Tag Archives: Virus

Protein binding: by chance or intelligent design?

Dr. Fazale Rana has this interesting post up on protein binding at Reasons to Believe.


Nobody likes getting the flu. In fact, the influenza virus represents a serious health challenge. For most people it causes a few days of misery, but tragically for others, it takes their lives.

Biomedical researchers are looking for ways to develop therapies against the strains of the influenza virus that avoid destruction by the immune system or fail to respond to antiviral drugs. Recently scientists from the University of Washington and The Scripps Institute made progress toward this end. They designed novel proteins from scratch that bind to the stem region of hemagglutinin, a viral protein that plays a central role in the infection process.1 The hope is that the new proteins will have therapeutic use and also help with diagnosis.

This advance has obvious biomedical importance. It also contributes toward understanding the fundamental nature of protein-protein interactions (PPIs), and with this insight comes powerful new evidence that life stems from a Creator.

Often, in order to carry out their function, proteins must interact and bind in a highly specific manner with other proteins. These PPIs are selective. If the wrong proteins bind to each other, the interaction is of no use to the cell.

A large and varied population of proteins crowds the cell’s interior. Even the simplest bacterium harbors several thousand different types of proteins, along with numerous copies of the other biomolecules inside it. The jam-packed environment complicates things. Proteins are more likely to encounter the “wrong” partners than the ones they are designed to interact with.

Biochemists are currently working to understand the specificity of PPIs and how proteins avoid unintended interactions. As it turns out, protein surfaces are carefully structured to allow strong interactions between protein pairs while minimizing the strength of the unwanted interactions. Recent work by Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also designed carefully.

In other words, protein structure and concentrations have to be precisely regulated to promote the PPIs critical for life.

The rest of the article talks about all the intricate and cutting-edge engineering and computation done by the scientists to create a situation where the proteins could bind, and then ends with this:

When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:

…cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2

If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?

If you have to involve human intelligence to this degree, then I think that the best explanation is intelligent design.

New CDC study says that gay/bisexual men 50 times for likely to be HIV-positive

Story from NPR. (H/T Neil Simpson)

Note: CDC = the Center for Disease Control, a US government agency.


Before doctors knew what HIV was, they referred to the virus as “Gay Cancer” because it overwhelmingly affected gay men.

More than 25 years later, AIDS activists say the CDC’s finding that gay and bisexual men are 50 times more likely to contract the virus is the first time the government has given a concrete view of HIV’s effect on that population.

“The CDC has never been willing to issue rates before. So we would only have absolute numbers, and whether these numbers are going up or down.”

Walt Senterfitt is an epidemiologist and board chair of CHAMP, the Community HIV/AIDS Mobilization Project.

“Starting with the facts and the truth, and then digging down into why these particular facts might be the case, is the best way to generate good public policy.”

The CDC declined to be interviewed for this story, saying the statistics are preliminary.

Neil Simpson comments on this story here. Nearly 100 comments have been posted there, so far.

NOTE: Comments will be strictly filtered for this post. Neil is a lot more lenient than I am, so you may want to comment on his site instead if you think your comment is too harsh.