scholarly journals Probing the local conformational flexibility in receptor recognition: mechanistic insight from an atomic-scale investigation

RSC Advances ◽  
2019 ◽  
Vol 9 (25) ◽  
pp. 13968-13980 ◽  
Author(s):  
Fei Ding ◽  
Wei Peng
Keyword(s):  
Structural Characteristics ◽  
Conformational Flexibility ◽  
Atomic Scale ◽  
Flexible Loop ◽  
Mechanistic Insight ◽  
Receptor Recognition ◽  
Loop Domains

The local conformational flexibility and dynamics have significant impacts on the receptor recognition processes, and this phenomenon is related closely to the structural characteristics of the flexible loop domains in biomacromolecules.

Conformational flexibility of inositol phosphates: influence of structural characteristics

2002 ◽  
Vol 43 (27) ◽  
pp. 4853-4856 ◽  
Author(s):  
Carla J. Volkmann ◽  
Ginger M. Chateauneuf ◽  
Jyotsna Pradhan ◽  
Andrew T. Bauman ◽  
Richard E. Brown ◽  
...  
Keyword(s):  
Inositol Phosphates ◽  
Structural Characteristics ◽  
Conformational Flexibility

Polymorphism of monotropic forms: relationships between thermochemical and structural characteristics

2020 ◽  
Vol 76 (1) ◽  
pp. 65-75 ◽  
Author(s):  
German Perlovich ◽  
Artem Surov
Keyword(s):  
Molecular Descriptors ◽  
Structural Information ◽  
Structural Characteristics ◽  
Conformational Flexibility ◽  
Similarity Coefficients ◽  
Tanimoto Similarity ◽  
Group I ◽  
Bivariate Statistical Analysis ◽  
Polymorphic Forms ◽  
Group Ii

In this work, a database containing thermochemical and structural information about 208 monotropic polymorphic forms has been created and analyzed. Most of the identified compounds (77 cases) have been found to have two polymorphs, 14 compounds have three forms and there are only three examples of systems with four polymorphs. The analysis of density distribution within the database has revealed that only 62 out of 114 metastable polymorphs (referred to as group I) obey the `density rule' proposed by Burger and Ramberger [(1979), Mikrochim. Acta, 72, 259–271], while the remaining 45% of the monotropic systems (group II) violate the rule. A number of physicochemical, structural and molecular descriptors have been used to find and highlight the differences between group I and group II of the polymorphs. Group II is characterized (on average) by higher values of descriptors, which are responsible for conformational flexibility of molecules. An algorithm has been proposed for carrying out bivariate statistical analysis. It implies partitioning the database into structurally related clusters based on Tanimoto similarity coefficients and subsequent analysis of each cluster in terms of the number of hydrogen bonds per molecule.

Examination of whewellite kidney stones by scanning electron microscopy and powder neutron diffraction techniques

2009 ◽  
Vol 42 (1) ◽  
pp. 109-115 ◽  
Author(s):  
Michel Daudon ◽  
Dominique Bazin ◽  
Gilles André ◽  
Paul Jungers ◽  
Alain Cousson ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Neutron Diffraction ◽  
Kidney Stones ◽  
Structural Characteristics ◽  
Calcium Oxalate Monohydrate ◽  
Atomic Scale ◽  
Mesoscopic Scale ◽  
Powder Neutron Diffraction ◽  
Scanning Electron

Kidney stones made of whewellite,i.e.calcium oxalate monohydrate, exhibit various morphological aspects. The crystalline structure of whewellite at the atomic scale was revisited through a single-crystal neutron study at room temperature using a four-circle automated diffractometer. The possible relationships between the various morphological types of whewellite stones and their structural characteristics were examined at the mesoscopic scale by the use of scanning electron microscopy and at the nanometric scale by powder neutron diffraction. All types of whewellite stones displayed a similar structure at the nanometric scale. However, significant differences were found at the mesoscopic scale. In particular, the crystallites in kidney stones resulting from a genetic hyperoxaluria exhibited a peculiar structure. There was a close relationship between stone morphology and crystallite organization at the mesoscopic level and the effectiveness of extracorporeal shockwave lithotripsy.

scholarly journals Structural Aspects of the Superionic Transition in AX2 Compounds With the Fluorite Structure

2021 ◽  
Vol 9 ◽  
Author(s):  
Paul C. M. Fossati ◽  
Alain Chartier ◽  
Alexandre Boulle
Keyword(s):  
Structural Changes ◽  
Structural Characteristics ◽  
Fluorite Structure ◽  
Atomic Scale ◽  
Small Scale ◽  
Empirical Potentials ◽  
Structure Changes ◽  
Local Environments ◽  
Binary Compounds ◽  
Liquid States

Some AX2 binary compounds with the fluorite structure (space group Fm3̄m) are well-known examples of materials exhibiting transitions to ionic superconducting phases at high temperatures below their melting points. Such superionic states have been described as either highly defective crystals or part-crystal, part-liquid states where the A ions retain their crystalline order whilst the X ions undergo partial melting. However, no detailed description of the structure of these phases exists. We present here the results of our investigation of the structural changes that occur during these transitions and the structural characteristics of the resulting superionic materials. This work is based on atomic-scale molecular dynamics modelling methods as well as computational diffraction techniques. We employed a set of empirical potentials representing several compounds with the fluorite structure to investigate any potential-dependent effect. We show the importance of small-scale structure changes, with some local environments showing a hexagonal symmetry similar to what is seen in the scrutinyite structure that has been documented for example in UO2.

scholarly journals COVID-19 Pandemic: Insights into Structure, Function, and hACE2 Receptor Recognition by the SARS-CoV-2

2020 ◽  
Author(s):  
Anshumali Mittal ◽  
Kavyashree Manjunath ◽  
Rajesh Kumar Ranjan ◽  
Sandeep Kaushik ◽  
Sujeet Kumar ◽  
...  
Keyword(s):  
Host Cell ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Large Scale ◽  
Current Knowledge ◽  
Structural Characteristics ◽  
Global Public Health ◽  
Host Cell Membrane ◽  
Origin And Evolution ◽  
Receptor Recognition

SARS-CoV-2 is a newly emerging, highly transmissible, and pathogenic coronavirus in humans, which has caused global public health emergency and economic crisis. To date, millions of infections and thousands of deaths have been reported worldwide, and the numbers continue to rise. Currently, there is no specific drug or vaccine against this deadly virus; therefore, there is a pressing need to understand the mechanism through which this deadly virus enters the host cell. Viral entry into the host cell is a multistep process in which SARS-CoV-2 utilizes the receptor binding domain of the spike glycoprotein (S) to recognize ACE2 receptors on the human cells; this initiates the host cell entry by promoting the viral-host cell membrane fusion through large scale conformational changes in the S protein. Receptor recognition and fusion are critical and essential steps of viral infections and are key determinants of the viral host range and cross-species transmission. In this review, we summarize the current knowledge on the origin and evolution of SARS-CoV-2, roles of key viral factors and discuss the receptor recognition mechanisms of coronaviruses. We provide a comparative analysis of the SARS-CoV and SARS-CoV-2 S proteins, receptor-binding specificity, and discuss the differences in their antigenicity based on biophysical and structural characteristics. Finally, we dive into available medications, and the current COVID-19 treatment options, which will be beneficial for the scientific community as well as for the general public.

scholarly journals Seeing Structural Mechanisms of Optimized Piezoelectric and Thermoelectric Bulk Materials through Structural Defect Engineering

Materials ◽  
2022 ◽  
Vol 15 (2) ◽  
pp. 487
Author(s):  
Yang Zhang ◽  
Wanbo Qu ◽  
Guyang Peng ◽  
Chenglong Zhang ◽  
Ziyu Liu ◽  
...  
Keyword(s):  
High Performance ◽  
Structural Characteristics ◽  
Functional Materials ◽  
Atomic Scale ◽  
Structural Defects ◽  
General Strategy ◽  
Defect Engineering ◽  
Scanning Transmission ◽  
Complex Structural ◽  
Manufacturing Platform

Aberration-corrected scanning transmission electron microscopy (AC-STEM) has evolved into the most powerful characterization and manufacturing platform for all materials, especially functional materials with complex structural characteristics that respond dynamically to external fields. It has become possible to directly observe and tune all kinds of defects, including those at the crucial atomic scale. In-depth understanding and technically tailoring structural defects will be of great significance for revealing the structure-performance relation of existing high-property materials, as well as for foreseeing paths to the design of high-performance materials. Insights would be gained from piezoelectrics and thermoelectrics, two representative functional materials. A general strategy is highlighted for optimizing these functional materials’ properties, namely defect engineering at the atomic scale.

scholarly journals Targeting structural features of viral genomes with a nano-sized supramolecular drug

2021 ◽  
Author(s):  
Lazaros Melidis ◽  
Iain B. Styles ◽  
Michael J. Hannon
Keyword(s):  
Experimental Data ◽  
Md Simulations ◽  
Structural Features ◽  
Conformational Flexibility ◽  
Viral Genomes ◽  
Markov State ◽  
Mechanistic Insight ◽  
Tar Rna ◽  
Markov State Modeling ◽  
Insight Into

MD simulations and Markov state modeling explore induced fit binding of metallo-helicates to bulges in dynamic TAR RNA, reproduce experimental data, show how RNA conformational flexibility is reduced, and give mechanistic insight into insertion.

scholarly journals COVID-19 Pandemic: Insights into Structure, Function, and hACE2 Receptor Recognition by SARS-CoV-2

2020 ◽  
Author(s):  
Anshumali Mittal ◽  
Kavyashree Manjunath ◽  
Rajesh Kumar Ranjan ◽  
Sandeep Kaushik ◽  
Sujeet Kumar ◽  
...  
Keyword(s):  
Host Cell ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Large Scale ◽  
Current Knowledge ◽  
Structural Characteristics ◽  
Global Public Health ◽  
Host Cell Membrane ◽  
Origin And Evolution ◽  
Receptor Recognition

SARS-CoV-2 is a newly emerging, highly transmissible, and pathogenic coronavirus in humans, which has caused global public health emergency and economic crisis. To date, millions of infections and thousands of deaths have been reported worldwide, and the numbers continue to rise. Currently, there is no specific drug or vaccine against this deadly virus; therefore, there is a pressing need to understand the mechanism through which this virus enters the host cell. Viral entry into the host cell is a multistep process in which SARS-CoV-2 utilizes the receptor binding domain of the spike glycoprotein (S) to recognize ACE2 receptors on the human cells; this initiates host cell entry by promoting viral-host cell membrane fusion through large scale conformational changes in the S protein. Receptor recognition and fusion are critical and essential steps of viral infections and are key determinants of the viral host range and cross-species transmission. In this review, we summarize the current knowledge on the origin and evolution of SARS-CoV-2 and the roles of key viral factors. We discuss the RNA dependent RNA polymerase structure of SARS-CoV-2, its significance in drug discovery, and explain the receptor recognition mechanisms of coronaviruses. We provide a comparative analysis of the SARS-CoV and SARS-CoV-2 S proteins, receptor-binding specificity, and discuss the differences in their antigenicity based on biophysical and structural characteristics.

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