Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Mapping protein–protein interactions by double-REDOR-filtered magic angle spinning NMR spectroscopy

REDOR-based experiments with simultaneous ¹H–¹³C and ¹H?¹⁵N dipolar dephasing are explored for investigating intermolecular protein–protein interfaces in complexes formed by a U–¹³C,¹⁵N-labeled protein and its natural abundance binding partner. The application of a double-REDOR filter (dREDOR) results in a complete dephasing of proton magnetization in the U–¹³C,¹⁵N-enriched molecule while the proton magnetization of the unlabeled binding partner is not dephased. This retained proton magnetization is then transferred across the intermolecular interface by ¹H–¹³C or ¹H–¹⁵N cross polarization, permitting to establish the residues of the U–¹³C,¹⁵N-labeled protein, which constitute the binding interface. To assign the interface residues, this dREDOR-CPMAS element is incorporated as a building block into ¹³C–¹³C correlation experiments. We established the validity of this approach on U–¹³C,¹⁵N-histidine and on a structurally characterized complex of dynactin’s U–¹³C,¹⁵N-CAP-Gly domain with end-binding protein 1 (EB1). The approach introduced here is broadly applicable to the analysis of intermolecular interfaces when one of the binding partners in a complex cannot be isotopically labeled.     

A study of the genetic polymorphism of human inter-alpha-trypsin-inhibitor (ITI) in the Han population,Chengdu, China

Phenotypes of inter-alpha-trypsin-inhibitor (ITI) have been determined by isoelectric focusing on polyacrylamide gels followed by immunofixation. The phenotype frequencies of ITI in the Han population in Chengdu, P. R. China have been investigated using this method. In addition, family studies have been conducted in 21 families. The results show that ITI is polymorphic in the Han population in Chengdu, China. The allele frequencies are as follows: ITI*1 = 0.5763. ITI*2 = 0.4107, ITI*3 = 0.0130. ITI is thus a new and promising genetic marker that can be used in the field of forensic haematogenetics.     

Umbilical cord-derived mesenchymal stem cell transplantation for treating elderly vascular dementia

This study aimed to determine the efficacy and safety of human umbilical cord-derived mesenchymal stem cell (HUC-MSC) transplantation for treating elderly vascular dementia (VaD). Ten VaD patients (average age, 73.88 years old) were treated. HUC-MSCs were isolated, cultured, stem cell-marked, and qualified and administered as a 3-course intravenous infusion to these patients. The Mini-Mental State Exam (MMSE) and the Activities of Daily Living Index (Barthel Index scoring system) were used to assess the cognitive function and daily living activity improvements in these patients before transplantation (T0), 3 months after transplantation (T1), and 6 months after transplantation (T2). The MMSE and Barthel Index scores were 15.80 ± 5.49 and 42.00 ± 9.33 points at T0, respectively, and were significantly different when compared with those at T1 (19.20 ± 6.39 and 49.20 ± 10.86 points, respectively, P < 0.05), whereas there was no difference when compared with those at T2 (14.00 ± 6.55 and 40.70 ± 10.37 points, respectively, P > 0.05). HUC-MSC transplantation was safe and feasible for VaD and improved early cognitive functions and daily living activities in VaD patients to a certain extent, thus improving patients’ quality of life.     

Identification and characterization of ten polymorphic microsatellite loci in the red panda Ailurus fulgens

Ten polymorphic microsatellite loci were characterized from two genomic DNA-enriched libraries of the red panda (Ailurus fulgens). The number of observed alleles among 35 samples of red pandas ranged from five to 12. Observed and expected heterozygosities were 0.286–0.971 and 0.443–0.894, and the mean polymorphic information content was 0.712. All loci followed Hardy–Weinberg expectations except Aifu-14 and Aifu-16, which may due to the presence of inbreeding or null alleles. Three pairs of loci exhibited significant linkage disequilibrium after Bonferroni correction for multiple comparisons. These microsatellites would be useful to strengthen population management, genetic diversity exploration, and demographic history speculation of this species.