Newton Katelyn, Yan Shuting, Schlick Tamar
University of Portland, Portland, OR 97203, USA.
Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA.
Int J Mol Sci. 2025 Jun 30;26(13):6297. doi: 10.3390/ijms26136297.
Human immunodeficiency virus (HIV) continues to be a threat to public health. An emerging technique with promise in the context of fighting HIV type 1 (HIV-1) focuses on targeting ribosomal frameshifting. A crucial -1 programmed ribosomal frameshift (PRF) has been observed in several pathogenic viruses, including HIV-1. Altered folds of the HIV-1 RNA frameshift element (FSE) have been shown to alter frameshifting efficiency. Here, we use RNA-As-Graphs (RAG), a graph-theory based framework for representing and analyzing RNA secondary structures, to perform conformational analysis in motif space to propose how sequence length may influence folding patterns. This combined analysis, along with all-atom modeling and experimental testing of our designed mutants, has already proven valuable for the SARS-CoV-2 FSE. As a first step to launching the same computational/experimental approach for HIV-1, we compare prior experiments and perform SHAPE-guided 2D-fold predictions for the HIV-1 FSE embedded in increasing sequence contexts and predict structure-altering mutations. We find a highly stable upper stem and highly flexible lower stem for the core FSE, with a three-way junction connecting to other motifs at increasing lengths. In particular, we find little support for a pseudoknot or triplex interaction in the core FSE, although pseudoknots can form separately as a connective motif at longer sequences. We also identify sensitive residues in the upper stem and central loop that, when minimally mutated, alter the core stem loop folding. These insights into the FSE fold and structure-altering mutations can be further pursued by all-atom simulations and experimental testing to advance the mechanistic understanding and therapeutic strategies for HIV-1.
人类免疫缺陷病毒（HIV）仍然是对公共卫生的一个威胁。在对抗1型人类免疫缺陷病毒（HIV-1）方面，一种有前景的新兴技术聚焦于靶向核糖体移码。在包括HIV-1在内的几种致病病毒中，已观察到一种关键的-1程序性核糖体移码（PRF）。HIV-1 RNA移码元件（FSE）折叠的改变已被证明会改变移码效率。在这里，我们使用RNA-As-Graphs（RAG），一种基于图论的用于表示和分析RNA二级结构的框架，在基序空间中进行构象分析，以提出序列长度可能如何影响折叠模式。这种综合分析，连同我们设计的突变体的全原子建模和实验测试，已被证明对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的FSE很有价值。作为对HIV-1采用相同计算/实验方法的第一步，我们比较先前的实验，并对嵌入在不断增加的序列背景中的HIV-1 FSE进行SHAPE引导的二维折叠预测，并预测改变结构的突变。我们发现核心FSE有一个高度稳定的上部茎和高度灵活的下部茎，随着长度增加，一个三岔接头连接到其他基序。特别是，我们发现核心FSE中几乎没有假结或三链体相互作用的证据，尽管假结可以作为一个连接基序在更长的序列中单独形成。我们还在上部茎和中心环中鉴定出敏感残基，当这些残基发生最小程度的突变时，会改变核心茎环的折叠。对FSE折叠和改变结构的突变的这些见解可以通过全原子模拟和实验测试进一步探究，以推进对HIV-1的机制理解和治疗策略。
