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Protein quaternary structure

About: Protein quaternary structure is a(n) research topic. Over the lifetime, 2010 publication(s) have been published within this topic receiving 87086 citation(s).

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Journal ArticleDOI
Joseph A. Loo1Institutions (1)
TL;DR: Several applications of ESI-MS are discussed, including protein interactions with metal ions and nucleic acids and subunit protein structures (quaternary structure) and mass spectrometry offers advantages in speed and sensitivity.

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Abstract: Electrospray ionization mass spectrometry has been used to study protein interactions driven by noncovalent forces The gentleness of the electrospray ionization process allows intact protein complexes to be directly detected by mass spectrometry Evidence from the growing body of literature suggests that the ESI-MS observations for these weakly bound systems reflect, to some extent, the nature of the interaction found in the condensed phase Stoichiometry of the complex can be easily obtained from the resulting mass spectrum because the molecular weight of the complex is directly measured For the study of protein interactions, ESI-MS is complementary to other biophysical methods, such as NMR and analytical ultracentrifugation However, mass spectrometry offers advantages in speed and sensitivity The experimental variables that play a role in the outcome of ESI-MS studies of noncovalently bound complexes are reviewed Several applications of ESI-MS are discussed, including protein interactions with metal ions and nucleic acids and subunit protein structures (quaternary structure)

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1,115 citations


Journal ArticleDOI
J.M. Baldwin1, Cyrus Chothia2Institutions (2)
TL;DR: These structural results, together with other work, particularly the calculations of Gelin & Karplus and of Warshel, support a description of the haemoglobin mechanism in which the binding of ligand to the deoxy form is accompanied by steric strain, so that the proportion of molecules in the high-affinity form increases as successive ligands bind.

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Abstract: The structural changes that occur on ligand binding to haemoglobin have been studied by comparison of the atomic co-ordinates of human deoxy, horse met and human carbonmonoxy haemoglobin, using computer graphics and least-squares fitting methods. The changes that occur on going from deoxy to either of the liganded forms are very similar. These include tertiary structure changes within the α1β1 dimer and a quaternary structure change in which the packing of α1β1 against α2β2 alters. On going from deoxy to liganded haemoglobin, no significant structural change occurs in the central regions of the α1β1 dimer, including the α1β1 interface and nearby helices B, C, G and H in both subunits. Movements occur in the outer parts of the dimer, where the haems, F helices and FG corners of both subunits move towards the centre of the molecule. The two haems and the two FG corners come ~2 A closer together. One important effect of the changes in both subunits is to translate the F helix across the face of the haem by ~1 A. This moves the haem-linked histidine F8 from a position that is asymmetric with respect to the porphyrin nitrogens in deoxy to a more symmetric position in liganded haemoglobin. The motion of the β haem removes the ligand-binding site from the vicinity of ValβE11, which hinders ligand binding in deoxy. The changes in tertiary structure are linked to the quaternary change through the motion of the FG corners. The C helices and FG corners of α1β1 are in contact with the FG corners and C helices of α2β2 in both quaternary structures. In the quaternary change the contacts between α1FG and β2C and between α2FG and β1C act as “flexible joints” allowing small relative motions. The same side-chains are involved in the contacts in both structures. The contacts between α1C and β2FG and between α2C and β1FG act as “switch” regions, having two different stable positions with different side-chains in contact. The change between the two positions involves a relative movement of ~6 A. The quaternary structure change to liganded haemoglobin destroys the contacts made by the C-terminal residues of each subunit in deoxy haemoglobin, and these residues rotate freely in the liganded form. These structural results, together with other work, particularly the calculations of Gelin & Karplus and of Warshel, support a description of the haemoglobin mechanism in which (1) the binding of ligand to the deoxy form is accompanied by steric strain, originating from the particular position of the F helix and of His F8 relative to the haem. (2) The strain leads to decreased stability of the deoxy quaternary structure relative to the liganded quaternary structure, so that the proportion of molecules in the high-affinity form increases as successive ligands bind. (3) The quaternary structure change to the high-affinity form induces tertiary structure changes that reposition the F helix and HisF8 relative to the haem and there is then no strain on ligand binding. In the absence of ligand the deoxy structure is favoured by the greater surface area buried between α1β1 and α2β2 in this quaternary structure. Further implications of the structural results are discussed.

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786 citations


Journal ArticleDOI
TL;DR: The major envelope protein from Escherichia coli has been purified by differential heat extraction in dodecyl sulfate and subsequently freed of the detergent, and its molecular weight agrees with that derived from the mobility of the major band observed in standard dodecYL sulfate gel electrophoretic analysis of unfractionated cell envelopes after treatment at 100°.

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Abstract: The major envelope protein from Escherichia coli has been purified by differential heat extraction in dodecyl sulfate and subsequently freed of the detergent The polypeptide is homogeneous and has a mass of 36,500 daltons Homogeneity is based on four criteria, three of which are independent of its behavior in detergents Its molecular weight was established by three methods independent of dodecyl sulfate binding and agrees with that derived from the mobility of the major band observed in standard dodecyl sulfate gel electrophoretic analysis of unfractionated cell envelopes after treatment at 100° The mass of the protein is accounted for entirely, or nearly entirely, by the mass of its constituent amino acids These results imply that dodecyl sulfate is bound in amounts corresponding to those found in most polypeptides The protein was also isolated in association with the rigid layer of the cell by extraction of cell envelopes in 2 % dodecyl sulfate at 60° This complex is composed of about 65 % envelope protein, the remaining mass being accounted for largely by the peptidoglycan-lipoprotein structure In this form the protein is completely resistant to trypsin, but upon dissociation it is quickly degraded to small fragments Unlike the dissociated polypeptide, the complexed form of the protein does not bind dodecyl sulfate tightly even upon prolonged exposure to high excess at 60° A large fraction of the polypeptide exists as β-structure, as determined by circular dichroism and infrared spectroscopy The 105 copies of this polypeptide per cell are arranged in a lattice structure with hexagonal symmetry and a periodicity of 75 nm on the outer face of the peptidoglycan The regular array observed appears to be closely related to its quaternary structure in vivo All strains of E coli tested contain this protein

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706 citations


Journal ArticleDOI
TL;DR: It is suggested that these oligomers assemble from preformed monomers with little change in conformation, and in oligomers with large interfaces, isolated subunits should be unstable given their excessively large accessible surface, and assembly is expected to require major structural changes.

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Abstract: The solvent-accessible surface area (As) of 23 oligomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. As is correlated with the protein molecular weight, and a power law predicts its value to within 5% on average. The accessible surface of the average oligomer is similar to that of monomeric proteins in its hydropathy and amino acid composition. The distribution of the 20 amino acid types between the protein surface and its interior is also the same as in monomers. Interfaces, i.e. surfaces involved in subunit contacts, differ from the rest of the subunit surface. They are enriched in hydrophobic side-chains, yet they contain a number of charged groups, especially from Arg residues, which are the most abundant residues at interfaces except for Leu. Buried Arg residues are involved in H-bonds between subunits. We counted H-bonds at interfaces and found that several have none, others have one H-bond per 200 A2 of interface area on average (1 A = 0.1 nm). A majority of interface H-bonds involve charged donor or acceptor groups, which should make their contribution to the free energy of dissociation significant, even when they are few. The smaller interfaces cover about 700 A2 of the subunit surface. The larger ones cover 3000 to 10,000 A2, up to 40% of the subunit surface area in catalase. The lower value corresponds to an estimate of the accessible surface area loss required for stabilizing subunit association through the hydrophobic effect alone. Oligomers with small interfaces have globular subunits with accessible surface areas similar to those of monomeric proteins. We suggest that these oligomers assemble from preformed monomers with little change in conformation. In oligomers with large interfaces, isolated subunits should be unstable given their excessively large accessible surface, and assembly is expected to require major structural changes.

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633 citations


Journal ArticleDOI
08 Apr 1988-Cell
TL;DR: A family of related multisubunit CCAAT-binding proteins that are composed of heterologous subunits are proposed that are related to each other and to the adenovirus origin of replication and is required for the initiation ofadenoviral replication.

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Abstract: We have characterized three distinct proteins present in HeLa cell extracts that specifically recognize different subsets of transcriptional elements containing the pentanucleotide sequence CCAAT. One of these CCAAT-binding proteins, CP1, binds with high affinity to CCAAT elements present in the human a-globin promoter and the adenovirus major late promoter (MLP). A second protein, CP2, binds with high affinity to a CCAAT element present in the rat γ-fibrinogen promoter. Finally, the third CCAAT-binding protein is nuclear factor I (NF-I), a cellular DNA-binding protein that binds to the adenovirus origin of replication and is required for the initiation of adenoviral replication. CPi, CP2, and NF-I are distinct activities in that each binds to its own recognition site with an affinity that is at least three orders of magnitude higher than that with which it binds to the recognition sites of the other two proteins. Surprisingly, CP1, CP2, and NF-I each appear to recognize their binding site with highest affinity as a multisubunit complex composed of heterologous subunits. In the case of CP1, two different types of subunits form a stable complex in the absence of a DNA-binding site. Moreover, both subunits are present in the CP1-DNA complex. We thus propose the existence of a family of related multisubunit CCAAT-binding proteins that are composed of heterologous subunits.

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595 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202132
202038
201929
201828
201737
201641

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Topic's top 5 most impactful authors

Carol V. Robinson

13 papers, 1.5K citations

Dmitri I. Svergun

12 papers, 607 citations

Rainer Jaenicke

6 papers, 220 citations

Virgil Simplaceanu

5 papers, 388 citations

William A. Eaton

5 papers, 270 citations