Can stem bromelain, a pineapple waste product, be used as a drug alternative? A mechanistic insight into protein–protein interactions

2020 ◽  
Vol 44 (45) ◽  
pp. 19450-19458
Author(s):  
Samima Khatun ◽  
Anamika Sindhu ◽  
Pannuru Venkatesu
Keyword(s):  
Bovine Serum Albumin ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Waste Product ◽  
Protein Protein Interactions ◽  
Pineapple Waste ◽  
Mechanistic Insight ◽  
Biophysical Techniques ◽  
Stem Bromelain ◽  
Insight Into

Binding of stem bromelain to bovine serum albumin induced conformational changes, as shown by various biophysical techniques.

scholarly journals Thermally induced conformational changes and protein–protein interactions of bovine serum albumin in aqueous solution under different pH and ionic strengths as revealed by SAXS measurements

2017 ◽  
Vol 19 (26) ◽  
pp. 17143-17155 ◽  
Author(s):  
Dmitry Molodenskiy ◽  
Evgeny Shirshin ◽  
Tatiana Tikhonova ◽  
Andrey Gruzinov ◽  
Georgy Peters ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Conformational Changes ◽  
Interaction Potential ◽  
Protein Interactions ◽  
Bovine Serum ◽  
Protein Protein Interactions ◽  
Thermally Induced ◽  
Before And After

Temperature-induced oligomerization of albumin before and after protein melting was studied using SAXS and interpreted in terms of interaction potential.

scholarly journals The Importance of Protein-Protein Interactions on the pH-Induced Conformational Changes of Bovine Serum Albumin: A Small Angle X-Ray Scattering Study

2010 ◽  
Vol 98 (3) ◽  
pp. 630a ◽  
Author(s):  
Leandro R.S. Barbosa ◽  
Maria Grazia Ortore ◽  
Francesco Spinozzi ◽  
Paolo Mariani ◽  
Sigrid Bernstorff ◽  
...  
Keyword(s):  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Small Angle ◽  
Bovine Serum ◽  
Protein Protein Interactions ◽  
X Ray ◽  
X Ray Scattering ◽  
Scattering Study

scholarly journals Mechanistic insight into light-dependent recognition of Timeless by Drosophila cryptochrome

2021 ◽  
Author(s):  
Changfan Lin ◽  
Connor M. Schneps ◽  
Siddarth Chandrasekaran ◽  
Abir Ganguly ◽  
Brian R. Crane
Keyword(s):  
Molecular Dynamics ◽  
Western Blot ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Esr Spectroscopy ◽  
Redox State ◽  
Protein Protein Interactions ◽  
Mechanistic Insight ◽  
Dynamics Simulations ◽  
Insight Into

SUMMARYCryptochrome (CRY) entrains the fly circadian clock by binding to Timeless (TIM) in light and triggering its degradation. Undocking of a helical C-terminal tail (CTT) in response to photoreduction of the CRY flavin cofactor gates TIM binding. A generally-applicable Select Western-blot-Free Tagged-protein Interaction (SWFTI) assay enables quantification of CRY binding to TIM in dark and light. The assay is utilized to study CRY variants with residue substitutions in the flavin pocket and correlate their TIM affinities with CTT undocking, as measured by pulse-dipolar ESR spectroscopy and evaluated by molecular dynamics simulations. CRY variants with the CTT removed or undocked bind TIM constitutively, whereas those incapable of photoreduction bind TIM weakly. In response to flavin redox state, two conserved histidine residues contribute to a robust on/off switch by mediating CTT interactions with the flavin pocket and TIM. Our approach provides an expeditious means to quantify protein-protein interactions and photoreceptor targeting.

scholarly journals The Importance of Protein-Protein Interactions on the pH-Induced Conformational Changes of Bovine Serum Albumin: A Small-Angle X-Ray Scattering Study

2010 ◽  
Vol 98 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Leandro R.S. Barbosa ◽  
Maria Grazia Ortore ◽  
Francesco Spinozzi ◽  
Paolo Mariani ◽  
Sigrid Bernstorff ◽  
...  
Keyword(s):  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Small Angle ◽  
Bovine Serum ◽  
Protein Protein Interactions ◽  
X Ray ◽  
X Ray Scattering ◽  
Scattering Study

scholarly journals POT1-TPP1 differentially regulates telomerase via POT1 His266 and as a function of single-stranded telomere DNA length

2019 ◽  
Vol 116 (47) ◽  
pp. 23527-23533 ◽  
Author(s):  
Mengyuan Xu ◽  
Janna Kiselar ◽  
Tawna L. Whited ◽  
Wilnelly Hernandez-Sanchez ◽  
Derek J. Taylor
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Environmental Changes ◽  
Lymphocytic Leukemia ◽  
Protein Protein Interactions ◽  
Cellular Environment ◽  
Multiple Protein ◽  
Linear Chromosomes ◽  
Hydroxyl Radical Footprinting ◽  
Regulate Telomere Length

Telomeres cap the ends of linear chromosomes and terminate in a single-stranded DNA (ssDNA) overhang recognized by POT1-TPP1 heterodimers to help regulate telomere length homeostasis. Here hydroxyl radical footprinting coupled with mass spectrometry was employed to probe protein–protein interactions and conformational changes involved in the assembly of telomere ssDNA substrates of differing lengths bound by POT1-TPP1 heterodimers. Our data identified environmental changes surrounding residue histidine 266 of POT1 that were dependent on telomere ssDNA substrate length. We further determined that the chronic lymphocytic leukemia-associated H266L substitution significantly reduced POT1-TPP1 binding to short ssDNA substrates; however, it only moderately impaired the heterodimer binding to long ssDNA substrates containing multiple protein binding sites. Additionally, we identified a telomerase inhibitory role when several native POT1-TPP1 proteins coat physiologically relevant lengths of telomere ssDNA. This POT1-TPP1 complex-mediated inhibition of telomerase is abrogated in the context of the POT1 H266L mutation, which leads to telomere overextension in a malignant cellular environment.

Quantitative analysis of the interactions between HIV-1 integrase and retroviral reverse transcriptases

2008 ◽  
Vol 412 (1) ◽  
pp. 163-170 ◽  
Author(s):  
Alon Herschhorn ◽  
Iris Oz-Gleenberg ◽  
Amnon Hizi
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Reaction Model ◽  
Protein Protein Interactions ◽  
Common Site ◽  
Leukaemia Virus ◽  
Reverse Transcriptases ◽  
Interaction Kinetics ◽  
Hiv 1

The RT (reverse transcriptase) of HIV-1 interacts with HIV-1 IN (integrase) and inhibits its enzymatic activities. However, the molecular mechanisms underling these interactions are not well understood. In order to study these mechanisms, we have analysed the interactions of HIV-1 IN with HIV-1 RT and with two other related RTs: those of HIV-2 and MLV (murine-leukaemia virus). All three RTs inhibited HIV-1 IN, albeit to a different extent, suggesting a common site of binding that could be slightly modified for each one of the studied RTs. Using surface plasmon resonance technology, which monitors direct protein–protein interactions, we performed kinetic analyses of the binding of HIV-1 IN to these three RTs and observed interesting binding patterns. The interaction of HIV-1 RT with HIV-1 IN was unique and followed a two-state reaction model. According to this model, the initial IN–RT complex formation was followed by a conformational change in the complex that led to an elevation of the total affinity between these two proteins. In contrast, HIV-2 and MLV RTs interacted with IN in a simple bi-molecular manner, without any apparent secondary conformational changes. Interestingly, HIV-1 and HIV-2 RTs were the most efficient inhibitors of HIV-1 IN activity, whereas HIV-1 and MLV RTs showed the highest affinity towards HIV-1 IN. These modes of direct protein interactions, along with the apparent rate constants calculated and the correlations of the interaction kinetics with the capacity of the RTs to inhibit IN activities, are all discussed.

scholarly journals Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

2021 ◽  
Vol 17 (5) ◽  
pp. e1008988
Author(s):  
Nikolina ŠoŠtarić ◽  
Vera van Noort
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Protein Structures ◽  
Cellular Protein ◽  
Free Energy Calculations ◽  
Protein Protein Interactions ◽  
Post Translational Modifications ◽  
Protein Properties ◽  
Dynamics Simulations

Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond.

scholarly journals Mitochondria: Regulators of Cell Death and Survival

2002 ◽  
Vol 2 ◽  
pp. 1569-1578 ◽  
Author(s):  
David J. Granville ◽  
Roberta A. Gottlieb
Keyword(s):  
Cell Death ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Apoptotic Cell ◽  
Critical Role ◽  
Death Process ◽  
Protein Protein Interactions ◽  
Ionic Changes ◽  
A Cell ◽  
Cyt C

The past 5 years has seen an intense surge in research devoted toward understanding the critical role of mitochondria in the regulation of cell death. Apoptosis can be initiated by a wide array of stimuli, inducing multiple signaling pathways that, for the most part, converge at the mitochondrion. Although classically considered the powerhouses of the cell, it is now understood that mitochondria are also “gatekeepers” that ultimately determine the fate of the cell. The mitochondrial decision as to whether a cell lives or dies is complex, involving protein-protein interactions, ionic changes, reactive oxygen species, and other mechanisms that require further elucidation. Once the death process is initiated, mitochondria undergo conformational changes, resulting in the release of cytochrome c (cyt c), caspases, endonucleases, and other factors leading to the onset and execution of apoptosis. The present review attempts to outline the complex milieu of events regulating the mitochondrial commitment to and processes involved in the implementation of the executioner phase of apoptotic cell death.

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