Category: Molecular Structures

Fifty Years of the Protein Data Bank!

Macromolecular structures in the shape of the number 50. Protein Data Bank’s 50 years logo. Credit: PDB website.

The Protein Data Bank (PDB), established in 1971, is the single global repository for 3D structural data of proteins, DNA, RNA, and even complexes these biological molecules form with drugs or other small molecules. More than 1 million people—including researchers, medical professionals, educators, and students—use the PDB each year. NIGMS and other parts of NIH have helped fund this free digital resource since 1978.

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More Than 25 Years of Competition and Collaboration Advance the Prediction of Protein Shapes


Proteins (such as hemoglobin, actin, and amylase) are workhorse molecules that contribute to virtually every activity in the body. Some of proteins’ many jobs include carrying oxygen from your lungs to the rest of your body (hemoglobin), allowing your muscles to move (actin and myosin), and digesting your food (amylase, pepsin, and lactase). All proteins are made up of chains of amino acids that fold into specific 3D structures, and each protein’s structure allows it to perform its distinct job. Proteins that are misfolded or misshapen can cause diseases such as Parkinson’s or cataracts.

While it’s straightforward to use the genetic code to predict amino acid sequences of proteins from gene sequences, the vast diversity of protein shapes and many factors that influence a protein’s 3D structure make it much more complicated to create simple folding rules that could be used to predict proteins’ structures from these sequences. Scientists have worked on this problem for nearly 50 years, and NIGMS has supported many of their efforts, including the Critical Assessment of Structure Prediction (CASP) program.

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A Focus on Microscopes: See Eye-Catching Images


Have you ever wondered what creates striking images of cells and other tiny structures? Most often, the answer is microscopes. Many of us have encountered basic light microscopes in science classes, but those are just one of many types that scientists use. Check out the slideshow to see images researchers have captured using different kinds of microscopes. For even more images of the microscopic world, visit the NIGMS Image and Video Gallery.

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Explore Scientific Imaging Through a Virtual “Internship”

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Students, teachers, and other curious minds can step into a scientific imaging lab with a free online interactive developed by NIGMS and Scholastic. Imaging tools help scientists unlock the mysteries of our cells and molecules. A better understanding of this tiny world can help researchers learn about the body’s normal and abnormal processes and lead to more effective, targeted treatments for illnesses.

Entrances to the virtual imaging labs.
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Quiz: Prove Your Knowledge of Proteins!


Proteins play a role in virtually every activity in the body. They make up hair and nails, help muscles move, protect against infection, and more. Many NIGMS-funded researchers study the rich variety of proteins in humans and other organisms to shed light on their roles in health and disease.

Take our quiz to test how much you know about proteins. Afterward, find more quizzes and other fun learning tools on our activities and multimedia webpage, which includes an interactive protein alphabet.

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Pathways: The Imaging Issue

Cover of Pathways student magazine showing geometric shapes, pom-pom-like structures, and text that reads, Dive into the microscopic world. What do you think this image shows? Hint: It’s NOT an underwater scene! (Answer inside). Cover of Pathways student magazine.

NIGMS and Scholastic bring you our latest issue of Pathways, which focuses on imaging tools that help scientists unlock the mysteries of our cells and molecules. A better understanding of this tiny world can help researchers learn about the body’s normal and abnormal processes and lead to more effective, targeted treatments for illnesses.

Pathways is designed for students in grades 6 through 12. This collection of free resources teaches students about basic science and its importance to health, as well as exciting research careers.

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Through the Looking Glass: Microscopic Structures in Many Sizes


We seldom see microscopic objects next to one another, so it can be difficult to picture how they compare. For instance, it might surprise you that a thousand cold-virus particles could line up across one human skin cell! The largest objects that scientists view through microscopes are about a millimeter (roughly the size of a poppyseed), and they’re about 10 million times larger than the smallest molecules scientists can view: atoms.

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Freezing a Moment in Time: Snapshots of Cryo-EM Research


To get a look at cell components that are too small to see with a normal light microscope, scientists often use cryo-electron microscopy (cryo-EM). As the prefix cryo- means “cold” or “freezing,” cryo-EM involves rapidly freezing a cell, virus, molecular complex, or other structure to prevent water molecules from forming crystals. This preserves the sample in its natural state and keeps it still so that it can be imaged with an electron microscope, which uses beams of electrons instead of light. Some electrons are scattered by the sample, while others pass through it and through magnetic lenses to land on a detector and form an image.

Typically, samples contain many copies of the object a scientist wants to study, frozen in a range of orientations. Researchers take images of these various positions and combine them into a detailed 3D model of the structure. Electron microscopes allow us to see much smaller structures than light microscopes do because the wavelengths of electrons are much shorter than the wavelength of light. NIGMS-funded researchers are using cryo-EM to investigate a range of scientific questions.

Caught in Translation

One cluster that is yellow, purple, and orange and another that is beige, purple, and green. 3D reconstructions of two stages in the assembly of the bacterial ribosome created from time-resolved cryo-EM images. Credit: Joachim Frank, Columbia University.

Joachim Frank, Ph.D., a professor of biochemistry and molecular biophysics and of biological sciences at Columbia University in New York, New York, along with two other researchers, won the 2017 Nobel Prize in Chemistry for developing cryo.

Dr. Frank’s lab focuses on the process of translation, where structures called ribosomes turn genetic instructions into proteins, which are needed for many chemical reactions that support life. Recently, Dr. Frank has adopted and further developed a technique called time-resolved cryo-EM. This method captures images of short-lived states in translation that disappear too quickly (after less than a second) for standard cryo-EM to capture. The ability to fully visualize translation could help researchers identify errors in the process that lead to disease and also to develop treatments.

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Cool Images: The Hidden Beauty Inside Plants


Spring brings with it a wide array of beautiful flowers, but the interior structures of plants can be just as stunning. Using powerful microscopes, researchers can peek into the many molecular bits and pieces that make up plants. Check out these cool plant images from our Image and Video Gallery that NIGMS-funded scientists created while doing their research.

Several round structures that are yellow at the center and pink and purple around the edges and have honeycomb-like interiors. Credit: Arun Sampathkumar and Elliot Meyerowitz, California Institute of Technology.

In plants and animals, stem cells can transform into a variety of different cell types. The stem cells at the growing tip of this Arabidopsis plant will soon become flowers. Cellular and molecular biologists frequently study Arabidopsis because it grows rapidly (its entire life cycle is only 6 weeks), produces lots of seeds, and has a genome that’s easy to manipulate.

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