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。了解蛋白质相互作用的细节将增强对许多生物过程的理解，并为药物设计提供更可靠的基础。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之间（分子间）相互作用的相互作用能，并将其与分子内情况进行了比较。比较的结果强烈地依赖于参考状态，即，无论相互作用对是通过取代水的相互作用还是通过取代其他残基的相互作用形成的。在前一种情况下，分子间和分子内的潜力是非常相似的，因为水的相互作用的主导作用。我们还研究了从蛋白质结构中提取短程相互作用能的替代方法，并将其与长程势能结合起来以改善线程。令人惊讶的是，短程相互作用项与长程项同样有效，并且当组合时，线程性能的增益相对较小。在新的研究中，我们一直在研究蛋白质的最极端保守的部分，并已表明，这些包括一小部分的结构，通常为6？10个残基。同时，我们也在研究各种分子性质，如包装，与序列保守区的相关性。了解序列保守性结构的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性的预测。分子生物学的另一个目标是了解分子机制。蛋白质结构与传统的分子动力学相结合，并没有提供如此丰富的信息。我们正在研究蛋白质动力学与一个新的粗粒度模型，每个残基只有一个点。这种新方法代表了从结构中推断功能行为的最简单方法。它考虑了基于高斯网络模型的已知蛋白质结构的波动。这一程序被证明是令人满意的样品的原子波动分布的天然构象蛋白质，并产生显着良好的协议与晶体温度因子和氢交换数据，为各种各样的蛋白质和核酸结构。虽然这种方法很简单，但结果是直观和引人注目的。该方法产生一系列的运动模式，通常是铰链弯曲运动，甚至包括最慢的，最全局的运动。这为理解超大甚至超分子结构的功能动力学开辟了新的令人兴奋的前景。我们用这种方法研究的例子包括：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/拇指结合位点和核糖核酸酶H位点的运动之间的反相关如何导致逐步加工机制; 3）t-RNA游离并与其同源合成酶结合;和4）拓扑异构酶II在试图推断个别模式的运动和酶之间的连接？的功能步骤。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，证明了该方法和其他一些核酸结合蛋白的能力。这种方法被应用于研究结合位点，通常是最灵活的区域，但也用于研究各种蛋白质的更刚性的铰链和折叠核。Z 01 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,