Vbp Leite

As proteinas com atividade enzimatica podem ser divididas em seis grandes classes de acordo com suas funcoes especificas, que sao: oxirredutases, hidrolases, transferases, lyases, isomerases e ligases. Utilizando algoritmo de agrupamento nao-parametrico, este trabalho tem como objetivo predizer diferentes classes enzimaticas usando parâmetros estruturais e fisico-quimicos.

Abstract Non-pharmaceutical fentanyls (NPFs) are synthetic substances analogous to fentanyl that have not been approved for medical use. Their clandestine synthesis involves chemical modification of an existing drug, which may cause unpredictable pharmacological effects. New structures are emerging rapidly, and there is a lack of information for characterization. It makes their chemical identification difficult. In this scenario, in silico methods have become an alternative to study these systems. Here, we have applied factorial design to decide the best conditions to perform quantum calculations to obtain the infrared spectra of 46 seized NPFs. A multivariate classification was used to establish the main spectral characteristics of these substances. Similarities between theoretical and experimental spectra were determined through vibrational frequencies comparison, Kullback-Leibler divergence, and SIMCA evaluation. The in silico methods provided valuable information about illegal substances and proved helpful in predict the spectroscopic properties of new fentanyl analogous drugs.

The energy landscape approach has played a fundamental role in advancing our understanding of protein folding. Here, we quantify protein folding energy landscapes by exploring the underlying density of states. We identify three quantities essential for characterizing landscape topography: the stabilizing energy gap between the native and nonnative ensembles δ E , the energetic roughness Δ E , and the scale of landscape measured by the entropy S . We show that the dimensionless ratio between the gap, roughness, and entropy of the system accurately predicts the thermodynamics, as well as the kinetics of folding. Large Λ implies that the energy gap (or landscape slope towards the native state) is dominant, leading to more funneled landscapes. We investigate the role of topological and energetic roughness for proteins of different sizes and for proteins of the same size, but with different structural topologies. The landscape topography ratio Λ is shown to be monotonically correlated wi...

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower tha...

ABSTRACT This paper aims to give an initial presentation to physics students of the area of electron transfer, addressing its major aspects. The subject is then presented in an introductory way, highlighting and discussing the key points. Primarily, the problem is approached in a simplified manner through a two-state system, and aspects of calculating the matrix-element are discussed. Then, the electron transfer problem, influenced by nuclear reaction coordinates, is addressed and treated by the Marcus theory. Time scales and the concepts of adiabatic and non-adiabatic phenomena are discussed in the context of electron transfer. The classical, semi-classical and quantum formalisms of for the nuclear reactions coordinates are presented, and aspects of solvents are also discussed. Finally, we conclude by examining some recent examples of problems discussed in the literature.

Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs. In this paper, we introduce a metric to describe the distance between any two conformations, which also allows us to go beyond the one-dimensional representation and visualize the folding funnel in 2D and 3D. In this way it is possible to assess the folding process in detail, e.g., by identifying the connectivity between conformations and establishing the paths to reach the native state, in addition to regions where trapping may occur. Unlike the disconnectivity maps method, which is based on the kinetic con...

... Using the Born-Oppenheimer ap-proximation, the electronic contributions Tx VeA(x,r) and Tx VeB(x,r,R) were replaced by the donor and acceptor eigenenergies EA(r) and EB(r)], respectively. ... 270, 229 1992. 33 L. Jaroszewski, B. Lesyng, JJ Tanner, and JA McCammon, Chem. ...