S*******l
发帖数: 4637 | 1 可能会那么紧么？
谁搞biophysics算一下。 | d****o
发帖数: 32610 | 2 affinity这玩意儿单位一般不是浓度吗
【在 S*******l 的大作中提到】
: 可能会那么紧么？
: 谁搞biophysics算一下。
| x****6
发帖数: 4339 | | S*******l
发帖数: 4637 | 4 delta G=RTln(Kd)
这个算下来紧得不可想象...
【在 d****o 的大作中提到】
: affinity这玩意儿单位一般不是浓度吗
| S*******l
发帖数: 4637 | 5 数量级太吓人了
【在 x****6 的大作中提到】
: 他那是 计算的，不靠谱。还需要实验测量。
| x****6
发帖数: 4339 | 6 蛋白结合，Kd也就nM水平。
【在 S*******l 的大作中提到】
: delta G=RTln(Kd)
: 这个算下来紧得不可想象...
| S*******l
发帖数: 4637 | 7 比SARS 低了28 kcal/mol,中科院文章，线上下不来原文，卡住了。
从别人转述那里看到的。
【在 x****6 的大作中提到】
: 蛋白结合，Kd也就nM水平。
| x****6
发帖数: 4339 | 8 . The binding free energy between the Wuhan CoV S-protein and human ACE2 was
–50.6 kcal mol–1, whereas that between SARS-CoV S-protein and
ACE2 was –78.6 kcal mol–1.
基于计算的 测量，绝对值没有相对值有意义
【在 S*******l 的大作中提到】
: 比SARS 低了28 kcal/mol,中科院文章，线上下不来原文，卡住了。
: 从别人转述那里看到的。
| x****6
发帖数: 4339 | 9
The occurrence of concentrated pneumonia cases in Wuhan city, Hubei province
of China was first reported on December 30, 2019 by the Wuhan Municipal
Health Commission (WHO, 2020). The pneumonia cases were found to be linked
to a large seafood and animal market in Wuhan, and measures for sanitation
and disinfection were taken swiftly by the local government agency. The
Centers for Disease Control and Prevention (CDC) and Chinese health
authorities later determined and announced that a novel coronavirus (CoV),
denoted as Wuhan CoV, had caused the pneumonia outbreak in Wuhan city (CDC,
2020). Scientists from multiple groups had obtained the virus samples from
hospitalized patients (Normile, 2020). The isolated viruses were
morphologically identical when observed under electron microscopy.
One genome sequence (WH-Human_1) of the Wuhan CoV was first released on Jan
10, 2020, and subsequently five additional Wuhan CoV genome sequences were
released (Zhang, 2020; Shu and McCauley, 2017) (Table S1 in Supporting
Information). The current public health emergency partially resembles the
emergence of the SARS outbreak in southern China in 2002. Both happened in
winter with initial cases linked to exposure to live animals sold at animal
markets, and both were caused by previously unknown coronaviruses. As of
January 15, 2020, there were more than 40 laboratory-confirmed cases of the
novel Wuhan CoV infection with one reported death. Although no obvious
evidence of human-to-human transmission was reported, there were exported
cases in Hong Kong China, Japan, and Thailand.
Under the current public health emergency, it is imperative to understand
the origin and native host(s) of the Wuhan CoV, and to evaluate the public
health risk of this novel coronavirus for transmission cross species or
between humans. To address these important issues related to this causative
agent responsible for the outbreak in Wuhan, we initially compared the
genome sequences of the Wuhan CoV to those known to infect humans, namely
the SARS-CoV and Middle East Respiratory Syndrome (MERS)-CoV (Cotten et al.,
2013). The sequences of the six Wuhan CoV genomes were found to be almost
identical (Figure S1A in Supporting Information). When compared to the
genomes of SARS-CoV and MERS-CoV, the WH-human_1 genome that was used as
representative of the Wuhan CoV, shared a better sequence homology toward
the genomes of SARS-CoV than that of MERS-CoV (Figure S1B in Supporting
Information). High sequence diversity between Wuhan-human_1 and SARS-CoV_
Tor2 was found mainly in ORF1a and spike (S-protein) gene, whereas sequence
homology was generally poor between Wuhan-human_1 and MERS-CoV.
To understand the origin of the Wuhan CoV and its genetic relationship with
other coronaviruses, we performed phylogenetic analysis on the collection of
coronavirus sequences from various sources. The results showed the Wuhan
CoVs were clustered together in the phylogenetic tree, which belong to the
Betacoronavirus genera (Figure 1A). Betacoronavirus is enveloped, single-
stranded RNA virus that infects wild animals, herds and humans, resulting in
occasional outbreaks and more often infections without apparent symptoms.
The Wuhan CoV cluster is situated with the groups of SARS/SARS-like
coronaviruses, with bat coronavirus HKU9-1 as the immediate outgroup. Its
inner joint neighbors are SARS or SARS-like coronaviruses, including the
human-infecting ones (Figure 1A, marked with red star). Most of the inner
joint neighbors and the outgroups were found in various bats as natural
hosts, e.g., bat coronaviruses HKU9-1 and HKU3-1 in Rousettus bats and bat
coronavirus HKU5-1 in Pipistrellus bats. Thus, bats being the native host of
the Wuhan CoV would be the logical and convenient reasoning, though it
remains likely there was intermediate host(s) in the transmission cascade
from bats to humans. Based on the unique phylogenetic position of the Wuhan
CoVs, it is likely that they share with the SARS/SARS-like coronaviruses, a
common ancestor that resembles the bat coronavirus HKU9-1. However, frequent
recombination events during their evolution may blur their path, evidenced
by patches of high-homologous sequences between their genomes (Figure S1B in
Supporting Information).
Click to view Download high-quality image
Figure 1
Evolutionary analysis of the coronaviruses and modeling of the Wuhan CoV S-
protein interacting with human ACE2. A, Phylogenetic tree of coronaviruses
based on full-length genome sequences. The tree was constructed with the
Maximum-likelihood method using RAxML with GTRGAMMA as the nucleotide
substitution model and 1,000 bootstrap replicates. Only bootstraps ≥50%
values are shown as filled circles. The host for each coronavirus is marked
with corresponding silhouette. Known human-infecting betacoronaviruses are
indicated with a red star. B, Amino acid sequence alignment of the RBD
domain of coronavirus S-protein. Residues 442, 472, 479, 487, and 491 (
numbered based on SARS-CoV S-protein sequence) are important residues for
interaction with human ACE2 molecule. C, Structural modeling of the Wuhan
CoV (WH-human_1 as representative) S-protein complexed with human ACE2
molecule. Middle panel: The model of the Wuhan CoV S-protein (brown ribbon)
is superimposed with the structural template of the SARS CoV S-protein (
light blue ribbon). The protein backbone structure of human ACE2 is
represented in magenta ribbon. Left panel: The region is shown for hydrogen
bonding interactions between Arg426 in S-protein and Gln325/Glu329 in ACE2.
The relevant residues are presented in ball and stick representations. Right
panel: The region is shown for hydrogen bonding interactions between Tyr436
in S-protein and Asp38/Gln42 in ACE2.
Overall, there is considerable genetics distance between the Wuhan CoV and
the human-infecting SARS-CoV, and even greater distance from MERS-CoV. This
observation raised an important question whether the Wuhan CoV adopted the
same mechanisms that SARS-CoV or MERS-CoV used for transmission cross
species/humans, or involved a new, different mechanism for transmission.
The S-protein of coronavirus is divided into two functional units, S1 and S2
. S1 facilitates virus infection by binding to host receptors. It comprises
two domains, the N-terminal domain and the C-terminal RBD domain that
directly interacts with host receptors (Li, 2012). To investigate the Wuhan
CoV and its host interaction, we looked into the RBD domain of its S-protein
. The S-protein was known to usually have the most variable amino acid
sequences compared to those of ORF1a and ORF1b from coronavirus (Hu et al.,
2017). However, despite the overall low homology of the Wuhan CoV S-protein
to that of SARS-CoV (Figure S1 in Supporting Information), the Wuhan CoV S-
protein had several patches of sequences in the RBD domain having a high
homology to that of SARS-CoV_Tor2 and HP03-GZ01 (Figure 1B). The residues at
positions 442, 472, 479, 487, and 491 in SARS-CoV S-protein were reported
to be at receptor complex interface and considered critical for cross-
species and human-to-human transmission of SARS-CoV (Li et al., 2005).
Despite the patches of highly conserved regions in the RBD domain of the
Wuhan CoV S-protein, four of the five critical residues are not preserved
except Tyr491 (Figure 1B). Although the polarity and hydrophobicity of the
replacing amino acids are similar, they raised serious questions about
whether the Wuhan CoV would infect humans via binding of S-protein to ACE2,
and how strong the interaction is for risk of human transmission. Note MERS-
CoV S-protein displayed very little homology toward that of SARS-CoV in the
RBD domain, due to the different binding target for its S-protein, the human
dipeptidyl peptidase 4 (DPP4) (Raj et al., 2013).
To answer the serious questions and assess the risk of human transmission of
the Wuhan CoV, we performed structural modeling of its S-protein and
evaluated its ability to interact with human ACE2 molecules. Based on the
computer-guided homology modeling method, the structural model of the Wuhan
CoV S-protein was constructed by Swiss-model using the crystal structure of
SARS coronavirus S-protein (PDB accession: 6ACD) as a template (Schwede et
al., 2003). Note the amino acid sequence identity between the Wuhan-CoV and
SARS-CoV S-proteins is 76.47%. Then according to the crystal structure of
SARS-CoV S-protein RBD domain complexed with its receptor ACE2 (PDB code:
2AJF), the 3-D complex structure of the Wuhan CoV S-protein binding to human
ACE2 was modeled with structural superimposition and molecular rigid
docking (Li et al., 2005) (Figure 1C).
The computational model of the Wuhan CoV S-protein (using the WH-human_1
sequence as representative) showed a Cα RMSD of 1.45 Å on the
RBD domain compared to the SARS-CoV S-protein structure (Figure 1C). The
binding free energies for the S-protein to human ACE2 binding complexes were
calculated by MOE 2019 with amber ff14SB force field parameters (Maier et
al., 2015). The binding free energy between the Wuhan CoV S-protein and
human ACE2 was –50.6 kcal mol–1, whereas that between SARS-CoV
S-protein and ACE2 was –78.6 kcal mol–1. A value of –10&#
8197;kcal mol–1 is usually considered significant. Because of the
loss of hydrogen bond interactions due to replacing Arg426 with Asn426 in
the Wuhan CoV S-protein, the binding free energy for the Wuhan CoV S-protein
increased by 28 kcal mol–1 when compared to the SARS-CoV S-
protein binding. Although comparably weaker, the Wuhan CoV S-protein is
regarded to have strong binding affinity to human ACE2. So to our surprise,
despite replacing four out of five important interface amino acid residues,
the Wuhan CoV S-protein was found to have a significant binding affinity to
human ACE2. Looking more closely, the replacing residues at positions 442,
472, 479, and 487 in the Wuhan CoV S-protein did not alter the structural
confirmation. The Wuhan CoV S-protein and SARS-CoV S-protein shared an
almost identical 3-D structure in the RBD domain, thus maintaining similar
van der Waals and electrostatic properties in the interaction interface.
In summary, our analysis showed that the Wuhan CoV shared with the SARS/SARS
-like coronaviruses a common ancestor that resembles the bat coronavirus
HKU9-1. Our work points to the important discovery that the RBD domain of
the Wuhan CoV S-protein supports strong interaction with human ACE2
molecules despite its sequence diversity with SARS-CoV S-protein. Thus the
Wuhan CoV poses a significant public health risk for human transmission via
the S-protein–ACE2 binding pathway. People also need to be reminded that
risk and dynamic of cross-species or human-to-human transmission of
coronaviruses are also affected by many other factors, like the host’s
immune response, viral replication efficiency, or virus mutation rate.
Acknowledgment
This work was supported in part by grants from the National Science and
Technology Major Projects for “Major New Drugs Innovation and Development”
(directed by Dr. Song Li) (2018ZX09711003) of China, the National Key R&D
Program (2018YFC0310600) of China, the National Natural Science Foundation
of China (31771412), and Special Fund for strategic bio-resources from
Chinese Academy of Sciences (ZSYS-014). We also acknowledge the National
Institute for Viral Disease Control and Prevention, China CDC; Wuhan
Institute of Virology, Chinese Academy of Sciences; Institute of Pathogen
Biology, Chinese Academy of Medical Sciences & Peking Union Medical College;
and Wuhan Jinyintan Hospital for their efforts in research and collecting
the data and genome sequencing sharing. In addition, we acknowledge GISAID (
https://www.gisaid.org/) for facilitating open data sharing.
rchangel) 的大作中提到: 】
【在 S*******l 的大作中提到】
: 比SARS 低了28 kcal/mol,中科院文章，线上下不来原文，卡住了。
: 从别人转述那里看到的。
| S*******l
发帖数: 4637 | 10 就是说这些是计算化学的理论值，和实际值会差很多。
但是怎么会差那么多？ | | | S*******l
发帖数: 4637 | 11 这么强的结合，传染性会很强。比SARS 弱也弱不到哪里。 | x****6
发帖数: 4339 | 12 首先，他的这个 新sars的结构是TM用swiss model计算出来了，根本就不靠谱。然后再
和人的ace2受体进行docking，也是不靠谱计算的。两个不靠谱相乘，有个毛的置信度。
【在 S*******l 的大作中提到】
: 这么强的结合，传染性会很强。比SARS 弱也弱不到哪里。
| S*******l
发帖数: 4637 | 13 好吧。
还是要靠wet bench.
度。
【在 x****6 的大作中提到】
: 首先，他的这个 新sars的结构是TM用swiss model计算出来了，根本就不靠谱。然后再
: 和人的ace2受体进行docking，也是不靠谱计算的。两个不靠谱相乘，有个毛的置信度。
| x****6
发帖数: 4339 | 14 属实。
你是做wet bench吧？
【在 S*******l 的大作中提到】
: 好吧。
: 还是要靠wet bench.
:
: 度。
| S*******l
发帖数: 4637 | 15 对，当年差点转了结构的说
【在 x****6 的大作中提到】
: 属实。
: 你是做wet bench吧？
|
|
