Regulative interactions of the osmosensing C-terminal domain in the trimeric glycine betaine transporter BetP from Corynebacterium glutamicum

2009 ◽  
Vol 390 (8) ◽  
Author(s):  
Reinhard Krämer ◽  
Christine Ziegler
Keyword(s):  
Amino Acid ◽  
Corynebacterium Glutamicum ◽  
Protein Interactions ◽  
Regulation Mechanism ◽  
Protein Protein Interactions ◽  
Molecular Switching ◽  
X Ray ◽  
X Ray Crystallography ◽  
Terminal Domain ◽  
Domain Reorientation

Abstract Activation of the osmoregulated trimeric betaine transporter BetP from Corynebacterium glutamicum was shown to depend mainly on the correct folding and integrity of its 55 amino acid long, partly α-helical C-terminal domain. Reorientation of the three C-terminal domains in the BetP trimer indicates different lipid-protein and protein-protein interactions of the C-terminal domain during osmoregulation. A regulation mechanism is suggested where this domain switches the transporter from the inactive to the active state. Interpretation of recently obtained electron and X-ray crystallography data of BetP led to a structure-function based model of C-terminal molecular switching involved in osmoregulation.

New perceptions of transcription factor properties from NMR

1998 ◽  
Vol 76 (2-3) ◽  
pp. 368-378 ◽  
Author(s):  
Stefan Bagby ◽  
Cheryl H Arrowsmith ◽  
Mitsuhiko Ikura
Keyword(s):  
Transcription Factor ◽  
Protein Interactions ◽  
Dna Interaction ◽  
Protein Protein Interactions ◽  
Nmr Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein Protein Interaction ◽  
Structural Problems ◽  
Induced Folding

The complementarity of NMR and X-ray crystallography for biomacromolecular studies has been particularly evident in analysis of transcription factor structures and interactions. While X-ray crystallography can be used to tackle relatively complicated structural problems including multicomponent (three and higher) complexes, NMR studies have provided new insights into the nature of protein-DNA and protein-protein interactions that would be difficult to obtain by other biophysical methods. We describe herein some of the novel and important information recently derived from NMR studies of transcription factors.Key words: protein-DNA interaction, protein-protein interaction, induced folding, conformational fluctuations, transcriptional regulation.

scholarly journals Copper(I)-mediated protein–protein interactions result from suboptimal interaction surfaces

2009 ◽  
Vol 422 (1) ◽  
pp. 37-42 ◽  
Author(s):  
Lucia Banci ◽  
Ivano Bertini ◽  
Vito Calderone ◽  
Nunzia Della-Malva ◽  
Isabella C. Felli ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Metal Binding ◽  
Site Directed Mutagenesis ◽  
Protein Protein Interactions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Metal Binding Domain ◽  
Modelling Techniques ◽  
Cellular Pathways ◽  
P Type

The homoeostasis of metal ions in cells is the result of the contribution of several cellular pathways that involve transient, often weak, protein–protein interactions. Metal transfer typically implies the formation of adducts where the metal itself acts as a bridge between proteins, by co-ordinating residues of both interacting partners. In the present study we address the interaction between the human copper(I)-chaperone HAH1 (human ATX1 homologue) and a metal-binding domain in one of its partners, namely the P-type copper-transporting ATPase, ATP7A (ATPase, Cu+ transporting, α polypeptide). The adduct was structurally characterized in solution, in the presence of copper(I), and through X-ray crystallography, upon replacing copper(I) with cadmium(II). Further insight was obtained through molecular modelling techniques and site-directed mutagenesis. It was found that the interaction involves a relatively small interface (less than 1000 Å2, 1 Å=0.1 nm) with a low fraction of non-polar atoms. These observations provide a possible explanation for the low affinity of the two apoproteins. It appears that electrostatics is important in selecting which domain of the ATPase is able to form detectable amounts of the metal-mediated adduct with HAH1.

Decoding Protein-protein Interactions: An Overview

2020 ◽  
Vol 20 (10) ◽  
pp. 855-882
Author(s):  
Olivia Slater ◽  
Bethany Miller ◽  
Maria Kontoyianni
Keyword(s):  
Drug Discovery ◽  
Protein Interactions ◽  
Drug Repurposing ◽  
Protein Docking ◽  
Target Space ◽  
Protein Protein Interactions ◽  
X Ray Crystallography ◽  
Protein Protein Interaction ◽  
Interaction Sites ◽  
Long Time

Drug discovery has focused on the paradigm “one drug, one target” for a long time. However, small molecules can act at multiple macromolecular targets, which serves as the basis for drug repurposing. In an effort to expand the target space, and given advances in X-ray crystallography, protein-protein interactions have become an emerging focus area of drug discovery enterprises. Proteins interact with other biomolecules and it is this intricate network of interactions that determines the behavior of the system and its biological processes. In this review, we briefly discuss networks in disease, followed by computational methods for protein-protein complex prediction. Computational methodologies and techniques employed towards objectives such as protein-protein docking, protein-protein interactions, and interface predictions are described extensively. Docking aims at producing a complex between proteins, while interface predictions identify a subset of residues on one protein that could interact with a partner, and protein-protein interaction sites address whether two proteins interact. In addition, approaches to predict hot spots and binding sites are presented along with a representative example of our internal project on the chemokine CXC receptor 3 B-isoform and predictive modeling with IP10 and PF4.

scholarly journals Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis

2020 ◽  
Vol 76 (12) ◽  
pp. 1244-1255
Author(s):  
Sandra Kozak ◽  
Yehudi Bloch ◽  
Steven De Munck ◽  
Aleksandra Mikula ◽  
Isabel Bento ◽  
...  
Keyword(s):  
Cell Line ◽  
Protein Interactions ◽  
Successful Implementation ◽  
Structural Studies ◽  
Protein Fragments ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Acid Protein ◽  
Stimulating Factor

Structural studies of glycoproteins and their complexes provide critical insights into their roles in normal physiology and disease. Most glycoproteins contain N-linked glycosylation, a key post-translation modification that critically affects protein folding and stability and the binding kinetics underlying protein interactions. However, N-linked glycosylation is often an impediment to yielding homogeneous protein preparations for structure determination by X-ray crystallography or other methods. In particular, obtaining diffraction-quality crystals of such proteins and their complexes often requires modification of both the type of glycosylation patterns and their extent. Here, we demonstrate the benefits of producing target glycoproteins in the GlycoDelete human embryonic kidney 293 cell line that has been engineered to produce N-glycans as short glycan stumps comprising N-acetylglucosamine, galactose and sialic acid. Protein fragments of human Down syndrome cell-adhesion molecule and colony-stimulating factor 1 receptor were obtained from the GlycoDelete cell line for crystallization. The ensuing reduction in the extent and complexity of N-glycosylation in both protein molecules compared with alternative glycoengineering approaches enabled their productive deployment in structural studies by X-ray crystallography. Furthermore, a third successful implementation of the GlycoDelete technology focusing on murine IL-12B is shown to lead to N-glycosylation featuring an immature glycan in diffraction-quality crystals. It is proposed that the GlycoDelete cell line could serve as a valuable go-to option for the production of homogeneous glycoproteins and their complexes for structural studies by X-ray crystallography and cryo-electron microscopy.

Engineering an acetyllysine reader with photocrosslinking amino acid for interactome profiling

2021 ◽  
Author(s):  
Babu Sudhamalla ◽  
Anirban Roy ◽  
Soumen Barman ◽  
Jyotirmayee Padhan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Interactions ◽  
Unnatural Amino Acids ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Powerful Approach

The site-specific installation of light-activable crosslinker unnatural amino acids offers a powerful approach to trap transient protein-protein interactions both in vitro and in vivo. Herein, we engineer a bromodomain to...

scholarly journals Engineering bromodomains with a photoactive amino acid by engaging ‘Privileged’ tRNA synthetases

2020 ◽  
Vol 56 (25) ◽  
pp. 3641-3644
Author(s):  
Shana Wagner ◽  
Babu Sudhamalla ◽  
Philip Mannes ◽  
Sushma Sappa ◽  
Sam Kavoosi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chemical Synthesis ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Trna Synthetases

An improved chemical synthesis, site-specific incorporation and enhanced photo-crosslinking ability of tmdF have been demonstrated in the context of protein–protein interactions.

scholarly journals Single Amino Acid Replacements in RocA Disrupt Protein-Protein Interactions To Alter the Molecular Pathogenesis of Group A Streptococcus

2020 ◽  
Vol 88 (11) ◽  
Author(s):  
Paul E. Bernard ◽  
Amey Duarte ◽  
Mikhail Bogdanov ◽  
James M. Musser ◽  
Randall J. Olsen
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Molecular Pathogenesis ◽  
Single Amino Acid ◽  
Accessory Protein ◽  
Protein Protein Interactions ◽  
Tissue Destruction ◽  
Intact Cells ◽  
Group A

ABSTRACT Group A Streptococcus (GAS) is a human-specific pathogen and major cause of disease worldwide. The molecular pathogenesis of GAS, like many pathogens, is dependent on the coordinated expression of genes encoding different virulence factors. The control of virulence regulator/sensor (CovRS) two-component system is a major virulence regulator of GAS that has been extensively studied. More recent investigations have also involved regulator of Cov (RocA), a regulatory accessory protein to CovRS. RocA interacts, in some manner, with CovRS; however, the precise molecular mechanism is unknown. Here, we demonstrate that RocA is a membrane protein containing seven transmembrane helices with an extracytoplasmically located N terminus and cytoplasmically located C terminus. For the first time, we demonstrate that RocA directly interacts with itself (RocA) and CovS, but not CovR, in intact cells. Single amino acid replacements along the entire length of RocA disrupt RocA-RocA and RocA-CovS interactions to significantly alter the GAS virulence phenotype as defined by secreted virulence factor activity in vitro and tissue destruction and mortality in vivo. In summary, we show that single amino acid replacements in a regulatory accessory protein can affect protein-protein interactions to significantly alter the virulence of a major human pathogen.

Address of the President Lord Todd at the anniversary meeting, 30 November 1976

1977 ◽  
Vol 352 (1671) ◽  
pp. 451-462
Keyword(s):  
Protein Interactions ◽  
Complex Analysis ◽  
Organic Molecules ◽  
Heavy Atom ◽  
Vitamin B ◽  
Protein Protein Interactions ◽  
X Ray Crystallography ◽  
Polypeptide Chains ◽  
Complex Organic

The Copley Medal is awarded to Professor Dorothy M. C. Hodgkin, O. M., F. R. S. Professor Dorothy Hodgkin is distinguished for her research on the structure of complex organic molecules by the method of X-ray crystallography. She was among the first to appreciate the importance of heavy-atom phase-determining methods and these she used to effect the first complete determination of the stereochemistry of a sterol derivative in her analysis of cholesteryl iodide. The same powerful method of analysis and in particular her extraordinary gift of being able to interpret correctly the complex, partially resolved and often misleading electron density patterns that are first obtained, have been responsible for her success in elucidating the structures of many other important natural products, especially penicillin and vitamin B 12 . This last is by far the most beautiful and complex analysis which has yet been completed in this field and it is of fundamental importance to chemical science. In recent years Professor Hodgkin’s main interest has been devoted to the structure of insulin, on which she has been working on and off since 1935. Carried out with characteristic precision, this work has become a mine of stereochemical information relating to contacts between polypeptide chains and is of great significance for our interpretation of protein-protein interactions.

Studies Directed Towards the Total Synthesis of Anticapsin. X-Ray Crystal-Structure of (1RS,2SR,4RS,5RS,6SR)-5-Hydroxy-2-phthalimido-1-trimethylsilyloxy-bicyclo[2.2.2]octane-2,6-carbolactone

1990 ◽  
Vol 43 (11) ◽  
pp. 1827 ◽  
Author(s):  
MJ Crossley ◽  
TW Hambley ◽  
AW Stamford
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Total Synthesis ◽  
Synthetic Approach ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
X Ray Crystallography ◽  
Relative Stereochemistry ◽  
Atomic Parameters

The relative stereochemistry of methyl 2-phthalimido-1- trimethylsilyloxybicyclo[2.2.2]oct-5-ene-2-carboxylate (9) and its 5,6-epoxide (10), intermediates in a synthetic approach to the amino acid antibiotic anticapsin, were established by the TiCl4-mediated cyclization of (10) to the carbolactone (12); the structure of which was proved by single-crystal X-ray crystallography. Full-matrix least- squares refinement of all atomic parameters with individual isotropic thermal parameters for the hydrogen atoms by using 1446 reflections converged at R 0.036. Crystals of (12) are monoclinic, P21/c, a 12.342(3), b 12.239(2), c 13.405(3) Ǻ, β 99.34(2)°, Z 4.

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