Conformational Properties of Glycosaminoglycan Disaccharides: A Molecular Dynamics Study

2021 ◽  
Author(s):  
Valery Lutsyk ◽  
Wojciech Plazinski
Keyword(s):  
Molecular Dynamics ◽  
Conformational Properties ◽  
Glycosaminoglycan Disaccharides

Molecular Origins of the Unique Conformational Properties of the Polysilanes: A Molecular Dynamics Study of Poly(Di-N-Hexylsilane)

1992 ◽  
Vol 278 ◽  
Author(s):  
William J. Welsh ◽  
Samuel H. Tersigni ◽  
Wangkan Lin
Keyword(s):  
Molecular Dynamics ◽  
Torsion Angle ◽  
Model Compound ◽  
Energy Surface ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Torsion Angles ◽  
Global Energy Minimum ◽  
Conformational Properties ◽  
Backbone Torsion Angle

AbstractThe conformational dynamics of a model compound for poly(di-n-hexylsilane) (PDHS) has been explored using the new molecular dynamics program MM3-MD. MM3-MD trajectories at variable temperatures reveal two abrupt conformational transitions, one near -182°C and another near -175°C, associated with two energy barriers on the potential-energy surface. The first transition near -182°C allows shifts in the backbone torsion angle from that defined by the global energy minimum designated off-trans to that corresponding to a statistical collection of torsion angles within the range trans ±30°. The second transition near -175°C allows the backbone torsion angle to explore the remainder of its torsional space. The sidechain dynamics follows a similar pattern. We suggest that the abrupt transition calculated here at -182°C for “gas.phase” PDHS corresponds to that observed for PDHS at -28°C in solution and at 42°C in the solid state.

Serological and conformational properties of E. coli K92 capsular polysaccharide and its N-propionylated derivative both illustrate that induced antibody does not recognize extended epitopes of polysialic acid: Implications for a comprehensive conjugate vaccine against groups B and C N. meningitidis

2002 ◽  
Vol 80 (8) ◽  
pp. 1055-1063 ◽  
Author(s):  
Robert A Pon ◽  
Nam Huan Khieu ◽  
Qing-Ling Yang ◽  
Jean-Robert Brisson ◽  
Harold J Jennings
Keyword(s):  
Molecular Dynamics ◽  
Immune Response ◽  
Conjugate Vaccine ◽  
Capsular Polysaccharide ◽  
Competitive Inhibition ◽  
Polysialic Acid ◽  
E Coli ◽  
Protective Epitope ◽  
Conformational Properties ◽  
Group B

The capsular polysaccharide of E. coli K92 (K92P) contains elements in common with the capsular polysaccharides of both groups B and C N. meningitidis, and may therefore form the basis of a bivalent vaccine. In an attempt to augment the cross-protective immune response to group B meningococci, the N-acetyl groups of the K92P were replaced by N-propionyl groups (NPrK92P) and conjugated to protein. This strategy had previously been applied with success to the poorly immunogenic capsular polysaccharide of group B meningococcus (GBMP), and the bactericidal epitope was found to be exclusively mimicked by extended helical segments of the NPrGBMP. The NPrK92P-conjugate, in relation to a K92P-conjugate, failed to enhance the response to GBMP but did generate a measurable response to NPrGBMP, but only at the expense of a greatly reduced GCMP response. Despite the presence of an immune response to NPrGBMP, the anti-NPrK92 serum was not bactericidal. Competitive inhibition studies with NPrGBMP oligosaccharides suggested the NPrK92 antibodies could not cross-react with the protective epitope on group B meningococci, as defined by extended helical segments of the NPrGBMP, but only recognized short non-bactericidal NPrGBMP epitopes. This hypothesis was supported from the conformational and molecular dynamics studies of the K92P, which demonstrated a lack of extended conformations that resemble the GBMP extended epitope. Indeed, the conformational properties of the K92P more closely resembled those of the GCMP, thereby explaining the observed moderate cross-protection of the K92P antiserum towards group C meningococci. Thus, on the basis of these results, it can be concluded that K92P, regardless of N-propionyl modification, will not serve as an effective single vaccine component against both groups B and C meningococci.Key words: conjugate vaccine, Neisseria meningitidis, polysialic acid, NMR, molecular dynamics.

Conformational and Dynamic Properties of Polymer Loops and Their Mixtures at an Impenetrable Interface

1996 ◽  
Vol 463 ◽  
Author(s):  
H. S. Gulati ◽  
D. C. Driscoll ◽  
R. L. Jones ◽  
R. J. Spontak ◽  
C. K. Hall
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamic Properties ◽  
Relaxation Behavior ◽  
Dynamics Simulation ◽  
Dynamic Relaxation ◽  
Conformational Properties ◽  
Fluctuation Method ◽  
Bond Fluctuation ◽  
The Individual

ABSTRACTIn this study we investigate the equilibrium conformational properties and dynamic relaxation behavior of polymer loops grafted at an interface using the discontinuous molecular dynamics simulation technique. Differences and similarities between the structural and dynamic properties of polymer loops and tails are identified. The conformational properties of mixtures of polymers loops and tails are also studied using the bond-fluctuation method. The effect of mixture composition on the conformational properties of the individual components in the mixture is discussed.

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