Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family

Chothia, Cyrus; Lesk, Arthur M.

doi:10.1016/0022-2836(85)90033-6

Cited by 68 publications

(45 citation statements)

References 18 publications

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“…The residues involved in inter-helical interactions are, respectively, 6, 7 and 10, and 93, 94, 97 and 98 [17]. These contacts are very well conserved in the mitochondrial cytochrome c family [49,50]. Other residues with sizable chemical shift changes are 15-20, 31, 34, 45, 60-61, 69, 72, 74, 77 and 87-89 (Fig.…”

Section: Nmr Experimentsmentioning

confidence: 91%

A further investigation of the cytochrome b 5–cytochrome c complex

et al. 2003

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The interaction of reduced rabbit cytochrome b 5 with reduced yeast iso-1 cytochrome c has been studied through the analysis of 1 H-15 N HSQC spectra, of 15 N longitudinal (R 1 ) and transverse (R 2 ) relaxation rates, and of the solvent exchange rates of protein backbone amides. For the first time, the adduct has been investigated also from the cytochrome c side. The analysis of the NMR data was integrated with docking calculations. The result is that cytochrome b 5 has two negative patches capable of interacting with a single positive surface area of cytochrome c. At low protein concentrations and in equimolar mixture, two different 1:1 adducts are formed. At high concentration and/or with excess cytochrome c, a 2:1 adduct is formed. All the species are in fast exchange on the scale of differences in chemical shift. By comparison with literature data, it appears that the structure of one 1:1 adduct changes with the origin or primary sequence of cytochrome b 5 .

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Section: Nmr Experimentsmentioning

confidence: 91%

A further investigation of the cytochrome b 5–cytochrome c complex

et al. 2003

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“…Indeed, a sequence homology of ~20% between proteins suggests ~1.6 to 2.3 Å rmsd within the helical core, caused by helical shifts. 104 Another problem is related to conformational rearrangement of the receptor during activation. …”

Section: Homology Modeling Of Opioid Receptorsmentioning

confidence: 99%

Homology modeling of opioid receptor-ligand complexes using experimental constraints

Pogozheva

Przydzial

Mosberg

2005

AAPS J

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A BSTRACTOpioid receptors interact with a variety of ligands, including endogenous peptides, opiates, and thousands of synthetic compounds with different structural scaffolds. In the absence of experimental structures of opioid receptors, theoretical modeling remains an important tool for structurefunction analysis. The combination of experimental studies and modeling approaches allows development of realistic models of ligand-receptor complexes helpful for elucidation of the molecular determinants of ligand affi nity and selectivity and for understanding mechanisms of functional agonism or antagonism. In this review we provide a brief critical assessment of the status of such theoretical modeling and describe some common problems and their possible solutions. Currently, there are no reliable theoretical methods to generate the models in a completely automatic fashion. Models of higher accuracy can be produced if homology modeling, based on the rhodopsin X-ray template, is supplemented by experimental structural constraints appropriate for the active or inactive receptor conformations, together with receptor-specifi c and ligand-specifi c interactions. The experimental constraints can be derived from mutagenesis and cross-linking studies, correlative replacements of ligand and receptor groups, and incorporation of metal binding sites between residues of receptors or receptors and ligands. This review focuses on the analysis of similarity and differences of the refi ned homology models of m , d , and k -opioid receptors in active and inactive states, emphasizing the molecular details of interaction of the receptors with some representative peptide and nonpeptide ligands, underlying the multiple modes of binding of small opiates, and the differences in binding modes of agonists and antagonists, and of peptides and alkaloids.K EYWORDS: ligand docking , modeling , opioid receptors , opioid ligands , pharmacophore model INTRODUCTIONClinical interest in opioid receptors (ORs) is related to the development of strong analgesics without potential for abuse or adverse side effects. This task, however, cannot be accomplished without understanding the differences in the OR subtypes as well as the modes of interactions of drugs/ ligands with these receptors.Research on ORs was signifi cantly advanced by the cloning of d -opioid (DOR), m -opioid (MOR), and k -opioid (KOR) receptors in the early 1990s. 1 , 2 Sequence comparison confi rmed that ORs belong to the rhodopsin-like family of G-protein-coupled receptors (GPCRs). 1 ORs are composed of a core domain of 7 transmembrane (TM) a -helices and an adjacent, peripheral helix 8 (IL4), are connected by 3 extracellular (EL1, EL2, EL3) and 3 intracellular (IL1, IL2, IL3) loops, and contain glycosylated N-terminal and palmitoylated C-terminal domains of different sizes. ORs demonstrate high sequence identity in their TM domain (73%-76%) and in ILs (63%-66%) and large divergence in N-and C-terminal domains and ELs (34%-40% identity). ORs are activated by either endogenous peptides o...

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“…It has been found in various studies that point mutations are in general accommodated by very minor readjustments of the protein structure and that "space" created by introducing smaller amino acids can be occupied by water molecules (17)(18)(19). Experimental evidence for [Gly54]DHFR supports this generalization.…”

mentioning

confidence: 95%

Importance of a hydrophobic residue in binding and catalysis by dihydrofolate reductase.

Mayer

Chen

Taira

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

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A conserved residue at the dihydrofolate binding site of dihydrofolate reductase (EC 1.5.1.3), leucine-54, was replaced with glycine to ascertain the role of this hydrophobic amino acid. The effect of the mutation is both to increase the dissociation rate of dihydrofolate and decrease the rate of hydride transfer thus changing the rate-limiting step in catalysis from product loss (leucine-54) to hydride transfer (glycine-54). The total stabilization by leucine-54 of the transition state for hydride transfer is ca. 104-fold (AAG 5.4 kcal/mol) at subsaturating dihydrofolate levels relative to free enzyme despite its location some 10 A from the site of chemical reaction.Classical mechanistic studies on enzyme catalysis have focused on active site residues involved as acid-base catalysts or in the formation of covalent intermediates. The importance of hydrophobic amino acids remote from or hydrophobic residues directly at the active site could not be readily ascertained. Site-directed mutagenesis provides a means to define the role of hydrophobic amino acids in enzymic catalysis. To date, the focus of most studies using site-directed mutagenesis remains on active site residues, deleting them or replacing amino acids with potentially more efficient catalysts (1-3). One striking mutagenesis study on t-RNATYr ligase (formerly t-RNATYr synthetase) (4) suggests the critical importance of remote amino acids in catalysis. Replacing two hydrogen-bonding residues in the binding site for the y-phosphate of ATP (nucleophilic attack occurs at the aPhosphate) decreased the rate of catalysis by a factor of 10 , while only weakening ATP binding by a factor of 5. We report here the effect on catalysis and binding of a mutation in dihydrofolate reductase (DHFR; EC 1.5. MATERIALS AND METHODSThe Gly-54 and Val-31 mutants were constructed by primer extension of oligonucleotides using as the template partially single-stranded pTY1 (8, 9), a derivative of pBR322 containing a 1-kilobase insert encoding forE. coli DHFR. The double mutant was constructed in the same manner, but using the Val-31 encoding plasmid as the template. The oligonucleotide sequence introduced a new restriction site (Fig. 1) 7718The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family

Cited by 68 publications

References 18 publications

A further investigation of the cytochrome b 5–cytochrome c complex

A further investigation of the cytochrome b 5–cytochrome c complex

Homology modeling of opioid receptor-ligand complexes using experimental constraints

Importance of a hydrophobic residue in binding and catalysis by dihydrofolate reductase.

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