The folding mechanism of several β-structures (e.g., β-hairpins and β-sheets) was studied using newly developed enhanced sampling methods along with MD simulations in all implicit solvent environments. The influence of different implicit solvent models on the folding simulation of β-structure was also tested. Through the analysis of the free energy landscape as the function of several suitable reaction coordinates, we observed that the folding of β-hairpins is actually a two-state transition. In addition, the folding free energy landscapes for those related hairpins indicate the apparent sequence dependence, which demonstrates different folding mechanisms of similar β-structures of varied sequence. We also found that the stability of backbone hydrogen bonds is determined by the turn sequence and the composition of hydrophobic core cluster in β-structures. Neither of these findings was reported before. The processive movement of kinesin was also studied at the mesoscopic level. We developed a simple physical model to understand the asymmetric hand-over-hand mechanism of the kinesin walking on the microtubule. The hand-over-hand motion of the conventional kinesin is reproduced in our model and good agreement is achieved between calculated and experimental results. The experimentally observed limping of the truncated kinesin is also perfectly described by our model. The global conformational change of kinesin heads (e.g., the power stroke of neck-linkers which works as lever-arms during the kinesin walking, the transition between open and closed states of the switch region of the nucleotide binding domain in each head induced by the nucleotide binding and release) was studied for both dimeric and monomeric kinesins using a coarse-grained model, anisotropic network model (ANM). At the same time Langevin mode analysis was used to study the solvent influence on the motions of the kinesin head mimicked by ANM. Additionally, the correlation between the neck-linker and the nucleotide binding site was also studied for dimeric and monomeric kinesins. The former shows the apparent correlation between two subdomains whereas the latter does not, which may explain the experimental observation that only the dimeric kinesin is capable of walking processively on the microtubule.

Simulações moleculares podem fornecer informações e detalhes mecanísticos que são difíceis de obter de experimentos. No entanto, fenômenos bioquímicos como formação de complexos proteína-ligante e desenovelamento de proteína são lentos e difíceis de amostrar na escala de tempo geralmente atingida por simulações de dinâmica molecular (MD) convencionais. Esses fenômenos moleculares foram estudados aqui pela combinação de simulações de MD com diversos métodos e aproximações para aumentar a amostragem configuracional: método de energia de interação linear (LIE), a aproximação de ensemble ponderado (WE) e dinâmica molecular dirigida (SMD). Uma equação foi parametrizada para prever afinidades entre pequenas moléculas e proteínas baseada na aproximação LIE, que foca a amostragem computacional nos estados complexado e não-complexado do ligante. A flexibilidade proteica foi introduzida usando ensembles de configurações obtidos de simulações de MD. Diferentes esquemas de média foram testados para obter afinidades totais de complexos proteína-ligante, revelando que muitas configurações de complexo contribuem para as afinidades de proteínas flexíveis, enquanto as afinidades de proteínas rígidas são dominadas por uma configuração de complexo. O mutante L99A da lisozima T4 (T4L) é provavelmente a proteína mais frequentemente usada para estudar complexação de ligantes. Estruturas cristalográficas mostram que a cavidade de ligação artificial criada pela mutação é pouco acessível, portanto movimentos proteicos ou uma respiração conformacional são necessários para permitir a entrada e saída de ligantes. Simulações de MD foram combinadas aqui com a aproximação de WE para aumentar a amostragem de eventos infrequentes de saída do benzeno de T4L. Quatro possíveis caminhos foram encontrados e movimentações de alfa-hélices e cadeias laterais envolvidas na saída do ligante foram caracterizadas. Os quatro caminhos correspondem a túneis da proteína previamente observados em simulações de MD longas de T4L apo, sugerindo que a heterogeneidade de caminhos ao longo de túneis intrínsecos é explorada por pequenas moléculas para sair de cavidades de ligação enterradas em proteínas. Experimentos de microscopia de força atômica revelaram informações detalhadas do desenovelamento forçado e da estabilidade mecânica da rubredoxina, uma proteína ferro-enxofre simples. O desenovelamento completo da rubredoxina envolve a ruptura de ligações covalentes. Portanto, o processo de desenovelamento foi simulado aqui por simulações de SMD acopladas a uma descrição clássica da dissociação de ligações. A amostragem de eventos de desenovelamento forçado foi aumentada pelo uso de velocidades rápidas de esticamento. Os resultados foram analisados usando um modelo teórico válido para regimes de desenovelamento forçado lentos e rápidos. As simulações revelaram que mudanças no ponto de aplicação de força ao longo da sequência da rubredoxina levam a diferentes mecanismos de desenovelamento, caracterizados por variáveis graus de rompimento de ligações de hidrogênio e estrutura secundária da proteína. / Molecular simulations may provide information and mechanistic insights that are difficult to obtain from experiments. However, biochemical phenomena such as ligand-protein binding and protein unfolding are slow and hard to sample on the timescales usually reached by conventional molecular dynamics (MD) simulations. These molecular phenomena were studied here by combining MD simulations with several methods or approximations to enhance configurational sampling: linear interaction energy (LIE) method, weighted ensemble (WE) approach and steered molecular dynamics (SMD). An equation was parametrized to predict affinities between small molecules and proteins based on the LIE approximation, which focus computational sampling in ligand bound and unbound states. Protein flexibility was introduced by using ensembles of configurations obtained from MD simulations. Different averaging schemes were tested to obtain overall affinities for ligand-protein complexes, revealing that many bound configurations contribute to affinities for flexible proteins, while affinities for rigid proteins are dominated by one bound configuration. T4 lysozyme (T4L) L99A mutant is probably the protein most often used to study ligand binding. Crystal structures show the artificial binding cavity created by the mutation has low accessibility, so protein movements or conformational breathing are necessary to allow the entry and egress of ligands. MD simulations were combined here with the WE approach to enhance sampling of infrequent benzene unbinding events from T4L. Four possible pathways were found and motions on alpha-helices and side chains involved in ligand egress were characterized. The four pathways correspond to protein tunnels previously observed in long MD simulations of apo T4L, suggesting that pathway heterogeneity along intrinsic tunnels is explored by small molecules to egress from binding cavities buried in proteins. Previous atomic force microscopy experiments revealed detailed information on the forced unfolding and mechanical stability of rubredoxin, a simple iron-sulfur protein. Complete unfolding of rubredoxin involves rupture of covalent bonds. Thus, the unfolding process was simulated here by SMD simulations coupled to a classical description of bond dissociation. Sampling of forced unfolding events was increased by using fast pulling velocities. Results were analyzed using a theoretical model valid for both slow and fast forced unfolding regimes. Simulations revealed that changing the points of force application along the rubredoxin sequence leads to different unfolding mechanisms, characterized by variable degrees of disruption of hydrogen bonds and secondary protein structure.

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