<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Acharya, Nirbhik</style></author><author><style face="normal" font="default" size="100%">Mishra, Prajna</style></author><author><style face="normal" font="default" size="100%">Jha, Santosh Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evidence for dry molten globule-like domains in the pH-induced equilibrium folding intermediate of a multidomain protein</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Physical Chemistry Letters</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">JAN</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">1</style></number><publisher><style face="normal" font="default" size="100%">AMER CHEMICAL SOC</style></publisher><pub-location><style face="normal" font="default" size="100%">1155 16TH ST, NW, WASHINGTON, DC 20036 USA</style></pub-location><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">173-179</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The role of van der Waals (vdW) packing interactions compared to the hydrophobic effect in stabilizing the functional structure of proteins is poorly understood. Here we show, using fluorescence resonance energy transfer, dynamic fluorescence quenching, red-edge excitation shift, and near- and far-UV circular dichroism, that the pH-induced structural perturbation of a multidomain protein leads to the formation of a state in which two out of the three domains have characteristics of dry molten globules, that is, the domains are expanded compared to the native protein with disrupted packing interactions but have dry cores. We quantitatively estimate the energetic contribution of vdW interactions and show that they play an important role in the stability of the native state and cooperativity of its structural transition, in addition to the hydrophobic effect. Our results also indicate that during the pH-induced unfolding, side-chain unlocking and hydrophobic solvation occur in two distinct steps and not in concerted manner, as commonly believed&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;</style></custom3><custom4><style face="normal" font="default" size="100%">8.539</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mishra, Prajna</style></author><author><style face="normal" font="default" size="100%">Jha, Santosh Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Alternatively packed dry molten globule-like intermediate in the native state ensemble of a multidomain protein</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Physical Chemistry B</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">OCT</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">121</style></volume><pages><style face="normal" font="default" size="100%">9336-9347</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It has been difficult to quantify the degree of side-chain conformational heterogeneity in the native (N) state ensemble of proteins and the relative energetic contributions of the side-chain packing and the hydrophobic effect in protein stability. Here, we show using multiple site specific spectroscopic probes and tools of thermodynamics that the N state ensemble of a multidomain protein contains an equilibrium intermediate (I) whose interdomain region resembles a dry molten globule. In the I state, a tryptophan residue in the interdomain region is alternatively packed, but its secondary structure and intradomain packing are N-like. The I state also has a larger interdomain distance, but the domain-domain interface is dry and molten. Our results indicate that hydrophobic desolvation and side-chain packing are decoupled during protein folding and that interdomain packing interactions have an important energetic contribution in protein stability. Dynamic interconversion between alternatively packed N-like states could be important for multiple allosteric and ligand binding functions of this protein.</style></abstract><issue><style face="normal" font="default" size="100%">40</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">3.177</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Acharya, Nirbhik</style></author><author><style face="normal" font="default" size="100%">Mishra, Prajna</style></author><author><style face="normal" font="default" size="100%">Jha, Santosh Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein</style></title><secondary-title><style face="normal" font="default" size="100%">Physical Chemistry Chemical Physics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">NOV</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">19</style></volume><pages><style face="normal" font="default" size="100%">30207-30216</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The nature of the initial structural events during the base-induced unfolding of the native (N) state of proteins is poorly understood. Combining site-specific fluorescence resonance energy transfer, size exclusion chromatography, dynamic fluorescence quenching, red-edge excitation shift and circular dichroism spectroscopy, we show here that an early intermediate during the base-induced unfolding of a multidomain protein, i.e., the B form, has features of a dry molten globule. We show that the N (sic) B transition involves protein expansion and loosening of packing of inter-domain helices near domains I and II without the disruption of intra-domain packing or any change in hydration of the inter-domain region which resembles a molten hydrocarbon. Surprisingly, the disruption of inter-domain packing accounts for 40-45% of the total change in free energy of complete unfolding. Our results show that the disruption of van der Waals packing can be decoupled in different regions of a protein and could occur prior to hydrophobic solvation during base-induced unfolding, challenging the existing notion.</style></abstract><issue><style face="normal" font="default" size="100%">44</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">4.449</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Acharya, Nirbhik</style></author><author><style face="normal" font="default" size="100%">Mishra, Prajna</style></author><author><style face="normal" font="default" size="100%">Jha, Santosh Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein (vol 19, pg 20307, 2017)</style></title><secondary-title><style face="normal" font="default" size="100%">Physical Chemistry Chemical Physics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">SEP</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">20499-20499</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">36</style></issue><work-type><style face="normal" font="default" size="100%">Correction</style></work-type><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;
</style></custom3><custom4><style face="normal" font="default" size="100%">&lt;p&gt;&lt;span class=&quot;LrzXr kno-fv&quot;&gt;3.567&lt;/span&gt;&lt;/p&gt;
</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mishra, Prajna</style></author><author><style face="normal" font="default" size="100%">Jha, Santosh Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Slow motion protein dance visualized using red-edge excitation shift of a buried fluorophore</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Physical Chemistry B</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">FEB</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">123</style></volume><pages><style face="normal" font="default" size="100%">1256-1264</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;It has been extremely challenging to detect protein structures with a dynamic core, such as dry molten globules, that remain in equilibrium with the tightly packed native (N) state and that are important for a myriad of entropy-driven protein functions. Here, we detect the higher entropy conformations of a human serum protein, using red-edge excitation shift experiments. We covalently introduced a fluorophore inside the protein core and observed that in a subset of native population, the side chains of the polar and buried residues have different spatial arrangements than the mean population and that they solvate the fluorophore on a timescale much slower than the nanosecond timescale of fluorescence. Our results provide direct evidence for the dense fluidity of protein core and show that alternate side-chain packing arrangements exist in the core that might be important for multiple binding functions of this protein.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;
</style></custom3><custom4><style face="normal" font="default" size="100%">&lt;p&gt;2.923&lt;/p&gt;
</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mishra, Prajna</style></author><author><style face="normal" font="default" size="100%">Patni, Divya</style></author><author><style face="normal" font="default" size="100%">Jha, Santosh Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">pH-dependent protein stability switch coupled to the perturbed pKa of a single ionizable residue</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical Chemistry</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">electrostatic interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Fluorescence spectroscopy</style></keyword><keyword><style  face="normal" font="default" size="100%">Thermodynamic stability</style></keyword><keyword><style  face="normal" font="default" size="100%">Unfolded proteins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">JUL</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">274</style></volume><pages><style face="normal" font="default" size="100%">106591</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The contribution of electrostatic interactions in protein stability has not been fully understood. Burial of an ionizable amino acid inside the hydrophobic protein core can affect its ionization equilibrium and shift its pKa differentially in the native (N) and unfolded (U) states of a protein and this coupling between the folding/ unfolding cycle and the ionization equilibria of the ionizable residue can substantially influence the protein stability. Here, we studied the coupling of the folding/unfolding cycle with the ionization of a buried ionizable residue in a multi-domain protein, Human Serum Albumin (HSA) using fluorescence spectroscopy. A pHdependent change in the stability of HSA was observed in the near native pH range (pH 6.0-9.0). The protonation-deprotonation equilibrium of a single thiol residue that is buried in the protein structure was identified to give rise to the pH-dependent protein stability. We quantified the pKa of the thiol residue in the N and the U states. The mean pKa of the thiol in the N state was upshifted by 0.5 units to 8.7 due to the burial of the thiol in the protein structure. Surprisingly, the mean pKa of the thiol in the U state was observed to be downshifted by 1.3 units to 6.9. These results indicate that some charged residues are spatially proximal to the thiol group in the U state. Our results suggest that, in addition to the N state, electrostatic interactions in the U state are important determinants of protein stability.&lt;/p&gt;</style></abstract><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;</style></custom3><custom4><style face="normal" font="default" size="100%">2.352</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mishra, Prajna</style></author><author><style face="normal" font="default" size="100%">Jha, Santosh Kumar</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Native state conformational heterogeneity in the energy landscape of protein folding</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical Chemistry</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Conformational heterogeneity</style></keyword><keyword><style  face="normal" font="default" size="100%">Dry molten globules</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy landscape model</style></keyword><keyword><style  face="normal" font="default" size="100%">Native state</style></keyword><keyword><style  face="normal" font="default" size="100%">Side-chain packing</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">APR</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">283</style></volume><pages><style face="normal" font="default" size="100%">106761</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The native structure of proteins is central to various functions performed by cells. A vital part of the structure-function paradigm of proteins is their inherent flexibility and dynamics. The dynamic interconversion between the conformational substates in the heterogeneous native state basin of the energy landscape enables a single protein molecule to perform multiple functions. The dynamics among the substates are assisted by the motion of different structural elements of a protein out of which side-chains of amino acids hold a significant position due to their involvement in various functions such as molecular recognition and dynamic allostery. This review briefly describes the origin of conformational heterogeneity in the native state ensemble and the motions of different structural modules that assist the equilibrium dynamics of the conformational substates. The review then centers the discussion on conformational heterogeneity due to side-chain movements in proteins, the experimental methods to detect and characterize them and their role in performing multiple functions.</style></abstract><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">2.352</style></custom4></record></records></xml>