Bucket with two ears catches DNA

Dutch PhD student Cathelijne Kloks has discovered that the so-called Cold Shock domain of the human YB-1 protein looks like a bucket with two extra ears. These ears lead the DNA to the binding site on the protein and keep it there.

Kloks investigated the structure and function of one of the three domains of the human protein YB-1. This protein plays an important role in the production of new proteins. The central domain, the so-called Cold Shock domain, ensures the binding of the protein to the DNA in the process.

The researcher from the University of Nijmegen discovered that the domain looks like a bucket with a handle and two extra ears. The ears attach to the DNA and push it to the binding site on the YB-1. This binding site was found to be located precisely in between the two ears. This means that the ears can hold the DNA firmly in place whilst it is being bound to the protein. The function of the handle is not yet clear.

Kloks dissolved the YB-1 protein and then studied the solution using NMR measurements. She used the NMR signals to draw up a distances table, which indicated the distance between the nuclei of atoms in the protein. With this information she then calculated the structure of the Cold Shock domain.

Furthermore, Kloks determined the strength of the binding to the DNA. The Cold Shock domain alone formed weak bonds to the DNA. This did not agree with previously made measurements of the binding strength of the complete YB-1 protein. The domain also exhibited little preference with respect to where it binds to the DNA, although previous experiments had shown that the Cold Shock domain binds more strongly to areas of DNA containing a lot of cytosine and thymine. Kloks concluded that the protein’s considerable binding strength and preference could only be clarified by including its other two domains.

In the cell YB-1 forms the link between the transcription of the DNA and the subsequent production of a new protein. YB-1 consists of three different domains. These are compact parts which can fold independently without using other parts of the protein.

The Cold Shock domain derives its name from its function in bacteria. In bacterial proteins the domain ensures that the bacteria resume growth, following a period of arrested growth due to a sudden drop in temperature.

For further information please contact Cathelijne Kloks (Department of Medicinal Chemistry, Organon) tel. +31 (0)412 662461 e-mail: c.kloks@organon.com. The doctoral thesis will be defended on 26 May 2003. Ms Kloks’’ supervisor is Prof. C.W. Hilbers (University of Nijmegen).