When you run, you fuel your muscles by burning calories in the form of complex carbohydrates. Your muscles are analogous to the engine of a car and the calories you consume are analogous to the gasoline used to fuel the car engine. It is important to keep in mind that in your body the muscles are the engine and not the fuel.
Muscle Is Not Fuel
A good place to start to understand that your muscle tissue will not be used as fuel when running is Dr. Tim Noakes' classic, "Lore of Running." Noakes notes that certain contributing factors when you run such as intensity, duration, fitness level, carbohydrate supplies before and during your run and type of fuel ingested while running help your body determine whether it burns fat, carbohydrate or protein to fuel your muscles. According to Noakes, submaximal or distance run training actually increases and strengthens your muscle mitochondria or fibers. Your muscle fibers will not be burned up,
Muscle Fiber Damage
One of the reasons you may think that your body is burning muscle is the soreness you experience after a long, hard run. An article about delayed onset muscle soreness (DOMS), published in Sports Fitness Advisor, noted that this muscle soreness is caused by actual muscle tissue breakdown resulting from your hard running effort. Muscle biopsies taken from marathon runners showed that the muscle mitochondria cell membranes actually ruptured during the long run, resulting in post-run muscle soreness. The soreness is your muscle's inflammatory response to the cellular-level damage. Even considering this damage, the muscle itself was not utilized as fuel for your long run.
Extreme Fuel Needs
The only time that there may ever a need for your body to turn to your muscles themselves for fuel is in the late stages of extreme endurance running. Suzanne Girard Eberle, a registered dietician, states that when glycogen or carbohydrate stores are depleted, your body will turn to the only fuel source left -- amino acid proteins in your skeletal muscles -- and turn them into glucose for fuel.
Fill Your Fuel Tank
To avoid ever requiring your body to burn amino acid proteins for fuel, make sure to regularly consume plenty of complex carbohydrates, particularly if you are training for a marathon or ultra-marathon. Taking that action will not only help reduce muscle fiber damage but also reduce post-run muscle soreness.