Rom each state and 1113-59-3 site observe the subsequent free evolutions of the protein conformation. The multiple simulations using the same protocol and initial structure can thus reveal the intrinsic diversity in the conformational dynamics of AdK. Although the unrestrained simulations above may provide valuable information on the stability of the given conformations, the currently affordable simulation time is orders-of-magnitude shorter than what is needed to fully sample the conformational space. If two metastable conformations are K162 web separated by some energetic barrier, it would be very unlikely to observe, even in multiple simulations, any spontaneous transition. Therefore, to complement the unrestrained simulations, we also carry out another type of calculation here, in which we employ a series of biased simulations to estimate the free energy in the conformational space. In general, protein conformations require high-dimensional representations, and are described by a relatively large number of chosen “coarse coordinates”, which can be either Cartesian coordinates [24] or collective variables [21]. These coarse coordinates define a high-dimensional configuration space, and each point in this space represents a conformation. A free energy as a function of the coarse coordinates can be defined by integrating out all other (such as solvent) degrees of freedom. The objective of the conventional string method is then to identify a “minimum-free-energy-pathway” [21] that 18204824 connects two free energy minima in the configuration space, each representing a metastable conformational state. However, although the configuration space represents a significant dimensionality reduction compared to the entire phase space, it is still of relatively high dimensions. The multidimensional free energy associated with this pathway, as obtained from the conventional string method, only describes the energetics on a single curve, and ignores information along the directions perpendicular to the curve. This is apparently not desired, given the high dimensionality of the configuration space. One approach to alleviate this problem is to adopt a lowdimensional configuration space, e.g., by using only a small number of linear modes from a principal component analysis to describe the protein conformation [18]. Alternatively, transitions between two conformations can be described by transition (or reaction) tubes [25,26] in the high-dimensional configuration space, as further discussed below. A transition tube [25,26] refers to a region in the configuration (conformational) space that connects the two metastable conformational states, such that most spontaneous transitions between the two states go through this tube. The center of the transition tube is defined as its principal curve [25], and a free energy can be defined along this curve. Unlike the multidimensional free energyassociated with the minimum-free-energy-pathway discussed earlier, however, this free energy has further integrated out all degrees of freedom perpendicular to the principal curve, and is thus a one-dimensional function of the curve parameter alone. Although the transition is now described by a single progression (curve) parameter, we note that the principal curve still lies in a high-dimensional configuration space, and the curve parameter is essentially a collective variable based on all coarse coordinates. This approach thus minimizes the possibility of ignoring important degrees of freedom from the.Rom each state and observe the subsequent free evolutions of the protein conformation. The multiple simulations using the same protocol and initial structure can thus reveal the intrinsic diversity in the conformational dynamics of AdK. Although the unrestrained simulations above may provide valuable information on the stability of the given conformations, the currently affordable simulation time is orders-of-magnitude shorter than what is needed to fully sample the conformational space. If two metastable conformations are separated by some energetic barrier, it would be very unlikely to observe, even in multiple simulations, any spontaneous transition. Therefore, to complement the unrestrained simulations, we also carry out another type of calculation here, in which we employ a series of biased simulations to estimate the free energy in the conformational space. In general, protein conformations require high-dimensional representations, and are described by a relatively large number of chosen “coarse coordinates”, which can be either Cartesian coordinates [24] or collective variables [21]. These coarse coordinates define a high-dimensional configuration space, and each point in this space represents a conformation. A free energy as a function of the coarse coordinates can be defined by integrating out all other (such as solvent) degrees of freedom. The objective of the conventional string method is then to identify a “minimum-free-energy-pathway” [21] that 18204824 connects two free energy minima in the configuration space, each representing a metastable conformational state. However, although the configuration space represents a significant dimensionality reduction compared to the entire phase space, it is still of relatively high dimensions. The multidimensional free energy associated with this pathway, as obtained from the conventional string method, only describes the energetics on a single curve, and ignores information along the directions perpendicular to the curve. This is apparently not desired, given the high dimensionality of the configuration space. One approach to alleviate this problem is to adopt a lowdimensional configuration space, e.g., by using only a small number of linear modes from a principal component analysis to describe the protein conformation [18]. Alternatively, transitions between two conformations can be described by transition (or reaction) tubes [25,26] in the high-dimensional configuration space, as further discussed below. A transition tube [25,26] refers to a region in the configuration (conformational) space that connects the two metastable conformational states, such that most spontaneous transitions between the two states go through this tube. The center of the transition tube is defined as its principal curve [25], and a free energy can be defined along this curve. Unlike the multidimensional free energyassociated with the minimum-free-energy-pathway discussed earlier, however, this free energy has further integrated out all degrees of freedom perpendicular to the principal curve, and is thus a one-dimensional function of the curve parameter alone. Although the transition is now described by a single progression (curve) parameter, we note that the principal curve still lies in a high-dimensional configuration space, and the curve parameter is essentially a collective variable based on all coarse coordinates. This approach thus minimizes the possibility of ignoring important degrees of freedom from the.