Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation

Somatic hypermutation (SHM), initiated by activation-induced cytidine deaminase (AID), generates mutations in the antibody-coding sequence to allow affinity maturation. Why these mutations intrinsically focus on the three nonconsecutive complementarity-determining regions (CDRs) remains enigmatic. Here, we found that predisposition mutagenesis depends on the single-strand (ss) DNA substrate flexibility determined by the mesoscale sequence surrounding AID deaminase motifs. Mesoscale DNA sequences containing flexible pyrimidine-pyrimidine bases bind effectively to the positively charged surface patches of AID, resulting in preferential deamination activities. The CDR hypermutability is mimicable in in vitro deaminase assays and is evolutionarily conserved among species using SHM as a major diversification strategy. We demonstrated that mesoscale sequence alterations tune the in vivo mutability and promote mutations in an otherwise cold region in mice. Our results show a non-coding role of antibody-coding sequence in directing hypermutation, paving the way for the synthetic design of humanized animal models for optimal antibody discovery and explaining the AID mutagenesis pattern in lymphoma.

A Cautionary Tale: Florid Splenic γδ T-cell Proliferation and False-Positive T-cell Clonality by PCR Leads to a Grave Misdiagnosis

The discrimination of benign from malignant lymphoproliferative disorders is sometimes difficult because there can be overlap in their histological and immunophenotypic features. In such situations, molecularly based clonality testing is often used to discriminate benign (polyclonal) from malignant (monoclonal) processes. Clonality testing by polymerase chain reaction (PCR) has a number of pitfalls that may result in spurious results. Here we report the case of a woman diagnosed by 2 major academic institutions with hepatosplenic T-cell lymphoma based on a dense infiltration of the spleen by a γδ T-cell population with mild cytologic atypia, resulting in expansion of the splenic red pulp, and a positive T-cell receptor clonality test by PCR. There was likewise mild involvement of the liver and bone marrow by the "atypical" T-cell population. Close attention to her uncharacteristically well clinical appearance led to repeat T-cell receptor clonality testing using next-generation sequencing. Definitive demonstration of polyclonality by this test showed that she in fact did not have hepatosplenic T-cell lymphoma but rather a reactive condition, and allogeneic stem cell transplantation could be safely avoided. As molecular clonality testing is widely used in the practice of hematology, this case brings attention to the pitfalls of clonality testing by PCR that practitioners may encounter. It is therefore a cautionary tale highlighting the need for critical interpretation of test results in full clinical context.

COVID-19 vaccines for patients with cancer: benefits likely outweigh risks

Less than a year since the start of the COVID-19 pandemic, ten vaccines against SARS-CoV-2 have been approved for at least limited use, with over sixty others in clinical trials. This swift achievement has generated excitement and arrives at a time of great need, as the number of COVID-19 cases worldwide continues to rapidly increase. Two vaccines are currently approved for full use, both built on mRNA and lipid nanotechnology platforms, a success story of mRNA technology 20 years in the making. For patients with cancer, questions arise around the safety and efficacy of these vaccines in the setting of immune alterations engendered by their malignancy and/or therapies. We summarize the current data on leading COVID-19 vaccine candidates and vaccination of patients undergoing immunomodulatory cancer treatments. Most current cancer therapeutics should not prevent the generation of protective immunity. We call for more research in this area and recommend that the majority of patients with cancer receive COVID vaccinations when possible.

Checking the Hippo in Sarcomatoid Renal Cell Carcinoma with Immunotherapy

Subset analysis of patients with sarcomatoid renal cell carcinoma (sRCC) included in the CheckMate 214 trial of ipilimumab-nivolumab versus sunitinib showed improved outcomes in sRCC with ipilimumab-nivolumab. The use of checkpoint inhibitor-based regimens in sRCC, for which therapeutic options were once limited, is further supported by additional clinical trials.See related article by Tannir et al., p. 78.

BCR selection and affinity maturation in Peyer's patch germinal centres

The antigen-binding variable regions of the B cell receptor (BCR) and of antibodies are encoded by exons that are assembled in developing B cells by V(D)J recombination1. The BCR repertoires of primary B cells are vast owing to mechanisms that create diversity at the junctions of V(D)J gene segments that contribute to complementarity-determining region 3 (CDR3), the region that binds antigen1. Primary B cells undergo antigen-driven BCR affinity maturation through somatic hypermutation and cellular selection in germinal centres (GCs)2,3. Although most GCs are transient3, those in intestinal Peyer's patches (PPs)-which depend on the gut microbiota-are chronic4, and little is known about their BCR repertoires or patterns of somatic hypermutation. Here, using a high-throughput assay that analyses both V(D)J segment usage and somatic hypermutation profiles, we elucidate physiological BCR repertoires in mouse PP GCs. PP GCs from different mice expand public BCR clonotypes (clonotypes that are shared between many mice) that often have canonical CDR3s in the immunoglobulin heavy chain that, owing to junctional biases during V(D)J recombination, appear much more frequently than predicted in naive B cell repertoires. Some public clonotypes are dependent on the gut microbiota and encode antibodies that are reactive to bacterial glycans, whereas others are independent of gut bacteria. Transfer of faeces from specific-pathogen-free mice to germ-free mice restored germ-dependent clonotypes, directly implicating BCR selection. We identified somatic hypermutations that were recurrently selected in such public clonotypes, indicating that affinity maturation occurs in mouse PP GCs under homeostatic conditions. Thus, persistent gut antigens select recurrent BCR clonotypes to seed chronic PP GC responses.

Deployment of Transchromosomal Bovine for Personalized Antimicrobial Therapy

For decades, intravenous immunoglobulin (IVIg) has provided safe and effective therapy for immunodeficient patients. This proof-of-principle study describes a novel approach to generate personalized IVIg for chronic, antibiotic-resistant infection in real time.

Kidney Transplantation Using Expanded-Criteria Deceased Donors: A Comparison With Ideal Deceased Donors and Non-Expanded-Criteria Deceased Donors

PURPOSE

The use of expanded-criteria deceased-donor (ECD) kidneys must be evaluated within the objective perspective of critical organ shortage and graft function and survival. In this study, we aimed to compare the clinical outcomes of ECD reliance with concurrent use of ideal-criteria deceased donors (IDDs) and non-ECDs in adult renal transplantation.

METHODS

Between February 2000 and December 2015, we analyzed 405 deceased-donor renal transplants, specifically 129 grafts (31.9%) from ECDs, 233 grafts (57.5%) from non-ECDs, and 43 grafts (10.6%) from IDDs. ECDs were classified according to the United Network for Organ Sharing guidelines, while an IDD was defined as a younger person (10-39 years of age) with no medical risk factors who died from a traumatic head injury. Donor and recipient risk factors were separately analyzed and correlated with recipient graft function, and survival was evaluated.

RESULTS

ECDs were older (56.8 ± 6.3 years); showed increased incidence of hypertension, diabetes, and cerebrovascular brain death; and had a higher pre-retrieval serum creatinine level than the other groups. ECD kidney recipients were also older (50.6 ± 9.8 years), had a shorter waiting time (P = .031), and demonstrated a low frequency of re-transplantation (P = .028). Long-term renal function followed longitudinally was lower in ECD kidney recipients until five years after transplantation, while the glomerular filtration rate (GFR) level at 7 and 10 years did not differ significantly among the groups (P = .074 and .262, respectively). There were no significant differences in terms of graft survival (P = .394) or patient survival (P = .737) among the groups.

CONCLUSIONS

Although the long-term renal function followed longitudinally was lower in ECD kidney recipients, the use of renal grafts from ECDs is an acceptable method to resolve the disparity of critical organ shortage. However, the classification of the high-risk group should be updated with consideration given to differences in regional characteristics.

Pharmacokinetics of Mycophenolic Acid after Intravenous Administration of Mycophenolate Mofetil to Healthy Cats

Background

Mycophenolate mofetil (MMF), the prodrug of mycophenolic acid (MPA), is becoming increasingly popular as an alternative immunosuppressant in feline medicine. Pharmacokinetic information is not available for cats.

Objective

The purpose of this study was to determine whether MMF is biotransformed into the active metabolite MPA and to evaluate the disposition of MPA after a 2‐hour constant rate intravenous (IV) infusion of MMF in healthy cats.

Animals

Healthy cats (n = 6).

Methods

This was a prospective pilot study. All cats were administered MMF at 20 mg/kg every 12 hours over a 2‐hour constant rate infusion for 1 day. The concentrations of MPA and its derivatives in blood were determined using a validated UHPLC–UV method.

Results

All cats biotransformed MMF into MPA. The mean AUC_0‐14 h ranged from 6 to 50 h*mg/L after IV dosing of MMF. Transient large bowel diarrhea was recorded in 2 of 6 cats after medication administration.

Conclusion and Clinical Importance

The disposition of MPA in plasma was highly variable, which could result in high interindividual variability in the safety and efficacy of treatment with MMF in cats.

AID Recognizes Structured DNA for Class Switch Recombination

Activation-induced cytidine deaminase (AID) initiates both class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. Mechanisms of AID targeting and catalysis remain elusive despite its critical immunological roles and off-target effects in tumorigenesis. Here, we produced active human AID and revealed its preferred recognition and deamination of structured substrates. G-quadruplex (G4)-containing substrates mimicking the mammalian immunoglobulin switch regions are particularly good AID substrates in vitro. By solving crystal structures of maltose binding protein (MBP)-fused AID alone and in complex with deoxycytidine monophosphate, we surprisingly identify a bifurcated substrate-binding surface that explains structured substrate recognition by capturing two adjacent single-stranded overhangs simultaneously. Moreover, G4 substrates induce cooperative AID oligomerization. Structure-based mutations that disrupt bifurcated substrate recognition or oligomerization both compromise CSR in splenic B cells. Collectively, our data implicate intrinsic preference of AID for structured substrates and uncover the importance of G4 recognition and oligomerization of AID in CSR.

Establishment of reference ranges and evaluation of in vitro concentration-dependent platelet inhibition by acetylsalicylic acid for multiple electrode impedance aggregometry in healthy dogs

Acetylsalicylic acid (ASA, aspirin) is an antiplatelet medication used for prevention of thromboembolism. Effects of ASA appear to vary widely between dogs, but the underlying mechanisms are not understood. The Multiplate analyzer is a newer form of whole-blood impedance aggregometry recently validated for use in healthy dogs. A method utilizing this instrument to measure ASA effects on platelet function has not been established. The goals of this study were to establish reference ranges for the Multiplate in healthy dogs and secondly, to develop a technique to determine the in vitro concentration of ASA needed to cause 50% inhibition of platelet aggregation (IC50). Reference ranges established from 40 dogs at multiple test times for three agonists were consistent with previously published values. In vitro IC50 values were calculated using the sigmoid E_max model in 20 healthy dogs on two occasions to determine individual repeatability. Calculated in vitro IC50 demonstrated four ASA response groups: responder (n = 16), poor responder (n = 1), variable responder (n = 2), and nonresponder (n = 1). Multiplate within-assay variability was  <10% for area under the curve (AUC), and between-assay baseline AUC variability was  <15%. The described technique allowed for determination of an in vitro IC50 for ASA in dogs using a multiple electrode impedance aggregometer.

Formalin Instillation for Hemorrhagic Radiation Proctitis

Although formalin instillation has been proven to be an effective treatment of hemorrhagic radiation proctitis, different tech niques with varying success rates have been reported. The aim of this study was to assess our experience with formalin instillation for the treatment of radiation proctitis. After Institutional Review Board approval, all patients who presented with radiation proctitis and were treated with 4% formalin instillation were identified from a prospective database. Techniques of instillation were as follows: a formalin-soaked sponge stick was applied via a proctoscope (SS) and placed at each quadrant with a mean contact of 2.5 minutes (range, 0.5-3 minutes), or the formalin solution was introduced through a proctoscope in aliquots for a total of 350 to 400 mL irrigation (IR), with a mean contact time of 30 seconds in each aliquot. The patients were divided into two groups according to the method of formalin instillation and their outcomes were compared. Between March 1995 and September 2003, 21 patients who underwent formalin treatment were identified: 17 patients were in the SS and 4 patients were in the IR group. The mean age was 74.8 6.4 years and 70.5 6.8 years and the male/female ratio was 16:1 and 3:1 in the SS and IR groups, respectively. Indications for radiation therapy were prostate cancer in 19 patients: 16 (95.1%) SS patients and 3 (75%) IR patients. Four (23.5%) patients in the SS group were receiving anticoagulants or antiplatelet medications before the procedure. The mean duration of bleeding before formalin instillation was 11.7 months (range, 2-48 months) in the SS and 10.5 months (range, 7-12 months) in the IR group. Sixteen (94.1%) patients in the SS and 4 (100%) in the IR group had previous treatments for radiation proctitis, including hydrocortisone enema, 5-aminosalicylate mesalamine, and endoscopic coagulation. Eight (47.1%) patients in the SS and 2 (50%) in the IR group received a preprocedural blood transfusion, and 1 patient in the SS group required a blood transfusion after the formalin instillation. This patient subsequently underwent restorative proctosigmoidectomy because of persistent bleeding. The mean length of the procedure was 27.1 10.8 minutes in the SS group and 22.5 6.5 minutes in the IR group. The bleeding was successfully stopped on the first attempt in 14 patients (82.4%) in the SS group and 3 (75%) in the IR group. The instillation was repeated in 1 patient (5.9%) in the SS group and in 1 (25%) in the IR group. Four patients (23.5%) in the SS group experienced rectal pain after the procedure. One patient (5.9%) developed a new onset of fecal incontinence, while another (5.9%) had anococcygeal pain accompanied by worsening of fecal incontinence. One patient (25%) in the IR group developed acute colitis consistent with formalin instillation, which was managed by intravenous antibiotics. The patients were followed for a mean of 10 months (range, 1 to 38 months). Formalin instillation is effective in controlling refractory hemorrhage secondary to radiation proctitis.

Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes

In activated B lymphocytes, AID initiates antibody variable (V) exon somatic hypermutation (SHM) for affinity maturation in germinal centers (GCs) and IgH switch (S) region DNA breaks (DSBs) for class-switch recombination (CSR). To resolve long-standing questions, we have developed an in vivo assay to study AID targeting of passenger sequences replacing a V exon. First, we find AID targets SHM hotspots within V exon and S region passengers at similar frequencies and that the normal SHM process frequently generates deletions, indicating that SHM and CSR employ the same mechanism. Second, AID mutates targets in diverse non-Ig passengers in GC B cells at levels similar to those of V exons, definitively establishing the V exon location as "privileged" for SHM. Finally, Peyer's patch GC B cells generate a reservoir of V exons that are highly mutated before selection for affinity maturation. We discuss the implications of these findings for harnessing antibody diversification mechanisms.

The early protective effect of glutamine pretreatment and ischemia preconditioning in renal ischemia-reperfusion injury of rat

BACKGROUND

Heat shock proteins (HSP) play an important role in protecting cells against stress.

METHODS

Using a rat model, we tested the hypothesis that pretreatment with glutamine (Gln) and ischemia preconditioning (IPC) increase the expression of HSP resulting in attenuation of renal ischemia/reperfusion (I/R) injury. Sprague-Dawley rats were randomized into 4 groups [group I, Gln injection (+), IPC (+); group II, Gln injection (+), IPC (-); group III, saline injection (+), IPC (+); group IV, saline injection (+), IPC (-)]. Renal HSP70 expression was determined by Western blotting and kidney function was assessed by blood urea nitrogen and serum creatinine. Renal cross-sections were microscopically examined for tubular necrosis, exfoliation of tubular epithelial cells, cast formation, and monocyte infiltration.

RESULTS

Gln pretreatment increased intrarenal HSP expression (P = .031). In group I, tubulointerstitial abnormalities were clearly slighter compared with the other groups (P < .001).

CONCLUSION

Our experiments suggest that (1) a single dose of Gln could induce HSP expression and (2) IPC could relieve renal I/R injury. In addition, IPC combined with Gln pretreatment had a synergic protective effect against renal I/R injury.

Contrast-enhanced magnetic resonance angiography in the early period after kidney transplantation

Our objective was to evaluate the usefulness of three-dimensional (3-D) contrast-enhanced (CE) magnetic resonance angiography (MRA) to assess renal parenchyma, arterial inflow stenosis, and peritransplant fluid collections in the early period after kidney transplantation (KT). Between January 2010 and April 2011, we examined a consecutive series of 144 renal transplants using 3-D CE MRA at 14 days after KT. MRA showed parenchyma infarctions (n = 17, 11.8%), arterial inflow stenoses (n = 23, 16%), lymphoceles (n = 14, 9.7%), and hematomas (n = 6, 4.2%). The degree of renal transplant artery inflow stenosis was graded qualitatively based on diameter criterion; <50% = mild, 50% to 70% = moderate, and >70% = severe in 10 (6.9%), 5 (3.5%), and 8 (5.6%) subjects, respectively. The study recipients were divided into 3 groups according to the degree of renal artery inflow stenosis (group I: normal; group II: mild and moderate, <70%; group III: severe, >70%). Among group III patients who underwent digital subtraction angiography, 5 had percutaneous transluminal angioplasty or stenting performed after 1 month. Their mean resume creatinine levels at 1, 6, and 12 months after transplantation were not significantly different from those in the other groups (P = .391, .447, .110). The prevalence of graft loss (n = 2) was high in group III (P = .012), although the frequency of acute rejection episodes was not different among the groups (P = .890). The incidences of renal parenchyma infarction, peritransplant fluid collection and arterial inflow stenosis were unexpectedly high in the early period after KT. Thus, 3-D CE MRA provided a rapid global assessment of the renal parenchyma, transplant arterial system, and peritransplant fluid collection that can be helpful to detect or exclude many causes of renal transplant dysfunction.

Glechoma hederacea Suppresses RANKL-mediated Osteoclastogenesis

Glechoma hederacea (GH), commonly known as ground-ivy or gill-over-the-ground, has been extensively used in folk remedies for relieving symptoms of inflammatory disorders. However, the molecular mechanisms underlying the therapeutic action of GH are poorly understood. Here, we demonstrate that GH constituents inhibit osteoclastogenesis by abrogating receptor activator of nuclear κ-B ligand (RANKL)-induced free cytosolic Ca(2+) ([Ca(2+)]i) oscillations. To evaluate the effect of GH on osteoclastogenesis, we assessed the formation of multi-nucleated cells (MNCs), enzymatic activity of tartrate-resistant acidic phosphatase (TRAP), expression of nuclear factor of activated T-cells cytoplasmic 1 (NFATc1), and [Ca(2+)]i alterations in response to treatment with GH ethanol extract (GHE) in primarily cultured bone marrow-derived macrophages (BMMs). Treatment of RANKL-stimulated or non-stimulated BMMs with GHE markedly suppressed MNC formation, TRAP activity, and NFATc1 expression in a dose-dependent manner. Additionally, GHE treatment induced a large transient elevation in [Ca(2+)]i while suppressing RANKL-induced [Ca(2+)]i oscillations, which are essential for NFATc1 activation. GHE-evoked increase in [Ca(2+)]i was dependent on extracellular Ca(2+) and was inhibited by 1,4-dihydropyridine (DHP), inhibitor of voltage-gated Ca(2+) channels (VGCCs), but was independent of store-operated Ca(2+) channels. Notably, after transient [Ca(2+)] elevation, treatment with GHE desensitized the VGCCs, resulting in an abrogation of RANKL-induced [Ca(2+)]i oscillations and MNC formation. These findings demonstrate that treatment of BMMs with GHE suppresses RANKL-mediated osteoclastogenesis by activating and then desensitizing DHP-sensitive VGCCs, suggesting potential applications of GH in the treatment of bone disorders, such as periodontitis, osteoporosis, and rheumatoid arthritis.

The natural history of arteriovenous access and risk factors associated with access thrombosis after successful kidney transplantation

INTRODUCTION

The purpose of this study was to determine the natural history of arteriovenous (AV) access after successful kidney transplantation (KT) and to identify the risk factors of spontaneous access closure in kidney transplant recipients.

METHODS

We performed a retrospective review of 115 patients who underwent KT with functioning access from June 2010 to July 2012. AV access patency was checked and recorded daily during the hospital stay and at every visit to the outpatient clinic. Patients were divided into 2 groups according to the patency of access, and risk factors of access thrombosis were assessed. Access patency was followed up until patency was lost or the study was closed.

RESULTS

At the end of follow-up, 18 (15.7%) AV accesses had spontaneously closed. Mean time to closure was 119 ± 163 days, and 12 of 18 were closed within 90 days after KT. AV access spontaneously closed in 8.5% of male patients, compared with 27.3% of female patients (P = .007), 12.2% of cases with native access compared with 35.3% of cases with artificial access (P = .016), and 11.3% of cases with wrist access compared with 25.7% of cases with elbow access (P = .049). Spontaneously closed AV accesses tended to have a lower mean access flow compared with functioning accesses (P = .019). On multivariate analysis, female sex and AV access flow volume affected spontaneous AV access closure (odds ratio 4.749, 95% confidence interval 1.919-35.383, P = .008; odds ratio 0.998, 95% confidence interval 0.996-0.999, P = .010, respectively).

CONCLUSIONS

Our results suggest that AV access thrombosis occurs more frequently during the early postoperative period, particularly in female patients or patients with low flow access, whereas it is a rare event in male patients or patients with high access flow, especially in the late postoperative period.

New half-lives of r-process Zn and Ga isotopes measured with electromagnetic separation

The β decays of neutron-rich nuclei near the doubly magic (78)Ni were studied at the Holifield Radioactive Ion Beam Facility using an electromagnetic isobar separator. The half-lives of (82)Zn (228±10  ms), (83)Zn (117±20  ms), and (85)Ga (93±7  ms) were determined for the first time. These half-lives were found to be very different from the predictions of the global model used in astrophysical simulations. A new calculation was developed using the density functional model, which properly reproduced the new experimental values. The robustness of the new model in the (78)Ni region allowed us to extrapolate data for more neutron-rich isotopes. The revised analysis of the rapid neutron capture process in low entropy environments with our new set of measured and calculated half-lives shows a significant redistribution of predicted isobaric abundances strengthening the yield of A>140 nuclei.

Does donor kidney to recipient body weight ratio influence long-term outcomes of living-donor kidney transplantation?

This study evaluated the effect of the donor kidney to recipient body weight (Kw/Rw) ratio on long-term graft function and survival. We investigated retrospectively whether there was any association between Kw/Rw ratio and long-term graft survival and function after a follow-up of >10 years. We studied a consecutive series of 123 adult-to-adult living kidney transplants. According to the Kw/Rw ratio, patients were divided into 3 groups: "low" (Kw/Rw <2.85; n = 29), "medium" (2.85 ≤ Kw/Rw < 4.04; n = 63), and "high" (≥4.04; n = 31). Among the 3 groups, the mean serum creatinine levels at 1 and 6 months as well as 1 year after transplantation were significantly lower among patients with a high Kw/Rw ratio than in those with a medium or low ratio, but serum creatinine levels at 3 and 5 years did not differ significantly (P = .394 and 0.620, respectively). Graft survival rates at 5 and 10 years after transplantation were significantly lower in the "low" group. We observed a significant association between Kw/Rw ratio and graft survival (P = .018). The Kw/Rw ratio is an important factor for long-term graft survival and early graft function. However, it did not significantly affect subsequent renal function.

SPA0355, a thiourea analogue, inhibits inflammatory responses and joint destruction in fibroblast-like synoviocytes and mice with collagen-induced arthritis

BACKGROUND AND PURPOSE

NF-κB has been implicated as a therapeutic target for the treatment of rheumatoid arthritis. We previously synthesized a thiourea analogue, SPA0355, which suppressed NF-κB activity. Here we have assessed the anti-inflammatory and anti-arthritic effects of SPA0355.

EXPERIMENTAL APPROACH

We evaluated the effects of SPA0355 on human rheumatoid fibroblast-like synoviocytes in vitro and on collagen-induced arthritis (CIA) in mice in vivo.

KEY RESULTS

In vitro experiments demonstrated that SPA0355 suppressed chemokine production, matrix metalloproteinase secretion and cell proliferation induced by TNF-α in rheumatoid fibroblast-like synoviocytes. In addition, SPA0355 inhibited osteoclast differentiation induced by macrophage colony-stimulating factor and the receptor activator of NF-κB ligand, in bone marrow macrophages. Mice with CIA that were pretreated with SPA0355 had a lower cumulative disease incidence and severity of arthritis, based on hind paw thickness, radiological and histopathological findings, and inflammatory cytokine levels, than mice treated with vehicle. Mice treated with SPA0355, after the onset of CIA, also showed significantly decreased disease incidence and joint oedema. The in vitro and in vivo protective effects of SPA0355 were mediated by inhibition of the NF-κB signalling pathway.

CONCLUSION AND IMPLICATIONS

Taken together, these results suggested that using SPA0355 to block the NF-κB pathway in rheumatoid joints reduced both the inflammatory responses and tissue destruction. Therefore, SPA0355 may have therapeutic value in preventing or delaying joint destruction in patients with rheumatoid arthritis.

The treatment of deep vein thrombosis immediately after kidney transplantation: a case report

Ipsilateral acute iliofemoral deep vein thrombosis (DVT) immediately after kidney transplantation is rare but highly morbid, resulting in allograft failure, rupture, or even death. Treatment modalities for iliofemoral DVT occurring just after transplantation are limited due to bleeding risk and impaired renal function. A 55-year-old woman with end-stage renal disease from hypertension underwent a living nonrelated donor procedure using a kidney from her husband. On postoperative day 1, the patient presented edema and pain in the right lower extremity associated with local heat and redness. The symptoms became aggravated with time. Duplex ultrasonography (US) revealed a DVT involving from the right femoral vein to the common iliac vein and an increased resistive index of 0.96 to 0.97. A venogram using carbon dioxide as the contrast medium showed also same findings as the duplex US. After inferior vena cava filter insertion, percutaneous transluminal thromboaspiration (PTA) was performed with complete removal of the thrombus. Early PTA with carbon dioxide as intravenous contrast material seemed to be an effective and safe procedure to treat this complication.

Differences in the prevalence of colorectal polyps in patients undergoing endoscopic removal of gastric adenoma or early gastric cancer and in healthy individuals

BACKGROUND AND AIMS

We compared the prevalence of adenomatous and cancerous colon polyps in patients who underwent endoscopic removal of gastric neoplasms and in healthy controls.

MATERIALS AND METHODS

This retrospective study reviewed the medical records of 186 patients with gastric neoplasms and 186 healthy subjects from January 2002 to October 2008. The gastric neoplasm group was comprised of patients undergoing endoscopic removal of gastric adenomas or early gastric cancers and serial fiberoptic colonoscopy (FCS) for checkups. The control group was comprised of subjects undergoing fiberoptic esophagogastroduodenoscopy (FEGD) and FCS for general checkup and was matched for age and sex with the gastric neoplasm group. Advanced colonic neoplasm was defined by any of the following: (1) the presence of three or more polyps; (2) polyp size at least 1.0 cm; (3) high-grade dysplasia or adenocarcinoma confirmed by histopathologic examination.

RESULTS

Of the 372 persons, colorectal polyps were detected in 124 (33.3 %), advanced colonic neoplasms in 44 (11.8 %), and adenocarcinomas in 10 (2.7 %). The overall prevalence of adenomatous or cancerous polyps ("all polyps") and the prevalence of advanced colonic neoplasms were significantly higher in the gastric neoplasm group than in the control group (all polyps: 40.9 % in the gastric neoplasm group vs. 25.8 % in the control group, P = 0.002; advanced colonic neoplasms: 15.6 % vs. 8.1 %, P = 0.025). The risk factors for all polyps were age, male sex, diabetes mellitus, and being assigned to the gastric neoplasm group, and those for advanced colonic neoplasms were age and being assigned to the gastric neoplasm group. Confining the analysis to the gastric neoplasm group, the risk factors for all polyps were identical with those for the total group; however, those for advanced colonic neoplasm were different (age vs. diabetes and hypertriglyceridemia).

CONCLUSION

Endoscopists should consider performing routine FCS in patients undergoing endoscopic removal of gastric neoplasms.

Alpha decay of 109I and its implications for the proton decay of 105Sb and the astrophysical rapid proton-capture process

An alpha-decay branch of (1.4+/-0.4) x 10(-4) has been discovered in the decay of 109I, which predominantly decays via proton emission. The measured Q(alpha) value of 3918+/-21 keV allows the indirect determination of the Q value for proton emission from 105Sb of 356+/-22 keV, which is approximately of 130 keV more bound than previously reported. This result is relevant for the astrophysical rapid proton-capture process, which would terminate in the 105Sn(p,gamma)106Sb(p,gamma)107Te(alpha decay)103Sn cycle at the densities expected in explosive hydrogen burning scenarios, unless unusually strong pairing effects result in a 103Sn(p,gamma)104Sb(p,gamma)105Te(alpha decay)101Sn) cycle.

Discovery of 109Xe and 105Te: superallowed alpha decay near doubly magic 100Sn

Two new alpha emitters 109Xe and 105Te were identified through the observation of the 109Xe --> 105Te --> 101Sn alpha-decay chain. The 109Xe nuclei were produced in the fusion-evaporation reaction 54Fe(58Ni,3n)109Xe and studied using the Recoil Mass Spectrometer at the Holifield Radioactive Ion Beam Facility. Two transitions at Ealpha = 4062 +/- 7 keV and Ealpha = 3918 +/- 9 keV were interpreted as the l = 2 and l = 0 transitions from the 7/2+ ground state in 109Xe (T1/2 = 13 +/- 2 ms) to the 5/2+ ground state and a 7/2+ excited state, located at 150 +/- 13 keV in 105Te. The observation of the subsequent decay of 105Te marks the discovery of the lightest known alpha-decaying nucleus. The measured transition energy Ealpha = 4703 +/- 5 keV and half-life T1/2 = 620 +/- 70 ns were used to determine the reduced alpha-decay width delta2. The ratio delta105Te(2)/delta213Po(2) of approximately 3 indicates a superallowed character of the alpha emission from 105Te.

Anticariogenic activity of macelignan isolated from Myristica fragrans (nutmeg) against Streptococcus mutans

The occurrence of dental caries is mainly associated with oral pathogens, especially cariogenic Streptococcus mutans. Preliminary antibacterial screening revealed that the extract of Myristica fragrans, widely cultivated for the spice and flavor of foods, possessed strong inhibitory activity against S. mutans. The anticariogenic compound was successfully isolated from the methanol extract of M. fragrans by repeated silica gel chromatography, and its structure was identified as macelignan by instrumental analysis using 1D-NMR, 2D-NMR and EI-MS. The minimum inhibitory concentration (MIC) of macelignan against S. mutans was 3.9 microg/ml, which was much lower than those of other natural anticariogenic agents such as 15.6 microg/ml of sanguinarine, 250 microg/ml of eucalyptol, 500 microg/ml of menthol and thymol, and 1000 microg/ml of methyl salicylate. Macelignan also possessed preferential activity against other oral microorganisms such as Streptococcus sobrinus, Streptococcus salivarius, Streptococcus sanguis, Lactobacillus acidophilus and Lactobacillus casei in the MIC range of 2-31.3 microg/ml. In particular, the bactericidal test showed that macelignan, at a concentration of 20 microg/ml, completely inactivated S. mutans in 1 min. The specific activity and fast-effectiveness of macelignan against oral bacteria strongly suggest that it could be employed as a natural antibacterial agent in functional foods or oral care products.

Effects of pH and dissolved oxygen on cellulose production by Acetobacter xylinum BRC5 in agitated culture

Acetobacter xylinum BRC5 was cultivated in a jar fermentor using glucose as the sole carbon source. Strain BRC5 oxidized almost all of the glucose to gluconic acid; thereafter, it biosynthesized cellulose by utilizing gluconic acid accumulated in the broth. The optimal pH for metabolizing glucose to gluconic acid was 4.0, while a pH of 5.5 was preferred for cell growth and cellulose production from the accumulated gluconic acid in the medium. Shifting the pH from 4.0 to 5.5 during the cellulose production phase in batch cultures improved cellulose production and reduced the total fermentation time, compared to batch cultures at constant pH. In constant fed-batch culture, 10 g/l of cellulose was obtained from 40 g/l of glucose, a yield which was approximately 2-fold higher than in batch culture with the same initial glucose concentration, even without control of the level of dissolved oxygen. The highest cellulose yield was obtained in fed-batch cultures in which the dissolved oxygen concentration was controlled at 10% saturation. Control of pH and dissolved oxygen to optimal levels was effective for improving the production rate and yield of cellulose, to achieve a high cellulose productivity of 0.3 g cellulose/l x h. Approximately 15 g/l of cellulose was considered to be the highest yield obtainable using conventional fermentors because the culture broth then became too viscous to allow satisfactory aeration.

Kuwanon G: an antibacterial agent from the root bark of Morus alba against oral pathogens

Kuwanon G was isolated from the ethyl acetate fraction of methanol extract of Morus alba and its structure was elucidated by 13C-NMR, 1H-NMR and FAB-MS. Antibacterial activity of kuwanon G was investigated by the minimum inhibitory concentration (MIC) test and the viable cell count method. MIC of kuwanon G against Streptococcus mutans causing dental caries was determined to be 8.0 microg/ml. The bactericidal test showed that kuwanon G completely inactivated S. mutans at the concentration 20 microg/ml in 1 min. Kuwanon G also significantly inhibited the growth of other cariogenic bacteria such as Streptococcus sobrinus and Streptococcus sanguis, and Porpyromonas gingivalis causing periodontitis. Transmission electron microscopy (TEM) of kuwanon G treated cells demonstrated remarkable morphological damage of the cell wall and condensation of the cytoplasm.

Focal fibrocartilaginous dysplasia of long bones: report of eight additional cases and literature review

We report eight additional cases of focal fibrocartilaginous dysplasia (FFCD) in the proximal tibia (five), distal ulna (one), and distal femur (two). Spontaneous, complete resolution of the lesion was observed in two tibiae and one ulna. Three tibial lesions with genu varum deformity were managed with osteotomy. Two femoral FFCDs caused persistent or progressive deformity: one genu valgum with patellar dislocation, and one genu varum. These patients underwent concomitant deformity correction and lengthening by the Ilizarov method. The final results were satisfactory in all patients except one, who underwent valgus tibial osteotomy and developed mild postoperative genu valgum. The analysis of a total of 46 cases in the literature and our experience suggests that (a) FFCD has a wide histopathologic spectrum, ranging from purely dense, fibrous tendon-like tissue to benign fibrocartilaginous tissue; (b) at least 45% of tibial FFCD demonstrates progressive, spontaneous resolution; (c) in contrast, femoral and humeral FFCDs appear to have a slim possibility of spontaneous regression of the deformity; and (d) corrective osteotomy is indicated when the deformity is increasing or persistent, or when the existing deformity is severe enough to jeopardize adjacent joint mechanics and alignment.

The Sprengel deformity. Morphometric analysis using 3D-CT and its clinical relevance

We evaluated scapular dysplasia and malposition in 15 patients with the Sprengel deformity using three-dimensional CT (3D-CT). The shape, height-to-width ratio, the areas of both scapulae, the anterior curvature of the supraspinous portion and glenoid version were assessed on scapular posterior, medial and inferior views. The degree of rotation and superior displacement were measured on the trunk posterior view. The omovertebral connection was also assessed and correlated with the operative findings. Most of the affected scapulae had a characteristic shape with a decrease in the height-to-width ratio and were larger than the contralateral scapulae. There was an inverse relationship between scapular rotation and superior displacement. The typical curve of the supraspinous portion of the scapula was seen in only three cases. There was no significant difference in glenoid version. The point of tethering of the omovertebral connection may determine the shape, rotation and superior displacement of the scapula. 3D-CT was helpful in delineating the deformity in detail, and in planning scapuloplasty.

Antibacterial activity of xanthorrhizol from Curcuma xanthorrhiza against oral pathogens

The antibacterial activity of xanthorrhizol, isolated from the methanol extract of Curcuma xanthorrhiza roots, was evaluated against oral microorganisms in comparison with chlorhexidine.

alpha-Glycosidase inhibitory activity of hexagalloylglucose from the galls of Quercus infectoria

Hexagalloylglucose (3-O-digalloyl-1,2,4,6-tetra-O-galloyl-beta-D- glucose), which was isolated from the methanol extract of the galls of Quercus infectoria, significantly inhibited alpha-glycosidases such as sucrase, maltase and isomaltase. Its inhibitory activity was comparable to acarbose being used as a hypoglycemic agent, while the inhibitory activity on alpha-amylase was approximately 10 times lower than that of acarbose. The results indicate that, when compared to acarbose, hexagalloylglucose might reduce the side effects by reducing inhibition of alpha-amylase.

A recombinogenic targeting method to modify large-inserts for cis-regulatory analysis in transgenic mice: construction and expression of a 100-kb, zebrafish Hoxa-11b-lacZ reporter gene

The identification of cis-sequences responsible for spatiotemporal patterns of gene expression often requires the functional analysis of large genomic regions. In this study a 100-kb zebrafish Hoxa-11b-lacZ reporter gene was constructed and expressed in transgenic mice. PAC clone 10-O19, containing a portion of the zebrafish HoxA-b cluster, was captured into the yeast-bacterial shuttle vector, pPAC-ResQ, by recombinogenic targeting. A lacZ reporter gene was then inserted in-frame into exon 1 of the zfHoxa-11b locus by a second round of recombinogenic targeting. Expression of the zfHoxa-11b-lacZ reporter gene in 10.5 d.p.f. transgenic mouse embryos was observed only in the posterior portion of the A-P axis, in the paraxial mesoderm, neural tube, and somites. These findings demonstrate the utility of recombinogenic targeting for the modification and expression of large inserts captured from P1/PAC clones.

Pseudoaneurysm of the uterine artery

BACKGROUND

Preexisting aneurysms in several arterial locations have been associated with an increased risk of rupture in pregnancy. We report a rare case of uterine artery pseudoaneurysm that presented during the puerperium.

CASE

A 31-year-old woman had moderate suprapubic pain on postpartum day 8. The diagnosis of uterine artery aneurysm was made by duplex Doppler sonography and confirmed by arteriography. It was successfully treated by embolization of the left uterine artery.

CONCLUSION

In a rare case of pseudoaneurysm of the uterine artery, the complications of pregnancy-related aneurysmal rupture were prevented by prompt sonographic diagnosis and embolization therapy.

Management of stage pTxN+ adenocarcinoma of the prostate: influence of radical prostatectomy on progression-free interval

BACKGROUND

Whether stage pN+ prostate cancer patients will benefit from radical prostatectomy remains a controversial issue. We assess the impact of radical prostatectomy on a progression-free interval for patients with stage pN+ prostate cancer.

METHODS

From October 1990 to June 1997, 25 patients were diagnosed with stage pTxN+ adenocarcinoma of the prostate in our institute. Ten of these patients were treated with radical retropubic prostatectomy (RRP) due to false-negative frozen sections at staging pelvic lymphadenectomy. In 15 patients, radical surgery was discontinued because of grossly enlarged lymph nodes and/or positive frozen section results during staging pelvic lymph node dissection (PLND). All patients received immediate androgen ablation therapy with or without radiotherapy. Serum prostate-specific antigen (PSA) was regularly monitored in all patients.

RESULTS

During a median follow-up period of 33 months (range, 15-89 months), eight patients (53%) in the PLND group and two (20%) in the RRP group experienced disease progression as defined by significant elevation of serum PSA concentrations. The median progression-free intervals were 46 and 51 months, respectively. Both univariate and multivariate analyses failed to show statistically significant differences in the progression-free survival between the RRP and PLND groups.

CONCLUSIONS

Based on our limited experience, surgical removal of the primary tumor may have only a marginal effect in terms of the progression-free interval for prostatic cancer patients with metastasized pelvic lymph nodes (p = 0.124, log-rank test). The follow-up period was not long enough to evaluate the difference in cancer-specific survival.

Calcium binding mode of gamma-carboxyglutamic acids in conantokins

Conantokin-T (con-T) and conantokin-G (con-G) are two highly homologous peptide toxins found in Conus venom. The former is a 21-residue peptide with four gamma-carboxyglutamic acid (Gla) residues (at positions 3, 4, 10 and 14), while the latter is a 17-residue peptide with five gamma-carboxyglutamic acid residues (at positions 3, 4, 7, 10 and 14). Despite the apparent similarity in number and relative positions of the gamma-carboxyglutamic acid residues, (113)Cd-NMR studies indicated a distinct metal binding behavior for con-G and con-T. There appears to be four binding sites in con-G in contrast to one metal binding site in con-T. To elucidate the mode of calcium binding by the gamma-carboxyglutamic acid residues in these conantokins, we designed various analogous peptides with their gamma-carboxyglutamic acid replaced by other amino acid residues. (113)Cd-NMR experiments on conantokin analogues reveal that the major difference in the number of metal binding sites between con-G and con-T is due to the residue at position 7. We also performed molecular simulations to calculate the relative binding free energies of several potential binding sites. Based on our theoretical and experimental results, we propose a 'four-site' binding model for conantokin-G and a 'single-site' binding model for conantokin-T.

Mixed quantum mechanical/molecular mechanical simulations of chemical reactions in solution and in enzymes by the classical trajectory mapping approach

We present a practical hybrid quantum mechanical/molecular mechanical approach to study chemical reactions in solution and in enzymes. In this method, referred to as the "Classical Trajectory Mapping" method, trajectories are calculated on the classical potential surfaces and, by using the classical surfaces as a reference state for the actual quantum mechanical ground state potential, the free energy profile of the chemical reaction is obtained by the free energy perturbation technique. This method was applied to proton-transfer reactions both in aqueous solution and in papain. The encouraging results indicate the applicability of our method to chemical reactions in the condensed phase and the biological systems.

Co-localization of endogenous and exogenous p53 proteins in nasopharyngeal carcinoma cells

Recently, we have established nine nasopharyngeal carcinoma (NPC) cell lines in which only one cell line showed the p53 mutation. For investigation of the p53 mutation in this line, immunostaining using anti-p53 antibody was applied and showed the presence of p53 protein in the cytoplasm but not in the nucleus. Single strand conformation polymorphism analysis of the p53 gene showed one normal and one additional DNA band. Cloning and sequencing of PCR-amplified DNA showed an AGA (arginine) to ACA (threonine) heterozygous point mutation at codon 280. Transfection of the p53 DNA binding sequence and chloramphenicol acetyltransferase assay revealed loss of transcriptional activation function of endogenous p53 protein. Co-localization of the endogenous and the transfected exogenous p53 protein by polyclonal antibodies to anti-p53 protein revealed strong exogenous p53 staining in the transfected nuclei and weak staining of endogenous p53 protein in the cytoplasm. We concluded that (a) a heterozygous point mutation at codon 280 was identified in the NPC-TW 06 cell line; (b) the point mutation may cause the stagnation of mutant p53 protein in the cytoplasm, and loss of its transcriptional activation function; (c) endogenous and exogenous p53 protein can be co-localized at the same time in the transfected cells; and (d) 280 mutant p53 protein in NPC cells does not cause a decrease or increase in sensitivity to chemotherapy.

Analysis of binding of cobra cardiotoxins to heparin reveals a new beta-sheet heparin-binding structural motif

Heparin and heparan sulfate have recently been shown to bind to snake cardiotoxin (CTX) and to potentiate its penetration into phospholipid monolayer under physiological ionic conditions. Herein we analyze the heparin-binding domain of CTX using 10 CTXs from Taiwan and African cobra venom. We also performed computer modeling to obtain more information of the binding at molecular level. The results provide a molecular model for interaction of CTX-heparin complex where the cationic belt of the conserved residues on the concave surface of three finger beta-sheet polypeptides initiates ionic interaction with heparin-like molecules followed by specific binding of Lys residues near the tip of loop 2 of CTX. The dissociation constants of CTXs differ by as much as 4 orders of magnitude, ranging from approximately 140 microM for toxin gamma to approximately 20 nM for CTX M3, depending on the presence of Lys residues near the tip of loop 2. High affinity heparin binding becomes possible due to the presence of Arg-28, Lys-33, or the so-called consensus heparin binding sequence of XKKXXXKRX near the tip of the loop. The well defined three-finger loop structure of CTX provides an interesting template for the design of high affinity heparin-binding polypeptides with beta-sheet structure. The finding that several cobra CTXs and phospholipase A2 bind to heparin with different affinity may provide information on the synergistic action of the two venom proteins.

Side-chain prediction by neural networks and simulated annealing optimization

The prediction of the side-chain positions of proteins of known tertiary backbone structure was accomplished by a combination of neural networks and a simulated annealing method. Neural networks were used to generate distributions of side-chain dihedral angles. By eliminating network outputs with low activities, we were able to generate a reduced conformational space in which Monte Carlo-simulated annealing was carried out to optimize side-chain positions. In this study of 12 proteins, the average fractions of correct chi 1, chi 2 and combined chi 1 and chi 2 (to within 40 degrees of actual structure) were 82, 72 and 68% respectively.

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase

Computer simulation approaches can provide a powerful tool for correlating the structure of enzymes with their catalytic activity. One of the most effective ways of simulating enzymatic reactions is provided by the empirical valence bond method. The general applicability of this method has been demonstrated in several enzymatic reactions and it is reexamined here in a study of the initial proton-transfer step in the catalytic reaction of carbonic anhydrase. The simulations produce a rate constant which is in agreement with the observed kinetic data and emphasizes the importance of the electrostatic effect associated with the catalytic zinc ion. The calculations are also used to examine the validity of linear free-energy relationships (LFERs) in enzyme catalysis and to evaluate quantum-mechanical corrections of the calculated rate constant. It is found that LFERs are valid in the present case and it is argued that this reflects the fact that the protein responds linearly to the development of electrostatic forces during the reaction. It is concluded that the present approach can be used to augment experimental studies in establishing the general validity of LFERs. It is noted, however, that such relationships are much more valid for transitions between different resonance structures than for transitions between reactants and product states.

Wells' syndrome (eosinophilic cellulitis)--case report and electron microscopic studies

We report a case of Wells' syndrome (eosinophilic cellulitis) with acute cutaneous swelling followed by indolent infiltration. The histopathology is characterized by a dense infiltrate of eosinophils and "flame figures" in the dermis. The electron microscopic findings are peculiar. This case responded well to oral antihistamines. The skin signs and symptoms disappeared completely two weeks later.

How do serine proteases really work?

Recent advances in genetic engineering have led to a growing acceptance of the fact that enzymes work like other catalysts by reducing the activation barriers of the corresponding reactions. However, the key question about the action of enzymes is not related to the fact that they stabilize transition states but to the question to how they accomplish this task. This work considers the catalytic reaction of serine proteases and demonstrates how one can use a combination of calculations and experimental information to elucidate the key contributions to the catalytic free energy. Recent reports about genetic modifications of the buried aspartic group in serine proteases, which established the large effect of this group (but could not determine its origin), are analyzed. Two independent methods indicate that the buried aspartic group in serine proteases stabilizes the transition state by electrostatic interactions rather than by alternative mechanisms. Simple free energy considerations are used to eliminate the double proton-transfer mechanism (which is depicted in many textbooks as the key catalytic factor in serine proteases). The electrostatic stabilization of the oxyanion side of the transition state is also considered. It is argued that serine proteases and other enzymes work by providing electrostatic complementarity to the changes in charge distribution occurring during the reactions they catalyze.

Why ion pair reversal by protein engineering is unlikely to succeed

Genetic engineering is a powerful tool for exploring correlations between structure and function in proteins, but as yet we are unable to use it for effective protein design. One of the most interesting examples, which would seem to be obvious, is reversing the polarity of an ion pair. Changing a positively charged protein group, that provides a strong binding for negative substrates, to a negative group is expected to provide an effective binding site for a positively charged substrate. But several recent experiments on aspartate aminotransferase, trypsin and aspartate transcarbamoylase (Schachman, H. K. personal communication) have indicated that polarity reversal is not so successful. Here we argue that the same factors that make the enzyme an effective system for the (-+) pair will make it a much less effective system for the (+-) pair. We also point out that the unusually low effective dielectric constant (epsilon approximately equal to 13) for the (-+) interaction is due to its microenvironment and this will destabilize a (+-) arrangement having an entirely different dielectric constant (epsilon approximately equal to 80). The calculations presented here evaluate the energetics of ion pairs in protein active sites on a semiquantitative level. This is particularly important when dealing with strong, functionally important interactions that are difficult to evaluate with macroscopic models.

Evaluation of catalytic free energies in genetically modified proteins

A combination of the empirical valence bond method and a free energy perturbation approach is used to simulate the activity of genetically modified enzymes. The simulations reproduce in a semiquantitative way the observed effects of mutations on the activity and binding free energies of trypsin and subtilisin. This suggests that we are approaching a stage of quantitative structure-function correlation of enzymes. The analysis of the calculations points towards the electrostatic energy of the reacting system as the key factor in enzyme catalysis. The changes in the charges of the reacting system and the corresponding changes in "solvation" free energy (generalized here as the interaction between the charges and the given microenvironment) are emphasized. It is argued that a reliable evaluation of these changes might be sufficient for correlating structure and catalysis. The use of free energy perturbation methods and thermodynamic cycles for evaluation of solvation energies and reactivity is discussed, pointing out our early contributions. The apparent elaborated nature of our treatment is clarified, explaining that such a treatment is essential for consistent calculations of chemical reactions in polar environments. The problems associated with seemingly more rigorous quantum mechanical methods are discussed, emphasizing the inconsistency associated with using gas phase charge distributions. The importance of dynamic aspects is examined by evaluating the autocorrelation of the protein "reaction field" on the reacting substrate. It is found that, at least in the present case, dynamic effects are not important. The nature of the catalytic free energy is considered, arguing that the protein provides preoriented dipoles (polarized to stabilize the transition state charge distribution) and small reorganization energy, thus reducing the activation free energy. The corresponding catalytic free energy is related to the folding free energy, which is being invested in aligning the active site dipoles.

Semiquantitative calculations of catalytic free energies in genetically modified enzymes

The catalytic free energy and binding free energies of the native and the Asn-155----Thr, Asn-155----Leu, and Asn-155----Ala mutants of subtilisin are calculated by the empirical valence bond method and a free energy perturbation method. Two simple procedures are used; one "mutates" the substrate, and the other "mutates" the enzyme. The calculated changes in free energies (delta delta G not equal to cat and delta delta Gbind) between the mutant and native enzymes are within 1 kcal/mol of the corresponding observed values. This indicates that we are approaching a quantitative structure-function correlation. The calculated changes in catalytic free energies are almost entirely due to the electrostatic interaction between the enzyme-water system and the charges of the reacting system. This supports the idea that the electrostatic free energy associated with the changes of charges of the reacting system is the key factor in enzyme catalysis.