosylmetalloporphyrins. 4. Molecular stereochemistry of the two crystalline forms of nitrosyl-a,b,g,d-tetraphenyl-porphinato(4-methylpiperidine)iron(I I). A structural correlation with v(NO)
150. Redox-induced conformational changes in myoglobin and hemoglobin: Electrochemistry and ultraviolet-visible and Fourier transform infrared difference spectroscopy at surface-modified gold electrodes in an ultra-thin-layer spectroelectrochemical cell
151. Crystal structure of cytochrome P-450cam complexed with the (1S)-camphor enantiomer
152. The catalytic pathway of cytochrome P450cam at atomic resolution
153. The protonic activity at cryogenic temperatures - A possible influence on the spin state of the heme-iron of cytochrome P450cam in super-cooled buffered solutions
154. The carbon monoxide stretching modes in camphor-bound cytochrome P450cam - The effect of solvent conditions, temperature, and pressure
155. Structural changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-camphor and (1S)-camphor
156. Mobility of norbornane-type substrates and water accessibility in cytochrome P450cam
157. ('s4')2- = 2,2-'(ethylenedithio)bis(thiophenolate) - Transition-metal complexes with sulfur-containing ligands .64. Proof of strong S-H...S bridges in (Ru(Sh2)(PPh3)('s4'))·THF, the 1s: H2S complex characterized by X-ray crystallography
158. Substrate binding to 15β-hydroxylase (CYP106A2) probed by FT infrared spectroscopic studies of the iron ligand CO stretch vibration
159. Time-resolved mid-infrared spectroscopy: Methods and biological applications
160. Infrared spectroscopic evidence of hydrogen bonding between carbon monoxide and protein in carbonylhorseradish peroxidase C
161. Raman and infrared spectra of cytochrome c peroxidase-carbon monoxide adducts in alternative conformational states
162. The resonance Raman spectroscopy of metalloporphyrins and heme proteins
163. Mechanisms of ligand recognition in myoglobin
164. Dynamics of dioxygen and carbon monoxide binding to soybean leghemoglobin
165. Mammalian nitric oxide synthases
166. The crystal structure of chloroperoxidase: A heme peroxidase-cytochrome P450 functional hybrid
167. Infrared absorption methods for examining protein structure
168. Infrared spectroscopy -conformation
169. Hydrogen bond network in the distal site of peroxidases: Spectroscopic properties of Asn70 → Asp horseradish peroxidase mutant
170. Effects of cholesterol side-chain groups and adrenodoxin binding on the vibrational modes of carbon monoxide bound to cytochrome P-450scc: Implication of the productive and nonproductive substrate binding
171. Infrared and EPR studies on cyanide binding to the hemecopper binuclear center of cytochrome bo-type ubiquinol oxidase from Escherichia coli
172. Resonance Raman, infrared, and EPR investigations on the binuclear site structure of the heme-copper ubiquinol oxidases from Acetobacter aceti: Effect of the heme peripheral formyl group substitution
173. Peptide backbone conformation and microenvironment of protein side chains
174. The effect of heme pocket hydrophobicity on the ligand binding dynamics in myoglobin as studied with leucine 29 mutants
175. Effects of intramolecular disulfide bond on ligand binding dynamics in myoglobin
176. Time-resolved FT-IR absorption spectroscopy using a step-scan interferometer
177. Resonance Raman investigations of cytochrome P450(cam) complexed with putidaredoxin
178. Two types of conformers with distinct Fe - C - O configuration in the ferrous CO complex of horseradish peroxidase
179. Similarities in the architecture of the active sites of Ni-hydrogenases and Fehydrogenases detected by means of infrared spectroscopy
180. 2O) solutions. I. Spectral parameters of amino acid residue absorption bands
181. Crystal structure of myoglobin-ligand complexes at near-atomic resolution
182. 3-type cytochrome c oxidase from Rhodobacter sphaeroides
183. Vibrational spectroscopy under high pressure
184. Water structural changes at the proton uptake site (the Thr46-Asp96 domain) in the L intermediate of bacteriorhodopsin
185. Fourier-transform infrared studies on conformation changes in bd-type ubiquinol oxidase from Escherichia coli upon photoreduction of the redox metal centers
186. Heart cytochrome c oxidase: An infrared study of effects of oxidation state on carbon monoxide binding
187. An infrared study of the CO binding to heart cytochrome c oxidase and hemoglobin A
188. Investigations of cyanide as an infrared probe of hemeprotein ligand binding sites
189. Infrared and electron paramagnetic resonance study of nitrosyl(protoporphyrin IX dimethyl ester)iron(II) and its complexes with nitrogenous bases as model systems for nitrosylhemoproteins: Effect of solvent polarity
190. Resonance Raman studies of ligand binding
191. The role of water in the catalytic efficiency of triosephosphate isomerase
192. Infrared characterization of nitric oxide bonding to bovine heart cytochrome c oxidase and myoglobin