Complete Relaxation and Conformational Exchange Matrix (CORCEMA) Analysis of Intermolecular Saturation Transfer Effects in Reversibly Forming Ligand–Receptor Complexes

Jayalakshmi, V.; Krishna, N. Rama

doi:10.1006/jmre.2001.2499

Cited by 210 publications

(241 citation statements)

References 29 publications

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“…25,52 Parameters employed in the CORCEMA-ST simulations were used as initially estimated; a free ligand correlation time of 253 ps calculated from the pulsed field gradient diffusion measurements, a correlation time of 23.9 µs when bound was calculated from the molecular mass of the protein as a trimer (165 kDa), an internal correlation time being one order of magnitude shorter 53 i.e. .…”

Section: Methodsmentioning

confidence: 99%

Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions

et al. 2016

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Understanding interactions of bacterial surface polysaccharides with receptor protein scaffolds is important for the development of antibiotic therapies. The corresponding protein recognition domains frequently form low-affinity complexes with polysaccharides that are difficult to address with experimental techniques because of the conformational flexibility of the polysaccharide. In this work, we studied the tailspike protein (TSP) of the bacteriophage Sf6. Sf6TSP binds and hydrolyzes the high-rhamnose, serotype Y O-antigen polysaccharide of the Gram-negative bacterium Shigella flexneri (S. flexneri) as a first step of bacteriophage infection. Spectroscopic analyses and enzymatic cleavage assays confirmed that Sf6TSP binds long stretches of this polysaccharide. Crystal structure analysis and saturation transfer difference (STD) NMR spectroscopy using an enhanced method to interpret the data permitted the detailed description of affinity contributions and flexibility in an Sf6TSP-octasaccharide complex. Dodecasaccharide fragments corresponding to three repeating units of the O-antigen in complex with Sf6TSP were studied computationally by molecular dynamics simulations. They showed that distortion away from the low-energy solution conformation found in the octasaccharide complex is necessary for ligand binding. This is in agreement with a weak-affinity functional polysaccharide-protein contact that facilitates correct placement and thus hydrolysis of the polysaccharide close to the catalytic residues. Our simulations stress that the flexibility of glycan epitopes together with a small number of specific protein contacts provide the driving force for Sf6TSP-polysaccharide complex formation in an overall weak-affinity interaction system.

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Section: Methodsmentioning

confidence: 99%

Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions

et al. 2016

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“…The saturation in the phospholipids is not limited within the vesicle but is transferred to the residues at the interface of sapecin through the cross-saturation phenomena. If the reversible exchange of the sapecin and phospholipid vesicle complex exhibits a dissociation rate approximately greater than 0.1 s Ϫ1 , then the effect of the cross-saturation is sufficiently observed in the free state of sapecin (21). However, the wild type sapecin slowly dissociates from the membrane.…”

Section: Resultsmentioning

confidence: 99%

“…The solution structure of sapecin was solved in methanol by NMR techniques (PDB code 1L4V) (9). The structure revealed that the peptide consists of an N-terminal loop (residues 4 -12), an ␣ helix (residues [15][16][17][18][19][20][21][22][23], and a two-stranded ␤ sheet (residues 24 -31 and 34 -40), with three disulfide bridges connecting these structural elements. Sapecin can inhibit the growth of Gram-positive bacteria (Staphylococcus aureus) at micromolar concentrations (3) and, furthermore, shows high affinity for an acidic phospholipid, cardiolipin (CL) 1 (3).…”

mentioning

confidence: 99%

Channel-forming Membrane Permeabilization by an Antibacterial Protein, Sapecin

Takeuchi

Takahashi

Sugai

et al. 2004

Journal of Biological Chemistry

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The action mechanism of sapecin, an antibacterial peptide with membrane permeabilization activity, was investigated. The dose dependence of the membrane permeabilization caused by sapecin was sigmoidal, suggesting that sapecin oligomerization leads to the membrane permeabilization. Solution nuclear magnetic resonance analysis of the sapecin-phospholipid vesicle complex revealed the surface buried in the membrane and oligomerization surface on the sapecin molecule. The membrane-buried surface of sapecin was determined by observing the transferred cross-saturation phenomena from the alkyl chains of the phospholipid vesicle to the amide protons of sapecin. The membraneburied surface contains basic and highly exposed hydrophobic residues, which are suitable for interacting with the acidic bacterial membrane. The oligomerization surface was also identified by comparisons between the results from hydrogen-deuterium exchange experiments and transferred cross-saturation experiments. On the basis of the results from the NMR experiments we built a putative model of sapecin oligomers, which provides insights into the membrane permeabilization caused by insect defensins.

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“…Methods for the simulation of NOESY-HSQC spectra [232] and for the simulation of relaxation and conformational exchange [233] were developed. The nuclear Overhauser effects (NOE), produced by magnetization transfer between protons, are depending on the structure, but also on the internal dynamics of the observed molecule.…”

Section: Overhauser Effect Analysismentioning

confidence: 99%

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Malliavin

2006

COC

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Nuclear Magnetic Resonance (NMR) became during the two last decades an important method for biomolecular structure determination. NMR permits to study biomolecules in solution and gives access to the molecular flexibility at atomic level on a complete structure: in that respect, it is occupying a unique place i n structural biology. During the first years of its development, NMR was trying to meet the requirements previously defined in X-ray crystallography. But, NMR then started to determine its own criteria for the definition of a structure. Indeed, the atomic coordinates of an NMR structure are calculated using restraints on geometrical parameters (angles and distances) of the structure, which are only indirectly related to atom positions: in that respect, NMR and X-ray crystallography are very different. The indirect relation between the NMR measurements and the molecular structure and dynamics makes critical the precision and the interpretation of the NMR parameters and the development of quantitative analysis methods. The methods published since 1997 for liquid-NMR of proteins are reviewed here. First, methods for structure determination are presented, as well as methods for spectral assignment and for structure quality assessment. Second, the quantitative analysis of structure mobility i s reviewed.

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Complete Relaxation and Conformational Exchange Matrix (CORCEMA) Analysis of Intermolecular Saturation Transfer Effects in Reversibly Forming Ligand–Receptor Complexes

Cited by 210 publications

References 29 publications

Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions

Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions

Channel-forming Membrane Permeabilization by an Antibacterial Protein, Sapecin

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

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