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I know that after depletion of glycogen body starts to use fat for fuel. If I continue working an hour or more in this state, does my body start to use proteins for energy after a while? I have some belly fat so I don't think I am losing proteins from my muscles? Am I right?

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On average, a person has more than 80,000 calories in fat storage. You'd need to burn through this first before your body targets protein for fat storage.

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Not to mention the 1500 calories of glycogen stored in your liver and muscles, which should last you a couple hours of exercise. –  J. Winchester Feb 28 '12 at 17:48
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Don't worry about it, proteins start getting consumed only after prolonged periods of starvation when adipose tissues are depleted. (Unless you are on a very low calorie diet.)

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