alternative conformation
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2022 ◽  
Author(s):  
Shuting Yan ◽  
Qiyao Zhu ◽  
Swati Jain ◽  
Tamar Schlick

Abstract Conserved SARS-CoV-2 RNA regions of critical biological functions define excellent targets for anti-viral therapeutics against Covid-19 variants. One such region is the frameshifting element (FSE), responsible for correct translation of viral polyproteins. Here, we analyze molecular-dynamics motions of three FSE conformations, discovered by graph-theory analysis, and associated mutants designed by graph-based inverse folding: two distinct 3-stem H-type pseudoknots and a 3-way junction. We find that the prevalent H-type pseudoknot in literature adopts ring-like conformations, which in combination with 5′ end threading could promote ribosomal pausing. An inherent shape switch from “L” to linear that may help trigger the frameshifting is suppressed in our designed mutant. The alternative conformation trajectories suggest a stable intermediate structure with mixed stem interactions of all three conformations, pointing to a possible transition pathway during ribosomal translation. These observations provide new insights into anti-viral strategies and frameshifting mechanisms.


Metabolites ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 865
Author(s):  
Francesc Xavier Ruiz ◽  
Xavier Parés ◽  
Jaume Farrés

Human aldo-keto reductase 1B10 (AKR1B10) is overexpressed in many cancer types and is involved in chemoresistance. This makes AKR1B10 to be an interesting drug target and thus many enzyme inhibitors have been investigated. High-resolution crystallographic structures of AKR1B10 with various reversible inhibitors were deeply analyzed and compared to those of analogous complexes with aldose reductase (AR). In both enzymes, the active site included an anion-binding pocket and, in some cases, inhibitor binding caused the opening of a transient specificity pocket. Different structural conformers were revealed upon inhibitor binding, emphasizing the importance of the highly variable loops, which participate in the transient opening of additional binding subpockets. Two key differences between AKR1B10 and AR were observed regarding the role of external loops in inhibitor binding. The first corresponded to the alternative conformation of Trp112 (Trp111 in AR). The second difference dealt with loop A mobility, which defined a larger and more loosely packed subpocket in AKR1B10. From this analysis, the general features that a selective AKR1B10 inhibitor should comply with are the following: an anchoring moiety to the anion-binding pocket, keeping Trp112 in its native conformation (AKR1B10-like), and not opening the specificity pocket in AR.


2021 ◽  
Author(s):  
Shawn M Costello ◽  
Sophie R Shoemaker ◽  
Helen T Hobbs ◽  
Annalee W Nguyen ◽  
Ching-Lin Hsieh ◽  
...  

Current COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 spike ectodomain. Using hydrogen deuterium exchange mass spectrometry, we have uncovered that, in addition to the prefusion structure determined by cryo-EM, this protein adopts an alternative conformation that interconverts slowly with the canonical prefusion structure. This new conformation-an open trimer-contains easily accessible RBDs. It exposes the conserved trimer interface buried in the prefusion conformation, thus exposing potential epitopes for pan-coronavirus antibody and ligand recognition. The population of this state and kinetics of interconversion are modulated by temperature, receptor binding, antibody binding, and sequence variants observed in the natural population. Knowledge of the structure and populations of this conformation will help improve existing diagnostics, therapeutics, and vaccines.


2021 ◽  
Vol 118 (17) ◽  
pp. e2022464118
Author(s):  
Lauriane Lecoq ◽  
Shishan Wang ◽  
Marie Dujardin ◽  
Peter Zimmermann ◽  
Leonard Schuster ◽  
...  

Viral hepatitis is growing into an epidemic illness, and it is urgent to neutralize the main culprit, hepatitis B virus (HBV), a small-enveloped retrotranscribing DNA virus. An intriguing observation in HB virion morphogenesis is that capsids with immature genomes are rarely enveloped and secreted. This prompted, in 1982, the postulate that a regulated conformation switch in the capsid triggers envelopment. Using solid-state NMR, we identified a stable alternative conformation of the capsid. The structural variations focus on the hydrophobic pocket of the core protein, a hot spot in capsid–envelope interactions. This structural switch is triggered by specific, high-affinity binding of a pocket factor. The conformational change induced by the binding is reminiscent of a maturation signal. This leads us to formulate the “synergistic double interaction” hypothesis, which explains the regulation of capsid envelopment and indicates a concept for therapeutic interference with HBV envelopment.


2021 ◽  
Author(s):  
Matthew Domnauer ◽  
Fan Zheng ◽  
Liying Li ◽  
Yanxiao Zhang ◽  
Catherine E. Chang ◽  
...  

Temperature is a variable component of the environment and all organisms must deal with or adapt to temperature change. Acute temperature change activates cellular stress responses resulting in the refolding or removal of damaged proteins. However, how organisms adapt to long-term temperature change remains largely unexplored. Here, we report that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to the reduction of temperature sensitive proteins and re-localizing a portion of its proteome. Surprisingly, we also find many proteins adopt an alternative conformation. Using Fet3p as an example, we find that the temperature-dependent conformational difference is accompanied by distinct thermostability, subcellular localization, and importantly, cellular functions. We postulate that in addition to the known mechanisms of adaptation, conformational plasticity allows some polypeptides to acquire new biophysical properties and functions when environmental change endures.


2020 ◽  
Vol 117 (46) ◽  
pp. 28838-28846
Author(s):  
Yunxiao Zhang ◽  
Wan-Jin Lu ◽  
David P. Bulkley ◽  
Jiahao Liang ◽  
Arthur Ralko ◽  
...  

Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental, and agents amenable to tissue targeting for therapeutic application have been lacking. We have developed an agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1 (PTCH1). This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 “switch helix,” as revealed by our cryogenic electron microscopy structure. Nanobody-binding likely traps Patched in one stage of its transport cycle, thus preventing substrate movement through the Patched1 sterol conduit. Unlike the native Hedgehog ligand, this nanobody does not require lipid modifications for its activity, facilitating mechanistic studies of Hedgehog pathway activation and the engineering of pathway activating agents for therapeutic use. Our conformation-selective nanobody approach may be generally applicable to the study of other PTCH1 homologs.


Author(s):  
David Vizarraga ◽  
Rosa Pérez-Luque ◽  
Jesús Martín ◽  
Ignacio Fita ◽  
David Aparicio

The human pathogen Mycoplasma genitalium is responsible for urethritis in men, and for cervicitis and pelvic inflammatory disease in women. The adherence of M. genitalium to host target epithelial cells is mediated through an adhesion complex called Nap, which is essential for infectivity. Nap is a transmembrane dimer of heterodimers of the immunodominant proteins P110 and P140. The M. genitalium genome contains multiple copies of portions that share homology with the extracellular regions of P140 and P110 encoded by the genes mg191 and mg192, respectively. Homologous recombination between the genes and the copies allows the generation of a large diversity of P140 and P110 variants to overcome surveillance by the host immune system. Interestingly, the C-terminal domain (C-domain) of the extracellular region of P140, which is essential for the function of Nap by acting as a flexible stalk anchoring the protein to the mycoplasma membrane, presents a low degree of sequence variability. In the present work, the X-ray crystal structures of two crystal forms of a construct of the P140 C-domain are reported. In both crystal forms, the construct forms a compact octamer with D4 point-group symmetry. The structure of the C-domain determined in this work presents significant differences with respect to the structure of the C-domain found recently in intact P140. The structural plasticity of the C-domain appears to be a possible mechanism that may help in the functioning of the mycoplasma adhesion complex.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yoonyoung Heo ◽  
Hye-Jin Yoon ◽  
Hanseo Ko ◽  
Soonmin Jang ◽  
Hyung Ho Lee

Author(s):  
Christos M. Kougentakis ◽  
Lauren Skerritt ◽  
Ananya Majumdar ◽  
Jamie L. Schlessman ◽  
Bertrand García-Moreno E.

AbstractCharges are incompatible with the hydrophobic interior of proteins, yet proteins use buried charges, often in pairs or networks, to drive energy transduction processes, catalysis, pH-sensing, and ion transport. The structural adaptations necessary to accommodate interacting charges in the protein interior are not well understood. According to continuum electrostatic calculations, the Coulomb interaction between two buried charges cannot offset the highly unfavorable penalty of dehydrating two charges. This was investigated experimentally with two variants of staphylococcal nuclease (SNase) with Glu:Lys or Lys:Glu pairs introduce at internal i, i+4 positions on an α-helix. Contrary to expectations from previous theoretical and experimental studies, the proteins tolerated the charged ion pairs in both orientations. Crystal structures and NMR spectroscopy studies showed that in both variants, side chains or backbone are reorganized. This leads to the exposure of at least one of the two buried groups to water. Comparison of these ion pairs with a highly stable buried ion pair in SNase shows that the location and the amplitude of structural reorganization can vary dramatically between ion pairs buried in the same general region of the protein. The propensity of the protein to populate alternative conformation states in which internal charges can contact water appears to be the factor that governs the magnitude of electrostatic effects in hydrophobic environments. The net effect of structural reorganization is to weaken the Coulomb interactions between charge pairs; however, the reorganized protein no longer has to pay the energetic penalty for burying charges. These results provide the framework necessary to understand the interplay between the dehydration of charges, Coulomb interactions and protein reorganization that tunes the functional properties of proteins.


2019 ◽  
Author(s):  
Yunxiao Zhang ◽  
Wan-Jin Lu ◽  
David P. Bulkley ◽  
Jiahao Liang ◽  
Arthur Ralko ◽  
...  

AbstractActivation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental and therapeutic application has been difficult for lack of agents amenable to tissue targeting. We have developed a novel agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1. This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 “switch helix”, as revealed by cryo-EM structure determination. Although this conformation likely constitutes part of the transport cycle, nanobody-trapping disrupts the cycle and prevents substrate movement through the Patched1 sterol conduit. Our conformation-selective nanobody approach provides a new route to the development of transporter-related pharmacologic agents and may be generally applicable to the study of other transporters.


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