Weikl Thomas R, Paul Fabian
Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany.
Protein Sci. 2014 Nov;23(11):1508-18. doi: 10.1002/pro.2539. Epub 2014 Sep 6.
Protein binding and function often involves conformational changes. Advanced nuclear magnetic resonance (NMR) experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may "select" protein conformations for binding (or unbinding). In this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in different conformations, which is plausible for small ligand molecules. Such a separation of timescales leads to a decoupling and temporal ordering of binding/unbinding events and conformational changes. We propose that conformational-selection and induced-change processes (such as induced fit) are two sides of the same coin, because the temporal ordering is reversed in binding and unbinding direction. Conformational-selection processes can be characterized by a conformational excitation that occurs prior to a binding or unbinding event, while induced-change processes exhibit a characteristic conformational relaxation that occurs after a binding or unbinding event. We discuss how the ordering of events can be determined from relaxation rates and effective on- and off-rates determined in mixing experiments, and from the conformational exchange rates measured in advanced NMR or single-molecule fluorescence resonance energy transfer experiments. For larger ligand molecules such as peptides, conformational changes and binding events can be intricately coupled and exhibit aspects of conformational-selection and induced-change processes in both binding and unbinding direction.
蛋白质结合与功能通常涉及构象变化。先进的核磁共振(NMR)实验表明,这些构象变化可在没有配体分子的情况下发生(或在有结合配体时发生),并且配体可能会“选择”蛋白质构象以进行结合(或解离)。在本综述中,我们认为这种构象选择需要配体结合和解离的转变时间,与蛋白质在不同构象中的停留时间相比要短,这对于小分子配体来说是合理的。这种时间尺度的分离导致结合/解离事件与构象变化的解耦和时间排序。我们提出构象选择和诱导变化过程(如诱导契合)是同一枚硬币的两面,因为在结合和解离方向上时间排序是相反的。构象选择过程的特征是在结合或解离事件之前发生构象激发,而诱导变化过程则表现为在结合或解离事件之后发生特征性的构象弛豫。我们讨论了如何从混合实验中测定的弛豫速率和有效结合与解离速率,以及从先进的核磁共振或单分子荧光共振能量转移实验中测量的构象交换速率来确定事件的排序。对于较大的配体分子,如肽,构象变化和结合事件可能会复杂地耦合,并在结合和解离方向上表现出构象选择和诱导变化过程的特征。