Effectively Communicate Your Science Using Accurate Protein Images 

• Proteins are biomolecules that carry out essential bodily functions and are used in various biotech and pharmaceutical applications.
• Protein function is intricately linked to its 3D structure, which can be visualized from the data collected by structural biologists.
• Accurate protein visualization is essential for communicating complex scientific concepts effectively.
• Samba Scientific’s team of scientists can help you create accurate and visually appealing protein representations to enhance your scientific storytelling.

Proteins are often referred to as the workhorses of the cell, and for good reason. These microscopic molecular machines are involved in virtually every biological process, from providing structural support to catalyzing complex chemical reactions. By visualizing a protein’s structure, we gain clues into its function. With these insights, we can better understand biological processes and develop innovative solutions that aid in, for example, the diagnosis and treatment of disease.

Let’s explore the importance of proteins and how you can accurately present proteins visually in your scientific communications assets.

What are Proteins and What Do They Do?

The instructions for building proteins are found within DNA. The DNA code is translated into a series of amino acids that bind to one another, forming a polypeptide chain. The specific sequence of amino acids determines the protein’s unique three-dimensional structure, which in turn dictates its function.

Let’s look at a few examples of the diverse biological roles of proteins:

• Structure and support: Collagen, a fibrous protein, provides strength and flexibility to our skin, bones, and tendons.
• Immune response: Antibodies are proteins that recognize and neutralize foreign invaders, such as bacteria and viruses.
• Messengers: Insulin, a small protein, acts as a messenger, regulating blood sugar levels.
• Transport and storage: Hemoglobin, found in red blood cells, carries oxygen throughout the body.
• Catalyze reactions: ATP synthase, a complex protein, acts as a catalyst, facilitating the production of ATP, the energy currency of cells.

Proteins can also be utilized by the biotechnology and pharmaceutical industries in the following ways:  

• Disease biomarkers: Amyloid-β, a protein found in the brain, is a biomarker for Alzheimer’s disease.
• Disease treatment: Antibody-drug conjugates are a promising class of therapeutics that use antibodies to deliver drugs specifically to cancer cells.
• Drug targets: The μ-opioid receptor is a protein that serves as a target for opioid drugs, such as morphine.
• Chemical synthesis: Enzymes, specialized proteins acting as biological catalysts, are increasingly used in chemical synthesis to produce small molecules with high efficiency and selectivity.

Protein Structure: The Key to Function

The ability of proteins to perform these diverse functions is intricately linked to their three-dimensional (3D) structures. To understand how proteins fold and function, we use a hierarchical system to describe their structures. The levels of protein structure are shown here (Figure 1):

• Primary structure: The linear sequence of amino acids in a polypeptide chain.
• Secondary structure: Local folding patterns, such as α-helices and β-sheets, formed by interactions between nearby amino acids.
• Tertiary structure: The overall 3D arrangement of a protein, resulting from long-range interactions between amino acids.
• Quaternary structure: The interaction between multiple polypeptide chains to form a functional protein complex.

For decades, structural biologists have painstakingly worked to solve protein structures using experimental techniques like X-ray crystallography, cryo-electron microscopy (CryoEM), and nuclear magnetic resonance (NMR). These methods are time-consuming and require specialized expertise. The advent of AI models like AlphaFold has revolutionized the field by enabling rapid and largely accurate prediction of protein structures from their amino acid sequences. However, as AI models are further refined, experimental methods remain the standard by which we verify protein structures.

To tie protein structure to function, computational biochemistry uses protein structural information to predict how proteins move and interact with other molecules, providing insights into their dynamic behavior and function. Techniques like molecular dynamics simulations use mathematical equations and principles of physics and chemistry to simulate protein movements and interactions over time.

The Power of Protein Visualization

Accurate visual representation of protein structure can help explain the science behind different technologies or natural phenomena. There are several common styles of protein visualization, each providing different levels of structural and functional information (Figure 2):

• Ball and stick: Shows the atoms and bonds between them, providing detailed chemical information.
• Space filling: Represents atoms as solid spheres, highlighting the overall shape and volume of the protein.
• Cartoon/ribbon: Emphasizes secondary structure elements, such as α-helices and β-sheets, providing a simplified view of the protein’s fold.
• Molecular surface: Depicts the protein’s surface, showing how it interacts with water and other molecules.