Low-frequency vibrational modes of the native photoactive yellow protein (PYP) and its several mutant and analogue systems have been investigated in "time" (femtosecond fluorescence up-conversion) and "frequency" (resonance Raman spectroscopy) domains to elucidate their role in ultrafast photoisomerization reaction dynamics of PYP. The oscillatory frequencies derived from time-domain analysis are in fair agreement with those obtained independently using spontaneous resonance Raman spectroscopy. Tentative assignments of the oscillatory components to particular vibrations are proposed supported by normal-mode calculations based on density-functional theory and ab initio MO methods. It is concluded that the out-of-plane skeleton bending mode of the chromophore, gamma(16), is responsible for the observed oscillations in native and all mutant PYPs (f(1) approximate to 135 cm(-1)), while in-plane nu'(42) and nu'(43) modes are probably responsible for oscillations observed in the PYP analogue with locked chromophore. The low-frequency mode (f(2) approximate to 50 cm(-1)) present in time-domain experiments of all systems examined could not be fully characterized. A dynamic model called "trigger mode mediated guidance" has been proposed to explain in simple terms the ultrafast primary process initiating PYP's photocycle. This work provides a framework for future investigations on PYP's low-frequency vibrational modes in connection with its primary structural photodynamics.