scholarly journals Crystal structure of human angiogenin with an engineered loop exhibits conformational flexibility at the functional regions of the molecule

FEBS Open Bio ◽  
2012 ◽  
Vol 3 (1) ◽  
pp. 65-70 ◽  
Author(s):  
Nethaji Thiyagarajan ◽  
K. Ravi Acharya
Keyword(s):  
Crystal Structure ◽  
Conformational Flexibility ◽  
Functional Regions

scholarly journals Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 532
Author(s):  
Jonathan H. Sheehan ◽  
Jarrod A. Smith ◽  
Pradeep S. Pallan ◽  
Terry P. Lybrand ◽  
Martin Egli
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Base Pair ◽  
Crystal Packing ◽  
Md Simulations ◽  
Conformational Flexibility ◽  
Dynamics Simulation ◽  
Dna Duplex ◽  
Solution Studies

The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.

Crystal structure and conformational flexibility of 2-(acetylamino)prop-2-enoic acid (N-acetyldehydroalanine)

1979 ◽  
pp. 927-929 ◽  
Author(s):  
David Ajò ◽  
Gaetano Granozzi ◽  
Eugenio Tondello ◽  
Antonio Del Prà ◽  
Giuseppe Zanotti
Keyword(s):  
Crystal Structure ◽  
Conformational Flexibility ◽  
Enoic Acid

scholarly journals Crystal Structure of Prothrombin Reveals Conformational Flexibility and Mechanism of Activation

2013 ◽  
Vol 288 (31) ◽  
pp. 22734-22744 ◽  
Author(s):  
Nicola Pozzi ◽  
Zhiwei Chen ◽  
David W. Gohara ◽  
Weiling Niu ◽  
Tomasz Heyduk ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Flexibility

scholarly journals Crystal Structure of YaeT: Conformational Flexibility and Substrate Recognition

Structure ◽  
2008 ◽  
Vol 16 (12) ◽  
pp. 1873-1881 ◽  
Author(s):  
Petia Z. Gatzeva-Topalova ◽  
Troy A. Walton ◽  
Marcelo C. Sousa
Keyword(s):  
Crystal Structure ◽  
Substrate Recognition ◽  
Conformational Flexibility

scholarly journals Conformational Flexibility in Respiratory Syncytial Virus G Neutralizing Epitopes

2019 ◽  
Vol 94 (6) ◽  
Author(s):  
Stanislav O. Fedechkin ◽  
Natasha L. George ◽  
Ana M. Nuñez Castrejon ◽  
Joshua R. Dillen ◽  
Lawrence M. Kauvar ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Monoclonal Antibody ◽  
Respiratory Syncytial Virus ◽  
Human Monoclonal Antibody ◽  
The Elderly ◽  
Conformational Flexibility ◽  
Surface Glycoprotein ◽  
Viral Attachment ◽  
Conserved Domain ◽  
Syncytial Virus

ABSTRACT Respiratory syncytial virus (RSV) is a top cause of severe lower respiratory tract disease and mortality in infants and the elderly. Currently, no vaccine or effective treatment exists for RSV. The RSV G glycoprotein mediates viral attachment to cells and contributes to pathogenesis by modulating host immunity through interactions with the human chemokine receptor CX3CR1. Antibodies targeting the RSV G central conserved domain are protective in both prophylactic and postinfection animal models. Here, we describe the crystal structure of the broadly neutralizing human monoclonal antibody 3G12 bound to the RSV G central conserved domain. Antibody 3G12 binds to a conformational epitope composed of highly conserved residues, explaining its broad neutralization activity. Surprisingly, RSV G complexed with 3G12 adopts a distinct conformation not observed in previously described RSV G-antibody structures. Comparison to other structures reveals that the RSV G central conserved domain is flexible and can adopt multiple conformations in the regions flanking the cysteine noose. We also show that restriction of RSV G flexibility with a proline mutation abolishes binding to antibody 3G12 but not antibody 3D3, which recognizes a different conformation of RSV G. Our studies provide new insights for rational vaccine design, indicating the importance of preserving both the global structural integrity of antigens and local conformational flexibility at antigenic sites, which may elicit a more diverse antibody response and broader protection against infection and disease. IMPORTANCE Respiratory syncytial virus (RSV) causes severe respiratory infections in infants, young children, and the elderly, and currently, no licensed vaccine exists. In this study, we describe the crystal structure of the RSV surface glycoprotein G in complex with a broadly neutralizing human monoclonal antibody. The antibody binds to RSV G at a highly conserved region stabilized by two disulfide bonds, but it captures RSV G in a conformation not previously observed, revealing that this region is both structured and flexible. Importantly, our findings provide insight for the design of vaccines that elicit diverse antibodies, which may provide broad protection from infection and disease.

Crystal structure of octakis(2,3,6-tri-O-methyl)-γ-cyclodextrin·4.5 H2O: evidence for conformational flexibility of permethylated cyclodextrins

2000 ◽  
Vol 328 (3) ◽  
pp. 399-407 ◽  
Author(s):  
Thammarat Aree ◽  
Helga Hoier ◽  
Burkhard Schulz ◽  
Günter Reck ◽  
Wolfram Saenger
Keyword(s):  
Crystal Structure ◽  
Conformational Flexibility
Sign in / Sign up

Export Citation Format

Share Document