Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from <i>Streptomyces lividans</i>

Gagné, Donald; Narayanan, C. S.; Nguyen-Thi, Nhung; Roux, Louise D.; Bernard, David; Brunzelle, J.S.; Couture, Jean; Agarwal, Pratul K.; Doucet, Nicolas

doi:10.1021/acs.biochem.6b00130

Cited by 22 publications

(21 citation statements)

References 63 publications

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“…Cross-correlation analyses of protein motions from MD trajectories have highlighted changes in correlated motions upon binding of effector molecules to IGPS 38,81 . NMR and MD were also recently integrated to characterize the dynamical properties of the Streptomyces lividans xylanase B2 (XlnB2) in the free and ligand-bound states 82 . Ligand binding was shown to induce enhanced conformational dynamics of residues that interact with the ligand in the thumb loop and finger regions of the enzyme.…”

Section: Enhancing the Structural And Time-evolution Throughput Ofmentioning

confidence: 99%

“…Further illustrating the power of this combined experimental-theoretical method, Gagné et al used 15 N-CPMG, microsecond time-scale MD simulations, and QAA to investigate the conformational fluctuations associated with the binding of substrates in xylanase B2 from Streptomyces lividans (XlnB2) 82 . Using simulations of the apo enzyme and 6- and 9-unit xylan substrates bound to the enzyme as input for QAA, they characterized the dynamic modes and structural interactions of the enzyme that facilitate substrate binding (Figure 4).…”

Section: Enhancing the Structural And Time-evolution Throughput Ofmentioning

confidence: 99%

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Applications of NMR and computational methodologies to study protein dynamics

Narayanan

Bafna

Roux

et al. 2017

Archives of Biochemistry and Biophysics

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Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.

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Section: Enhancing the Structural And Time-evolution Throughput Ofmentioning

confidence: 99%

Section: Enhancing the Structural And Time-evolution Throughput Ofmentioning

confidence: 99%

Applications of NMR and computational methodologies to study protein dynamics

Narayanan

Bafna

Roux

et al. 2017

Archives of Biochemistry and Biophysics

Self Cite

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“…[22] Such ac orrelation could not be found for the data reported here ( Figure S6), in line with as imilar analysis on aB CX related protein, XlnB2. [23] The combination of alack of enzyme conformational changes and the strong enhancement of the chemical exchange for the states in which the enzyme interacts non-covalently with substrate or product molecules ((ES) 1 and EP states), suggests the presence of multiple binding modes of the substrate in the active site.Asmentioned above,itcan be expected that both X6 and X2 can bind in different "registers" and positions of the six binding subsites,with different affinities.Each binding mode would change the hydrogen bond network of amides Figure 3. Non-covalentinteractions enhance BCX millisecond time scale dynamics in the (ES) 1 and EP states.…”

Section: Resultsmentioning

confidence: 99%

Dynamics of Ligand Binding to a Rigid Glycosidase**

et al. 2020

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The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose,w hich is one of the most abundant renewable biomaterials in nature.W ed emonstrate that BCX in solution undergoes minimal structural changes during turnover.N MR spectroscopyresults showthat the rigid protein matrix provides af rame for fast substrate binding in multiple conformations, accompanied by slow conversion, whichi sa ttributed to an enzyme-induced substrate distortion. Am odel is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce aconformation that facilitates the acyl formation step of the hydrolysis reaction.

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“…The energy for the APE1:DNA interactions ( E Ape1-DNA ) were calculated as a sum of electrostatic ( E el ) and van der Waals ( E vdw ) energy between atom pairs, based on an approach developed in previous publications ( 34 , 35 ). All APE1 and DNA atom pairs were included in the calculations and the resulting interaction energies were summed up per residue pair.…”

Section: Methodsmentioning

confidence: 99%

AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop

Hoitsma

Whitaker

Beckwitt

et al. 2020

Nucleic Acids Research

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Base excision repair (BER) maintains genomic stability through the repair of DNA damage. Within BER, AP-endonuclease 1 (APE1) is a multifunctional enzyme that processes DNA intermediates through its backbone cleavage activity. To accomplish these repair activities, APE1 must recognize and accommodate several diverse DNA substrates. This is hypothesized to occur through a DNA sculpting mechanism where structural adjustments of the DNA substrate are imposed by the protein; however, how APE1 uniquely sculpts each substrate within a single rigid active site remains unclear. Here, we utilize structural and biochemical approaches to probe the DNA sculpting mechanism of APE1, specifically by characterizing a protein loop that intercalates the minor groove of the DNA (termed the intercalating loop). Pre-steady-state kinetics reveal a tyrosine residue within the intercalating loop (Y269) that is critical for AP-endonuclease activity. Using X-ray crystallography and molecular dynamics simulations, we determined the Y269 residue acts to anchor the intercalating loop on abasic DNA. Atomic force microscopy reveals the Y269 residue is required for proper DNA bending by APE1, providing evidence for the importance of this mechanism. We conclude that this previously unappreciated tyrosine residue is key to anchoring the intercalating loop and stabilizing the DNA in the APE1 active site.

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Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans

Abstract: Graphical abstract

Cited by 22 publications

References 63 publications

Applications of NMR and computational methodologies to study protein dynamics

Applications of NMR and computational methodologies to study protein dynamics

Dynamics of Ligand Binding to a Rigid Glycosidase**

AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop

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