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Book: Xue ye xi tong yi nan bing li jing xi ji zhen duan si lu

Li, Juan

2014

Author's details	Li Juan, Xiao Yang, Liu Junru zhu bian
MeSH term(s)	Hematologic Diseases/diagnosis ; Rare Diseases/diagnosis
Language	Chinese
Size	2, 5, 574 pages :, illustrations, portraits
Edition	Di 1 ban.
Document type	Book
ISBN	9787535963369 ; 7535963366
Database	Catalogue of the US National Library of Medicine (NLM)

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Article: Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity.

Li, Zhen-Lu / Buck, Matthias

Computational and structural biotechnology journal

2022 Volume 20, Page(s) 6078–6086

Abstract: SARS-CoV-2 variants often include surface mutations in the Spike protein that are important for viruses to recognize host receptors and evade antibody neutralization. The Spike protein also has mutations in the interior of the protein likely to affect ... ...

Abstract	SARS-CoV-2 variants often include surface mutations in the Spike protein that are important for viruses to recognize host receptors and evade antibody neutralization. The Spike protein also has mutations in the interior of the protein likely to affect the Spike protein S1 - S2 subunit's separation propensity, the most important of which is the D614G mutation. Remarkably, the Omicron variant contains a large number of internal mutations at the S2: S1 interface, which have not been investigated yet. In this study, we examined the effects of such interfacial mutations on the S2: S1 and subunit domain interactions and on the subunit's dissociation process. We found that the interaction with S2 is mainly contributed by the three encapsulation domains, named INT, ED1 and ED2 of S1, which are sandwiched between the S1 RBD and
Language	English
Publishing date	2022-11-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.10.044
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Article ; Online: A proteome-scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics.

Li, Zhen-Lu / Buck, Matthias

Proteins

2022 Volume 91, Issue 1, Page(s) 3–15

Abstract: Despite differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins, often with subtle differences in amino acid sequence. Here, we present a simple way to analyze the difference in amino acid occurrence by ... ...

Abstract	Despite differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins, often with subtle differences in amino acid sequence. Here, we present a simple way to analyze the difference in amino acid occurrence by comparing highly homologous proteins on a subproteome level between several vertebrate model organisms. Specifically, we use this method to identify a pattern of amino acid conservation as well as a shift in amino acid occurrence between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, this general analysis and a specific example further establish a broad correlation, if not likely connection between the thermal adaptation of protein sequences and two of their physical features: on average a change in their protein dynamics and, even more strongly, in their solvation. For poikilotherms, such as frog and fish, the lower body temperature is expected to increase the protein-protein interaction due to a decrease in protein internal dynamics. In order to counteract the tendency for enhanced binding caused by low temperatures, poikilotherms enhance the solvation of their proteins by favoring polar amino acids. This feature appears to dominate over possible changes in dynamics for some proteins. The results suggest that a general trend for amino acid choice is part of the mechanism for thermoadaptation of vertebrate organisms at the molecular level.
MeSH term(s)	Animals ; Proteome/metabolism ; Vertebrates/metabolism ; Amino Acid Sequence ; Cold Temperature ; Amino Acids/metabolism
Chemical Substances	Proteome ; Amino Acids
Language	English
Publishing date	2022-08-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.26404
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Article: Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2.

Li, Zhen-Lu / Buck, Matthias

bioRxiv : the preprint server for biology

2021

Abstract: The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. As the Spike protein of SARS-CoV-2 is cleaved into the S1 and the S2 domain by furin protease, Nrp1 binds to the newly created C-terminal RRAR ... ...

Abstract	The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. As the Spike protein of SARS-CoV-2 is cleaved into the S1 and the S2 domain by furin protease, Nrp1 binds to the newly created C-terminal RRAR amino acid sequence of the S1 domain. In this study, we model the association of a Nrp1 (a2-b1-b2) protein with the Spike protein computationally and analyze the topological constraints in the SARS-CoV-2 Spike protein for binding with Nrp1 and ACE2. Importantly, we study the exit mechanism of S2 from the S1 domain with the assistance of ACE2 as well as Nrp1 by molecular dynamics pulling simulations. In the presence of Nrp1, by binding the S1 more strongly to the host membrane, there is a high probability of S2 being pulled out, rather than S1 being stretched. Thus, Nrp1 binding could stimulate the exit of S2 from the S1 domain, which will likely increase virus infectivity as the liberated S2 domain mediates the fusion of virus and host membranes. Understanding of such a Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future combination therapy.
Language	English
Publishing date	2021-01-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.01.06.425627
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Article ; Online: Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2.

Li, Zhen-Lu / Buck, Matthias

Biophysical journal

2021 Volume 120, Issue 14, Page(s) 2828–2837

Abstract: The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. The Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (residues (res.) 1-685) ... ...

Abstract	The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. The Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (residues (res.) 1-685) and the S2 (res. 686-1273) domains by furin protease. Nrp1 predominantly binds to the C-terminal RRAR amino acid motif (res. 682-685) of the S1 domain. In this study, we firstly modeled the association of an Nrp1 protein (consisting of domains a2-b1-b2) with the Spike protein. Next, we studied the separation of S2 from the S1 domain, with and without Nrp1 bound, by utilizing molecular dynamics pulling simulations. During the separation, Nrp1 stabilizes the S1 C-terminal region (res. 640-685) and thereby assists the detachment of S2 N-terminal region (res. 686-700). Without Nrp1 bound, S1 tends to become stretched, whereas the bound Nrp1 stimulates an earlier separation of S2 from the S1 domain. The liberated S2 domain is known to mediate the fusion of virus and host membranes; thus, Nrp1 likely increases virus infectivity by facilitating the S1 and S2 separation. We further analyzed the possible topological structure of the SARS-CoV-2 Spike protein when bound with Nrp1 and angiotensin-converting enzyme 2 (ACE2). Understanding of such an Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future Nrp1-ACE2 targeted combination therapy.
Language	English
Publishing date	2021-06-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.05.026
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Article ; Online: Beyond history and "on a roll": The list of the most well-studied human protein structures and overall trends in the protein data bank.

Li, Zhen-Lu / Buck, Matthias

Protein science : a publication of the Protein Society

2021 Volume 30, Issue 4, Page(s) 745–760

Abstract: Of the roughly 20,000 canonical human protein sequences, as of January 20, 2021, 7,077 proteins have had their full or partial, medium- to high-resolution structures determined by x-ray crystallography or other methods. Which of these proteins dominate ... ...

Abstract	Of the roughly 20,000 canonical human protein sequences, as of January 20, 2021, 7,077 proteins have had their full or partial, medium- to high-resolution structures determined by x-ray crystallography or other methods. Which of these proteins dominate the protein data bank (the PDB) and why? In this paper, we list the 273 top human protein structures based on the number of their PDB entries. This set of proteins accounts for more than 40% of all available human PDB entries and represent past trends as well as current status for protein structural biology. We briefly discuss the relationship which some of the prominent protein structures have with protein research as a whole and mention their relevance to human diseases. The top-10 soluble and membrane proteins are all well-known (most of their first structures being deposited more than 30 years ago). Overall, there is no dramatic change in recent trends in the PDB. Remarkably, the number of structure depositions has grown nearly exponentially over the last 10 or more years (with a doubling time of 7 years for proteins, obtained from any organism). Growth in human protein structures is slightly faster (at 5.9 years). The information in this paper may be informative to senior scientists but also inspire researchers who are new to protein science, providing the year 2021 snap-shot for the state of protein structural biology.
MeSH term(s)	Algorithms ; Computational Biology ; Crystallography, X-Ray ; Databases, Protein ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Models, Molecular ; Protein Conformation
Chemical Substances	Membrane Proteins
Language	English
Publishing date	2021-03-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4038
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Article ; Online: The impact of conversion during minimally invasive pancreatoduodenectomy: A meta-analysis.

Li, Zhen-Lu / Li, Mao / Xiong, Jun-Jie / Lu, Hui-Min

Asian journal of surgery

2022 Volume 46, Issue 3, Page(s) 1539–1540

MeSH term(s)	Humans ; Pancreaticoduodenectomy ; Postoperative Complications/epidemiology ; Postoperative Complications/etiology ; Postoperative Complications/prevention & control ; Pancreatic Neoplasms/surgery ; Laparoscopy ; Minimally Invasive Surgical Procedures ; Robotic Surgical Procedures
Language	English
Publishing date	2022-10-14
Publishing country	China
Document type	Meta-Analysis ; Letter
ZDB-ID	1068461-x
ISSN	0219-3108 ; 1015-9584
ISSN (online)	0219-3108
ISSN	1015-9584
DOI	10.1016/j.asjsur.2022.09.074
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Article ; Online: Computational studies of the principle of dynamic-change-driven protein interactions.

Li, Zhen-Lu / Mattos, Carla / Buck, Matthias

Structure (London, England : 1993)

2022 Volume 30, Issue 6, Page(s) 909–916.e2

Abstract: Dynamic allostery emphasizes a role of entropy change manifested as a sole change in protein fluctuations without structural changes. This kind of entropy-driven effect remains largely understudied. The most significant examples involve protein-ligand ... ...

Abstract	Dynamic allostery emphasizes a role of entropy change manifested as a sole change in protein fluctuations without structural changes. This kind of entropy-driven effect remains largely understudied. The most significant examples involve protein-ligand interactions, leaving protein-protein interactions, which are critical in signaling and other cellular events, largely unexplored. Here we study an example of how protein-protein interaction (binding of Ras to the Ras binding domain [RBD] of the effector protein Raf) affects a subsequent protein association process (Ras dimerization) by quenching Ras internal motions through dynamic allostery. We also investigate the influence of point mutations or ambient temperature, respectively, on the protein dynamics and interaction of two other systems: in adenylate kinase (ADK) and in the EphA2 SAM:Ship2 SAM complex. Based on these examples, we postulate that there are different ways in which dynamic-change-driven protein interactions are manifested and that it is likely a general biological phenomenon.
MeSH term(s)	Dimerization ; Ligands ; Protein Binding ; Proteins
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2022-04-04
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2022.03.008
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Article ; Online: Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein-Protein Interactions.

Li, Zhen-Lu / Buck, Matthias

Journal of chemical theory and computation

2019 Volume 15, Issue 8, Page(s) 4318–4331

Abstract: The relative prevalence of native protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we develop a scheme for scaling the protein-water ... ...

Abstract	The relative prevalence of native protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we develop a scheme for scaling the protein-water interaction in the CHARMM36 force field, in order to better fit the solvation free energy of amino acids side-chain analogues. We find that the molecular dynamics simulation with the scaled force field, CHARMM36s, as well as a recently released version, CHARMM36m, effectively improve on the overly sticky association of proteins, such as ubiquitin. We investigate the formation of a heterodimer protein complex between the SAM domains of the EphA2 receptor and the SHIP2 enzyme by performing a combined total of 48 μs simulations with the different potential functions. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% with CHARMM36s, and to 18.3% with CHARMM36m. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a preorientation guided by Coulomb interactions, consistent with an electrostatic steering mechanism. In 12 cases, the complex could directly transform to the native protein interaction surfaces with only small adjustments in domain orientation. In the other 13 cases, orientational and/or translational adjustments are needed to reach the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a dissociation followed by a reassociation to the correct complex structure is still rare. Instead, the remaining non-native complexes undergo configurational changes/surface searching, which, however, rarely leads to native structures on a time scale of 250 ns. These observations provide a rich picture of the mechanisms of protein-protein complex formation and suggest that computational predictions of native complex PPIs could be improved further.
MeSH term(s)	Humans ; Molecular Dynamics Simulation ; Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry ; Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism ; Protein Binding ; Protein Conformation ; Protein Interaction Maps ; Protein Multimerization ; Proteins/chemistry ; Proteins/metabolism ; Receptor, EphA2/chemistry ; Receptor, EphA2/metabolism ; Static Electricity ; Thermodynamics ; Ubiquitin/chemistry ; Ubiquitin/metabolism ; Water/metabolism
Chemical Substances	Proteins ; Ubiquitin ; Water (059QF0KO0R) ; Receptor, EphA2 (EC 2.7.10.1) ; INPPL1 protein, human (EC 3.1.3.86) ; Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases (EC 3.1.3.86)
Language	English
Publishing date	2019-07-23
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.9b00195
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Article ; Online: The AP2/ERF transcription factor MdDREB2A regulates nitrogen utilisation and sucrose transport under drought stress.

Zhang, Ting-Ting / Lin, Yu-Jing / Liu, Hao-Feng / Liu, Ya-Qi / Zeng, Zhi-Feng / Lu, Xiao-Yan / Li, Xue-Wei / Zhang, Zhen-Lu / Zhang, Shuai / You, Chun-Xiang / Guan, Qing-Mei / Lang, Zhao-Bo / Wang, Xiao-Fei

Plant, cell & environment

2024 Volume 47, Issue 5, Page(s) 1668–1684

Abstract: Drought stress is one of the main environmental factors limiting plant growth and development. Plants adapt to changing soil moisture by modifying root architecture, inducing stomatal closure, and inhibiting shoot growth. The AP2/ERF transcription factor ...

Abstract	Drought stress is one of the main environmental factors limiting plant growth and development. Plants adapt to changing soil moisture by modifying root architecture, inducing stomatal closure, and inhibiting shoot growth. The AP2/ERF transcription factor DREB2A plays a key role in maintaining plant growth in response to drought stress, but the molecular mechanism underlying this process remains to be elucidated. Here, it was found that overexpression of MdDREB2A positively regulated nitrogen utilisation by interacting with DRE cis-elements of the MdNIR1 promoter. Meanwhile, MdDREB2A could also directly bind to the promoter of MdSWEET12, which may enhance root development and nitrogen assimilation, ultimately promoting plant growth. Overall, this regulatory mechanism provides an idea for plants in coordinating with drought tolerance and nitrogen assimilation to maintain optimal plant growth and development under drought stress.
MeSH term(s)	Plant Proteins/genetics ; Plant Proteins/metabolism ; Droughts ; Plants, Genetically Modified/metabolism ; Promoter Regions, Genetic ; Sucrose/metabolism ; Gene Expression Regulation, Plant ; Stress, Physiological/genetics
Chemical Substances	Plant Proteins ; Sucrose (57-50-1)
Language	English
Publishing date	2024-01-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.14834
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