INTERACTIONS IN GLOBULAR PROTEINS AND RELATING PROTEIN STRUCTURES TO MECHANISMS

结构生物学的一个主要目标是了解分子如何识别和相互作用。理解蛋白质相互作用的细节将增强对众多生物过程的理解，并为药物设计提供更坚实的基础。了解分子相互作用一直是我们许多研究的目标，特别是通过使用粗粒度模型。从结构中提取相互作用能，以及总能量分布的一般形式是我们的主要努力之一。在此期间，我们收集了不同蛋白质(分子间)之间相互作用的相互作用能，并将它们与分子内情况下的相互作用能进行了比较。比较的结果强烈依赖于参考态，即相互作用对是通过取代水相互作用还是通过取代其他残基相互作用形成的。在前一种情况下，由于水相互作用的主导作用，分子间和分子内的势非常相似。我们还研究了从蛋白质结构中提取短程相互作用能量的替代方法，并将它们与长程势结合起来，以改进线程。令人惊讶的是，短程交互项与长程交互项同样有效，当组合在一起时，线程性能的收益相对较小。在新的研究中，我们一直在研究蛋白质中最保守的部分，并表明这些部分只占结构的一小部分，通常是6？10个残基。同时，我们也在研究各种分子性质，如堆积，与序列保守区的相关性。了解序列保守的结构物理基础将使我们能够仅从序列中对蛋白质核心做出一些关键的预测。分子生物学的另一个目标是了解分子机制。与传统分子动力学相结合的蛋白质结构并没有提供关于这些的信息。我们正在用一种新的粗粒度模型研究蛋白质动力学，每个残基只有一个点。这一新方法代表了从结构推断功能行为的最简单方法。它基于高斯网络模型考虑已知蛋白质结构的波动。这一过程被证明是令人满意的采样关于蛋白质天然构象的原子涨落的分布，并对广泛的蛋白质和核酸结构产生与晶体温度因素和氢交换数据非常好的一致性。虽然这种方法很简单，但结果是直观和引人注目的。这种方法产生了一系列运动模式，通常是铰链弯曲运动，甚至包括最慢、最全局的运动。这为理解超大型甚至超分子结构的功能动力学开辟了新的和令人兴奋的前景。我们用这种方法进行研究的例子包括：1)色氨酸合成酶内的亚基通讯；2)逆转录酶，其中我们展示了手指/拇指结合部位的运动和核糖核酸酶H位点之间的反相关性如何导致分步处理机制；3)t-RNA游离并与其同源合成酶结合；以及4)拓扑异构酶II试图推断单独的运动方式和酶？S功能步骤之间的联系。其他正在进行的研究包括GroEL-groes蛋白伴侣系统(约8800个残基)，这是一个非常大的系统，展示了该方法的力量，以及其他一些核酸结合蛋白。这种方法正被应用于研究结合部位，通常是最灵活的区域，但也被用于研究更刚性的铰链和折叠核，对于各种各样的蛋白质。Z01 BC 08370-16-数据库，分子相互作用，分子模型，蛋白质折叠，蛋白质结构，超级计算，

A major goal of structural biology is to understand how molecules recognize and interact with one another. Comprehension of the details of protein interactions would enhance the understanding of numerous biological processes, as well as provide a sounder basis for drug design. Learning about molecular interactions has been the goal of many of our studies, particularly through the use of coarse-grained models. Extracting interaction energies from structures, together with the general forms of the overall energy distributions represents one of our major efforts. During this period we have collected interaction energies for interactions between separate proteins (intermolecular) and compared them to those for intramolecular cases. The results of the comparison depend strongly on the reference state, i.e., whether the interacting pairs are formed by replacing water interactions or by replacing other residue interactions. In the former case, the intermolecular and intramolecular potentials are extremely similar, because of the dominant effect of water interactions. We have also investigated alternative ways to extract short-range interaction energies from protein structures and combined them with long-range potentials to improve threading. Surprisingly the short-range interaction terms are similarly effective as the long-range terms, and when combined the gains in threading performance are relatively small. In new studies we have been studying the most extremely conserved parts of proteins and have shown that these comprise a small fraction of the structure, typically 6 ? 10 residues. At the same time we are also investigating the correlations of various molecular properties, such as packing, with the sequence conserved regions. Understanding the physical basis in structure for sequence conservation would enable us to make some critical predictions of protein cores from sequences alone.Another goal of molecular biology is to understand molecular mechanisms. Protein structures combined with conventional molecular dynamics have not been so informative about these. We are investigating protein dynamics with a new coarse-grained model having only one point per residue. This new approach represents a simplest way to infer functional behavior from structures. It considers fluctuations about known protein structures based on a Gaussian network model. This procedure is being shown to sample satisfactorily the distribution of atomic fluctuations about the native conformation in proteins, and to yield remarkably good agreement with crystallographic temperature factors and hydrogen exchange data, for a broad variety of proteins and nucleic acid structures. Although this method is simple, results are intuitive and compelling. The approach yields a series of modes of motion, typically hinge bending motions, including even the slowest, most global motions. This opens new and exciting prospects for comprehending the functional dynamics of extremely large, even supra- molecular structures. Examples of our studies with this approach include: 1) subunit communications within tryptophan synthase; 2) reverse transcriptase in which we showed how the anti-correlations between the motions of the fingers/thumb binding site and the ribonuclease H site could lead to a step-wise processing mechanism; 3) t-RNA free and bound to its cognate synthetase; and 4) topoisomerase II in trying to infer connections between individual modes of motion and the enzyme?s functional steps. Other studies underway include the GroEl-GroES protein chaperone system (about 8800 residues) which is an extremely large system that demonstrates the power of the approach and some other nucleic acid binding proteins. This approach is being applied to investigate binding sites, typically the most flexible regions, but also to investigate the more rigid hinges and folding nuclei for a broad variety of proteins.Z01 BC 08370-16 - databases, molecular interactions, molecular models, protein folding, protein structure, supercomputing,