Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors

In recent years, elastic network models (ENM) have been widely used to describe low-frequency collective motions in proteins. These models are often validated and calibrated by fitting mean-square atomic displacements estimated from x-ray crystallography (B-factors). We show that a proper calibration procedure must account for the rigid-body motion and constraints imposed by the crystalline environment on the protein. These fundamental aspects of protein dynamics in crystals are often ignored in currently used ENMs, leading to potentially erroneous network parameters. Here we develop an ENM that properly takes the rigid-body motion and crystalline constraints into account. Its application to the crystallographic B-factors reveals that they are dominated by rigid-body motion and thus are poorly suited for the calibration of models for internal protein dynamics. Furthermore, the translation libration screw (TLS) model that treats proteins as rigid bodies is considerably more successful in interpreting the experimental B-factors than ENMs. This conclusion is reached on the basis of a comparative study of various models of protein dynamics. To evaluate their performance, we used a data set of 330 protein structures that combined the sets previously used in the literature to test and validate different models. We further propose an extended TLS model that treats the bulk of the protein as a rigid body while allowing for flexibility of chain ends. This model outperforms other simple models of protein dynamics in interpreting the crystallographic B-factors.     

Comparison of different tomato puree production phases from an environmental point of view

The International Journal of Life Cycle Assessment - Agro-food systems are involved with considerable environmental impacts. Tomato as an important vegetable crop is processed into some products...     

The effect of the degradation pattern of biodegradable bone plates on the healing process using a biphasic mechano-regulation theory

Biomechanics and Modeling in Mechanobiology - Bone plates are used to treat bone fractures by stabilizing the fracture site and allowing treatments to take place. Mechanical properties of the...