Comparative Analysis of Protein Surface Hydrophobicity Maps Determined by Sparse Sampling INDUS and Spatial Aggregation Propensity

生物系统 背景(考古学) 化学 折叠(DSP实现) 表面蛋白 蛋白质折叠 曲面(拓扑) 疏水效应 化学物理 有机化学 数学 生物化学 几何学 生物 古生物学 病毒学 电气工程 工程类
作者
Imee Sinha,Shekhar Garde,Steven M. Cramer
出处
期刊:Journal of Physical Chemistry B [American Chemical Society]
卷期号:127 (48): 10304-10314 被引量:3
标识
DOI:10.1021/acs.jpcb.3c04902
摘要

Protein surface hydrophobicity plays a central role in various biological processes such as protein folding and aggregation, as well as in the design and manufacturing of biotherapeutics. While the hydrophobicity of protein surface patches has been linked to their constituent residue hydropathies, recent research has shown that protein surface hydrophobicity is more complex and characterized by the response of water to these surfaces. In this work, we employ water density perturbations to map the surface hydrophobicity of a set of model proteins using sparse indirect umbrella sampling simulations (SSI). This technique is used to identify hydrophobic surface patches for the set of model proteins, and the results are compared to those obtained from the widely adopted spatial aggregation propensity (SAP) technique. While SAP-based calculations show agreement with SSI in some cases, there are several examples of disagreement. We identify four general classes of difference in behavior and study factors that contribute to these differences. We find that the SAP method can sometimes mask the effect of weakly nonpolar or isolated nonpolar residues that can lead to strong hydrophobic patches on the protein surface. In addition, hydrophobic patches identified by SAP can exhibit shifts in both position and strength on the SSI map. Our results demonstrate that the combination of topography and chemical context controls the hydrophobicity of a given patch above and beyond the intrinsic polarity of the residues present on the patch surface. The availability of more accurate protein hydrophobicity maps in concert with new classes of hydrophobic molecular descriptors may create significant opportunities for in silico prediction of protein behavior for a range of applications, such as protein design, biomanufacturability, and downstream bioprocessing.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
谨慎的擎宇完成签到,获得积分10
刚刚
Thomas完成签到,获得积分10
1秒前
小白鞋完成签到 ,获得积分10
1秒前
maying0318发布了新的文献求助10
3秒前
宣以晴完成签到,获得积分10
3秒前
Nnn完成签到,获得积分10
4秒前
baby完成签到,获得积分10
7秒前
123完成签到,获得积分10
7秒前
8秒前
学术牛马完成签到,获得积分10
8秒前
sl发布了新的文献求助10
10秒前
完美的鹤完成签到,获得积分10
11秒前
hky完成签到,获得积分10
12秒前
TTTHANKS完成签到 ,获得积分10
13秒前
WW完成签到,获得积分10
13秒前
LL完成签到,获得积分10
14秒前
量子星尘发布了新的文献求助10
14秒前
小马的可爱老婆2完成签到,获得积分10
14秒前
缥缈纲完成签到,获得积分10
15秒前
TY完成签到 ,获得积分10
15秒前
迷路的小蚂蚁完成签到,获得积分10
16秒前
哈儿的跟班完成签到,获得积分10
16秒前
醉熏的鑫完成签到,获得积分20
17秒前
远_09完成签到 ,获得积分10
18秒前
网站技术人员完成签到,获得积分10
19秒前
eazin完成签到 ,获得积分10
20秒前
山野桃饼完成签到,获得积分10
20秒前
无私代芹完成签到,获得积分10
21秒前
画风湖湘卷完成签到,获得积分10
21秒前
段一帆完成签到,获得积分10
22秒前
结实的老虎完成签到,获得积分10
22秒前
22秒前
邓希静完成签到,获得积分10
23秒前
26秒前
27秒前
27秒前
29秒前
是冬天完成签到,获得积分10
30秒前
mengwensi完成签到,获得积分10
30秒前
单纯血茗发布了新的文献求助10
30秒前
高分求助中
【提示信息,请勿应助】关于scihub 10000
Les Mantodea de Guyane: Insecta, Polyneoptera [The Mantids of French Guiana] 3000
徐淮辽南地区新元古代叠层石及生物地层 3000
The Mother of All Tableaux: Order, Equivalence, and Geometry in the Large-scale Structure of Optimality Theory 3000
Global Eyelash Assessment scale (GEA) 1000
Picture Books with Same-sex Parented Families: Unintentional Censorship 550
Research on Disturbance Rejection Control Algorithm for Aerial Operation Robots 500
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 4038426
求助须知:如何正确求助?哪些是违规求助? 3576119
关于积分的说明 11374556
捐赠科研通 3305834
什么是DOI,文献DOI怎么找? 1819339
邀请新用户注册赠送积分活动 892678
科研通“疑难数据库(出版商)”最低求助积分说明 815029