The protein folding problem: a major conundrum of science: Ken Dill at TEDxSBU

Summary

Proteins are the microscopic machines that drive every process in living organisms, from movement and thought to digestion and immunity. This lecture explores protein structure, the long-standing folding problem, and recent advances in predicting how amino acid sequences determine 3D shapes. Proteins function through motion and shape changes, acting as pumps, rotary motors, sliding motors, and valves, with implications for muscle activity, bacterial movement, and disease treatment. Beyond biology, understanding protein mechanisms offers exciting potential for scaling these efficient natural machines to human-scale technologies, promising innovations in energy, transportation, and health. Proteins truly reveal the blueprint of life and engineering.

Takeaways

• 🧬 Proteins are essential molecular machines in the body, responsible for nearly all biological functions including movement, thought, immunity, and digestion.
• 🔗 Proteins are composed of long chains of amino acids, which can be visualized as beads on a necklace, with each sequence determining the protein's final shape and function.
• 🌀 The protein folding problem involves predicting how a sequence of amino acids folds into a three-dimensional structure that determines its biological role.
• 💻 Advances in computational biology now allow scientists to predict protein structures, helping to solve both high-level and detailed folding challenges.
• ⚙️ Proteins function as real microscopic machines, including rotary motors, sliding motors, pumps, and valves, using energy to perform work.
• 🎯 Protein mechanisms rely on shape changes rather than electricity or explosions, making them fundamentally different from human-engineered machines.
• 💊 Understanding protein structure and function is critical for drug design, as pharmaceuticals often target proteins to inhibit or modify their activity.
• 🌊 Proteins operate in a dynamic, jiggly environment influenced by surrounding water molecules, which affects their motion and interactions.
• 🌍 Studying protein machines at the microscopic scale offers insights for scaling up to macro-scale technology in areas like energy, water, and transportation.
• 🔬 Proteins are highly versatile, with tens of thousands of different types acting as machines across living organisms, offering vast potential for scientific and technological innovation.
• 🧩 The key principle behind protein function is the binding and shape change process, where the interaction with other molecules enables motion and activity.
• 🚀 The potential to harness protein principles for large-scale machines could transform human life by improving efficiency, energy usage, and technological capabilities.

Q & A

What are protein molecules and why are they important in the body?

Protein molecules are complex chemicals that perform nearly all essential biological functions. They enable movement, brain function, digestion, immune responses, and cellular processes, making them vital for sustaining life.

What are the building blocks of proteins, and how do they determine protein structure?

Proteins are made of amino acids, of which there are 20 different types. The sequence of these amino acids dictates how the long protein chain folds into a three-dimensional shape, which ultimately determines its function.

What is the protein folding problem?

The protein folding problem is the challenge of predicting a protein's three-dimensional structure based solely on its amino acid sequence. Solving this allows scientists to understand how proteins function and interact in the body.

How have recent advances in computational biology impacted protein research?

Recent advances allow scientists to compute protein structures using computers, effectively decoding the folding process and predicting how proteins will shape themselves, which accelerates research in medicine and bioengineering.

In what ways do proteins act as molecular machines?

Proteins can function as motors, pumps, valves, and rotary mechanisms at the microscopic level. They convert energy into motion or mechanical work, such as pumping ions, propelling bacterial flagella, and enabling muscle contraction.

How do protein motors differ from macroscopic machines like electric motors or combustion engines?

Protein motors do not rely on electricity or explosions. Instead, they operate through shape changes triggered by chemical interactions, allowing them to work efficiently at microscopic scales in a watery, dynamic environment.

How do proteins function in drug design and disease treatment?

Pharmaceutical drugs often target proteins by binding to them and inducing shape changes. This can inhibit harmful proteins in pathogens or correct dysfunctional proteins in diseases, making proteins central to medical therapies.

Why is the study of protein mechanisms important for future technology?

Understanding protein mechanisms could allow humans to scale up their principles to develop highly efficient, bio-inspired machines for energy, transportation, and other applications, mimicking nature’s microscopic solutions on a macroscopic level.

What metaphor does the speaker use to illustrate the abundance of protein molecules in the human body?

The speaker compares the number of protein molecules in the human body to the number of pennies that would fill the Pacific Ocean, emphasizing their immense quantity despite their microscopic size.

What role does shape and shape change play in protein function?

A protein's function is determined by its three-dimensional shape. Proteins often perform their tasks by changing shape in response to interactions with other molecules, which is the fundamental principle behind their mechanisms and medical targeting.

Can you provide examples of different types of protein machines?

Examples include rotary motors (bacterial flagella), sliding motors (muscle contraction), pumps and valves (ion transport in cell membranes), and ATP/ADP-driven motors that convert chemical energy into motion.

How do proteins handle their microscopic environment, such as water molecules?

Proteins operate in a dynamic environment and are constantly jostled by water molecules. Despite this, they can reliably find their folded shape and perform their functions due to systematic folding and chemical interactions.