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Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin

Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin

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The cover art--composed of the 1918 antibody (Ig-2D1) binding to the 2009 hemagglutinin (09HA)--is generated from visual molecular dynamics and enhanced in GIMP (GNU image manipulation program). The protein at the bottom is the 09HA, colored by residue name, and the protein on top is the antibody, colored in grey. The protein system was solvated in a water box and simulated in NAMD. We aimed to study the interactions between the antibody and antigen under ...

Tags: influenza1918 antibody (Ig-2D1)2009 hemagglutinin (09HA)antibodyh1n1molecular dynamics
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SAHELI MITRA:

A must read.

Coronavirus Structure, Vaccine and Therapy Development
Brennan Weaver:

Pretty nice read. I wish I could have written something about Pi. It's my 2nd favorite number value. Also, I don't think Pi is as mysterious as everyone thinks it is. It's just a number with a lot of personalities. And I do believe there is a last digit.

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Harel Weinstein:

Just perused the article "From Dynamics to Membrane Organization- Experimental Breakthroughs Occasion a ‘‘Modeling Manifesto’’ in the August 21 issue. While the Perspective is intriguing, the sheer Chutzpah of writing a "manifesto" about a field of modeling with lists of "demands" based on experiments that in many cases are more limited in scope or reality than any physics-based model, is quite astounding. Neither artificial membrane slabs, nor "live cells" imaged under conditions in which cells have a shabby life that doesn't last long (how much of this is due to the mistreatment of the membrane proteins?) share established behaviors that must be matched or else.... No experiment, computational or using imaging, is meant to mimic reality, only to probe it based on models and assumptions that can be falsified.

As to the role of the cytoskeleton, what does this tell us about the membrane itself, or the behavior of membrane proteins as individual molecules in their interplay with the membrane? And since this unrelated scaffold differs greatly between cells, what is the "correct matching standard"? All models are wrong, some (computational, or on the stage of a microscope) are useful, but in my opinion, self-critical, humble, and rigorous scientific reasoning are preferable to a manifesto in order to foster progress.

In Search of…Protein Interaction Partners
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