A variety of optical studies reveal coherent low-frequency oscillations during photochemical reactions in proteins. We recently argued [New J. Phys. 12, Art. No. 085004 (2010)] that the vibrational eigenstates of an isolated chromophore may be localized, which can give rise to long-lived low-frequency vibrational modes when the chromophore is embedded in a protein. Here we show that, even if vibrational eigenstates are not localized, bottlenecks to vibrational energy flow that are absent in much larger molecules give rise to slow damping of low-frequency modes in many protein chromophores. Examples including rhodopsin, photoactive yellow protein and green fluorescent protein are discussed. (C) 2012 Elsevier B. V. All rights reserved.