A cross-section of the glomerulus, a capillary-rich capsule in the kidney where waste material passes from the blood into the urine. The yellow structure is the basement membrane that develops holes in certain diseases. Three different NC1 domain proteins are found in the glomerulus, as indicated; the top box illustrates the ubiquitous form crystallized by Sundaramoorthy.
Protein structure key to diabetes, kidney disease
Space-filling model of the NC1 domain protein illustrating how the two identical trimers come together to form the hexameric protein. Each trimer is attached to a ropelike, triple-helix collagen molecule.
Model showing detail of the secondary structure of the two trimers of the NC1 domain protein.
You can imagine the consequences if the thin, amorphous membrane that surrounds and supports the various tubes, organs, and other soft tissues inside our bodies were to develop holes. But that’s exactly what happens, in limited areas, in diseases such as diabetes and certain kidney disorders.
Understanding how and why these holes form may be easier now due to the work of Munirathinam Sundaramoorthy, Ph.D., an X-ray crystallographer soon to be joining Vanderbilt’s faculty who determined the atomic architecture of a protein critical to the warp and woof of this so-called basement membrane.
A paper describing the structure of the protein — the NC1 domain of type IV collagen — and giving insight into how it affects the integrity of basement membrane was made available in the online version of the Journal of Biological Chemistry in April and will appear in print later this summer. Collagen is a protein that bundles into fibers and lends enormous strength to the thin but tough membrane.
According to Sundaramoorthy, the NC1 domain governs the assembly of the type IV collagen network underlying all basement membranes. “Having a clear picture of the structure of the NC1 domain in type IV collagen molecules will help us better understand the disease process that occurs when the network is malformed.”
Sundaramoorthy was recruited from the University of Kansas Medical Center to join the Vanderbilt faculty as an assistant professor of Medicine in the division of Nephrology, and to be part of the newly established Center for Matrix Biology. The present work resulted from a collaboration between Sundaramoorthy and Billy G. Hudson, Ph.D., Elliot V. Newman Professor of Medicine in the division of Nephrology and director of the Center, while they were both at the medical center in Kansas.
“Sundar has solved the most complicated, complex connecting point of all the collagens, and his work will help us in our investigation of many projects related to type IV collagen and the extracellular matrix,” Hudson said.
Type IV collagen is one of two predominant molecules making up the basement membrane (BM), a specialized form of the matrix that separates pockets of cells in all human tissues. The NC1 domain protein is located at the end of each ropelike collagen molecule. Separate collagen molecules link up with one another via the NC1 domain protein in such a way that, ultimately, a complex, interwoven mesh of molecules is assembled.
The BM lies like a scaffold beneath cells. Hudson likens the role of the BM in tissues to that of walls in a building; the membranous walls hold cells in place and help to compartmentalize the various rooms. But, he says, scientists are learning that the wall serves more than simply a structural role. Evidence suggests that it directly assists in maintaining tissue-specific functions, as well as in modulating cell and tissue function during growth and development.
“What’s emerging — with some excitement — is that this wall is telling the cells what should happen in the room,” Hudson said, “like how painting a room a certain color influences how we feel in that room. As chemists and biologists, we’re interested in what the wall is made of and how it’s decorated.”
In all tissues of the body — and identically in other organisms as well — the BM wall is “decorated” with the hexameric, or six-parted, NC1 domain protein (each part is called a monomer) that Sundaramoorthy crystallized and dissected. In the paper he describes how two identical trimeric protein structures abut to create the larger protein. He defines in precise detail the atomic structure — the intricate loops and pleats and folds — of each monomer, how each monomer is oriented in relation to the others, and the forces that hold the monomers together.
In the human kidney, however, another family of related type IV collagen molecules exists where the NC1 domain varies from the ubiquitous version. In these molecules, two or more of the six monomers making up the NC1 domain protein appear to have a uniquely different structural identity.
“One of the discoveries that came out of my lab is that there is this other family of molecules, with a different set of genes that encode them. We need to know what’s selecting for each variety,” Hudson said. “Sundar is going to crystallize the other molecules to compare them and get the code for each.”
Sundaramoorthy has set his sights on this set of molecules since it is these other types of collagen that are known to be disease-associated.
One of these special types of collagen is found in the basement membrane that surrounds the capillaries in the kidney. Here, the BM acts as a coarse sieve, holding back large molecules in the capillary-borne blood from passing into the urine. In Alport’s Syndrome, a rare and fatal kidney disease, a mutation causes one of the NC1 domain monomers to fold incorrectly. As a consequence, the collagen network in the BM develops holes and is unable to filter properly. Patients with this disease must have a kidney transplant or rely on dialysis to survive.
In diabetes, this same BM wall found inside the kidney is thickened, but still has structural defects that let large molecules seep through. Hudson, who has spent 30 years focusing on the role of the extracellular matrix in diabetes, is excited about how Sundaramoorthy’s work will facilitate his research.
“What we’re working on is the hypothesis that glucose attaches to the kidney BM and deranges it,” Hudson said. “I want to spend the next five to 10 years exploring parts of the kidney.”
Other germane research applications include inhibition of angiogenesis by introducing a specific mutation into a monomer of the NC1 domain — Hudson holds a patent related to this particular application — and an investigation into Goodpasture Syndrome, another fatal kidney disease where the body develops an antibody against an NC1 domain monomer.
Sundaramoorthy, whose first day on the job at Vanderbilt will be September 1, says he looks forward to the opportunities for collaboration that await him and the three colleagues he brings with him.
“With the emergence of proteomics and structural genomics, this is a most exciting and competitive time for structural biologists,” he said. “The enormous infrastructure and intellectual resources available at Vanderbilt will help me to be an active participant of this revolution. My colleagues and I are excited about this move.”
Sundaramoorthy holds an undergraduate degree in physics, mathematics, and chemistry and a master’s degree in materials science. After earning his doctoral degree in biophysics at the Indian Institute of Science in Bangalore, India, he spent a year at the Center for Advanced Research in Biotechnology at the University of Maryland, followed by several years as a post-doctoral researcher and then faculty member in the department of Molecular Biology and Biochemistry at the University of California-Irvine. Since 1999, he has been assistant professor of Biochemistry and Molecular Biology at the University of Kansas Medical Center.
The work reported in the Journal of Biological Chemistry was supported by grants from the Ernst F. Lied Basic Science Program of University of Kansas Medical Center, the National Institutes of Health, and the Plan Nacional I+D, Spain.