Biomedical subjects

Guohui Li

Publications and source records attributed to Guohui Li.

10 recordsLinked to original sources

PubMed2025

Decoding Arginine Dimethylation Isomers via pH-Tuned Reactivity with Methylglyoxal: A Chemical Approach for Functional Proteomics.

Arginine dimethylation, encompassing asymmetric and symmetric configurations, represents a fundamental post-translational modification. Despite sharing identical chemical formulas, the two arginine dimethylation isomers exhibit different or even opposite biological effects. Therefore, it is necessary to determine their specific structure before conducting a further biological investigation. However, current methods for arginine dimethylation analysis face great challenges in efficient isomer differentiation, preventing the functional investigation of arginine dimethylation. To overcome this obstacle, herein, we introduce a novel chemical strategy leveraging pH-tuned reactivity with methylglyoxal (MGO) to decode these dimethylation isomers. By utilizing molecular dynamics simulation analysis, we revealed the different chemical reactivities of asymmetrically and symmetrically dimethylated arginine when reacted with MGO at different pH conditions. This property enabled the development of a pH-tuned chemical strategy by combining the MGO reaction with boronate affinity enrichment to simultaneously enrich and differentiate the dimethylation isomers. This strategy can effectively distinguish dimethylated arginine isomers in complex cell samples, and the good feasibility of this strategy was verified by orthogonal validation with the neutral loss. Of the obtained data set, this strategy identified sDMA at R112 of SNRPN, which is confirmed to be modified by PRMT5. Further functional analysis reveals its crucial role in maintaining protein stability and in regulating spliceosome assembly. Overall, by transforming the inherent pH sensitivity of MGO reactions into a powerful analytical tool, our work establishes the first chemical platform for functional proteomic dissection of arginine dimethylation isomers, which paves the way for further regulating mechanism investigations of protein methylation.

Pyruvaldehyde↗

PubMed2004

Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase.

The structural flexibilities of two molecular machines, myosin and Ca(2+)-ATPase, have been analyzed with normal mode analysis and discussed in the context of their energy conversion functions. The normal mode analysis with physical intermolecular interactions was made possible by an improved implementation of the block normal mode (BNM) approach. The BNM results clearly illustrated that the large-scale conformational transitions implicated in the functional cycles of the two motor systems can be largely captured with a small number of low-frequency normal modes. Therefore, the results support the idea that structural flexibility is an essential part of the construction principle of molecular motors through evolution. Such a feature is expected to be more prevalent in motor proteins than in simpler systems (e.g., signal transduction proteins) because in the former, large-scale conformational transitions often have to occur before the chemical events (e.g., ATP hydrolysis in myosin and ATP binding/phosphorylation in Ca(2+)-ATPase). This highlights the importance of Brownian motions associated with the protein domains that are involved in the functional transitions; in this sense, Brownian molecular machines is an appropriate description of molecular motors, although the normal mode results do not address the origin of the ratchet effect. The results also suggest that it might be more appropriate to describe functional transitions in some molecular motors as intrinsic elastic motions modulating local structural changes in the active site, which in turn gets stabilized by the subsequent chemical events, in contrast with the conventional idea of local changes somehow getting amplified into larger-scale motions. In the case of myosin, for example, we favor the idea that Brownian motions associated with the flexible converter propagates to the Switch I/II region, where the salt-bridge formation gets stabilized by ATP hydrolysis, in contrast with the textbook notion that ATP hydrolysis drives the converter motion. Another useful aspect of the BNM results is that selected low-frequency normal modes have been identified to form a set of collective coordinates that can be used to characterize the progress of a significant fraction of large-scale conformational transitions. Therefore, the present normal mode analysis has provided a stepping-stone toward more elaborate microscopic simulations for addressing critical issues in free energy conversions in molecular machines, such as the coupling and the causal relationship between collective motions and essential local changes at the catalytic active site where ATP hydrolysis occurs.

Algorithms↗

PubMed2003

What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations.

Potential of mean force (PMF) simulations with a hybrid QM/MM potential function were used to analyze the catalytic mechanism of human cyclophilin A (CypA). PMF calculations were performed for proline isomerization of peptides in solution, the wild-type CypA, and several CypA mutants. With an approximate density functional theory, the self-consistent-charge density functional tight binding (SCC-DFTB) as the QM level, and CHARMM 22 force field as MM, satisfactory energetics compared to available experiments were obtained. Calculations for the Arg55Ala and zero-charge-Arg55 mutants clearly indicated that Arg 55 significantly stabilizes the isomerization transition state through electrostatic interactions. However, the decrease in the average distance (thus the increase in interaction) between Arg 55 and the substrate amide N in going from the stable states to the transition state is mainly due to the pyramidalization of the amide N rather than motions associated with Arg 55. Although the nanosecond simulations cannot exclude the existence of sub-millisecond collective motions proposed on the basis of recent elegant NMR relaxation and line-shape analyses, the energetics obtained for the various enzyme systems here indicate that the contribution from motions of active site residues to catalysis is expected to be small. Instead, the present simulations support that the structural stability rather than mobility of the preorganized active site is more important. Through hydrogen-bonding interactions among the substrate, Arg 55, Gln 63, and Asn 102, the active site of the wild-type enzyme is structurally very stable and puts Arg 55 in a favorable position to perform its catalytic role in the transition state. This is further illustrated with the somewhat unexpected prediction that Arg55Lys is largely catalytically inactive, because Lys does not have the unique bifurcating construct of the guanidino group in Arg and thus the active site of Arg55Lys cannot accommodate Lys in a position capable of providing electrostatic stabilization of the isomerization transition state. Among all the enzyme systems studied, the wild-type CypA is the only one that selects the syn/exo transition state, while the syn/endo conformation is also present in the mutants, which is another reason for their higher barriers. Finally, the present analysis indicated that the population of near-attack-conformations (NAC) is not relevant to catalysis in CypA.

Arginine↗

PubMed2003

Human epithelial cancers secrete immunoglobulin g with unidentified specificity to promote growth and survival of tumor cells.

Immunoglobulins (Igs) are found thus far only to be produced by differentiated B lymphocytes. By immunohistochemistry analysis, in situ hybridization, and laser capture microdissection-assisted single-cell PCR, we demonstrate that human cancers of epithelial origin, including carcinomas of breast, colon, liver, lung, established epithelial cancer lines, as well as some normal lung tissues, also produce IgG in both cytoplasmic and secreted forms. Furthermore, blockade of tumor-derived IgG by either antisense DNA or antihuman IgG antibody increased programmed cell death and inhibited growth of cancer cells in vitro. More importantly, administration of antihuman IgG antibody also suppressed the growth of an IgG-secreting carcinoma line in immunodeficient nude mice. Our results support a role of tumor-derived IgG as growth factor for epithelial cancers. Prevalent expression of IgG in human carcinomas and its growth-promoting functions may have important implications in growth regulation and targeted therapy of human cancers.

Amino Acid Sequence↗

PubMed2002

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase.

A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the hessian matrix into local translation/rotation basis vectors and, therefore, dramatically reduces the size of the matrix involved in diagonalization. In the current work, by constructing the atomic hessian elements required in the projection operation on the fly, the memory requirement for the BNM approach has been significantly reduced from that of standard normal mode analysis and previous implementation of BNM. As a result, low frequency modes, which are of interest in large-scale conformational changes of large proteins or protein-nucleic acid complexes, can be readily obtained. Comparison of the BNM results with standard normal mode analysis for a number of small proteins and nucleic acids indicates that many properties dominated by low frequency motions are well reproduced by BNM; these include atomic fluctuations, the displacement covariance matrix, vibrational entropies, and involvement coefficients for conformational transitions. Preliminary application to a fairly large system, Ca(2+)-ATPase (994 residues), is described as an example. The structural flexibility of the cytoplasmic domains (especially domain N), correlated motions among residues on domain interfaces and displacement patterns for the transmembrane helices observed in the BNM results are discussed in relation to the function of Ca(2+)-ATPase. The current implementation of the BNM approach has paved the way for developing efficient sampling algorithms with molecular dynamics or Monte Carlo for studying long-time scale dynamics of macromolecules.

Algorithms↗

PubMed2002

[The relationship between arterial blood oxygen pressure and the changes in blood biochemical indices after partial liquid ventilation in canine inhalation injury].

OBJECTIVE: To explore the therapeutic effects of partial liquid ventilation on canine inhalation injury. METHODS: Mongrel dogs were inflicted with steam inhalation injury and were employed as the model. Partial liquid ventilation was accomplished by slow instillation of into the lungs. The changes in blood superoxide dismutase (SOD), malondialdehyde (MDA), nitric oxide (NO) and arterial oxygen pressure (PaO(2)) were determined. RESULTS: The blood levels of MDA and NO at 2 postburn hours (PBHs) increased obviously but those of SOD and PaO(2) decreased significantly when compared with those before injury (P < 0.05). The blood levels of SOD, MDA, NO and PaO(2) recovered to near preinjury levels after partial liquid ventilation. CONCLUSION: Partial liquid ventilation might be helpful in the management of inhalation injury by raising blood oxygen pressure, antagonizing lipid peroxidation and reducing the in vivo NO production.

Animals↗

PubMed2002

[Respiratory support with high frequency jet ventilation in severely burned patients with inhalation injury during early postburn stage].

OBJECTIVE: To observe the effects of respiratory support with high frequency jet ventilation (HFJV) in severely burned patients with inhalation injury during early postburn stage. METHODS: Twenty severely burned patients with TBSA of 79.6 +/- 29.3% and inhalation injury were enrolled in the study. Nineteen cases received tracheostomy after admission and only one received nasal intubation. All the patients underwent HFJV to correct hypoxia. The changes in blood gas analysis, respiratory rate and pulse were recorded before and 11 days after the ventilation. RESULTS: Tracheostomy was performed on 2.7 +/- 2.4 postburn days (PBDs), and HFJV was given during 4.4 +/- 2.9 PBDs. PaO(2) was evidently higher during 1 - 3 days after HFJV than that before the ventilation (P < 0.01) and remained at high level for 1 week after HFJV. There was no change in PaCO(2), respiratory rate and pulse during the ventilation. CONCLUSION: HFJV was beneficial in improving oxygenation and without any obvious side effects during the early management of severely burned patients with inhalation injury. This might be an optimal respiratory support pattern.

Adult↗

PubMed2002

[An exploration of the preventive effects on lanthanum chloride on enteral bacterial translocation in scalded rats].

OBJECTIVE: To explore the preventive effect of lanthanum chloride on enteral bacterial translocation in scalded rats. METHODS: Ninety Sprague-Dawley (SD) rats were employed in the study and randomly divided into three groups, i.e. normal control (A), burn control (B) and treatment (C) groups. Plasmid PUC19 labelled by JM109 was transfected to Escherichia coli (E. coli), so that restriction endonuclease finger - print image spectrum analysis could be applied to the tracing and quantification of the translocation of E. coli from intestine to mesenteric lymph nodes (MLNs) and blood. The intestinal tissue contents of endotoxin (ET), nitric oxide (NO), nitric oxide synthase (NOS), malondialdehyde (MDA) and superoxide dismutase (SOD) were determined. RESULTS: It was identified that the bacteria in MLNs and blood exhibited the same gene map with those from gastric gavage in B and C groups. But the bacterial quantity in MLNs in C group on 3 postburn day (PBD) was much lower than that in B group (P < 0.05). The intestinal MDA content in C group on 1 and 3 PBDs was obviously higher than that in B group (P < 0.05). CONCLUSION: Bacteria (E. coli) could be translocated from gut to MLNs and blood, which could be evidently alleviated by lanthanum chloride by means of its bactericidal property, inhibition of NOS activity, so that NO production decreased, and its ability to increase SOD activity leading to less production of MDA.

Animals↗

PubMed2002

[The influence of lanthanum chloride on the TNFalpha expression of murine peritoneal macrophages stimulated by lipopolysaccharide].

OBJECTIVE: To explore the influence of lanthanum chloride on the TNFalpha expression of murine peritoneal macrophages stimulated by lipopolysaccharide (LPS). METHODS: Murine peritoneal macrophages (Mphi) were isolated, cultured and then stimulated by LPS. The influence of lanthanum chloride on the TNFalpha secretion and TNFalphamRNA expression of murine Mphi stimulated by LPS was determined by ELISA method and SYBR green fluorescence quantitative RT-PCR. Forty BALB/C mice were randomly divided into two groups and were treated by lethal dose of LPS and lanthanum chloride processed LPS, respectively. The mortality within 7 days was observed. RESULTS: The TNFalpha secretion and TNFalphamRNA expression level of the Mphi from mice treated by lanthanum chloride processed LPS were obviously lower than those by LPS only (P < 0.01). The mortality of the mice treated by lethal dose of LPS which has been processed by lanthanum chloride was significantly lower than that by lethal dose of LPS only. CONCLUSION: Lanthanum chloride possessed the capacity of lowering down the toxicity of LPS and inhibiting the TNFalpha secretion and TNFalphamRNA expression in murine Mphi stimulated by LPS.

Animals↗

PubMed2002

[The influence of high frequency partial liquid ventilation on the cardiopulmonary function in dogs with inhalation injury].

OBJECTIVE: To investigate the influence of high frequency partial liquid ventilation (HFJV) on the cardiopulmonary function in dogs with inhalation injury. METHODS: Sixteen mongrel dogs inflicted by hot steam inhalation were subjected to severe inhalation injury and were randomly divided into control (C) and treatment (T) groups. The dogs in both groups were all given HFJV. In addition, the dogs in T group were simultaneously supplied with perfluorocarbon liquid (3 ml/kg) into the lungs slowly via tracheal intubation for liquid ventilation. The blood gas analysis, pulmonary compliance, airway resistance and hemodynamic parameters were determined at 30, 60 and 90 minutes after ventilation. RESULTS: The PaO(2) in T group increased progressively, which was significantly higher than the post-injury value at all time points (P < 0.05). While the PaO(2) in C group exhibited no difference to the post-injury value at all time points. The PaCO(2) in T group increased obviously and was higher than the post-injury value at 60 and 90 post-ventilation minutes (P < 0.05). Furthermore, the PaO(2) in all the time points in T group was a little higher than that in C group (P > 0.05) and PaCO(2) in T group was much higher than that in C group at 90 min after ventilation (P < 0.05). But there was no difference between the two groups in terms of dynamic/static pulmonary compliance and airway resistance as well as the hemodynamics. CONCLUSION: Compared with simple HFJV, high frequency partial liquid ventilation seemed to be beneficial to the oxygenation after inhalation injury and to be no influence on the hemodynamics.

Airway Resistance↗